JOHN TAINER to Binding Sites
This is a "connection" page, showing publications JOHN TAINER has written about Binding Sites.
Connection Strength
2.849
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X-ray scattering reveals disordered linkers and dynamic interfaces in complexes and mechanisms for DNA double-strand break repair impacting cell and cancer biology. Protein Sci. 2021 09; 30(9):1735-1756.
Score: 0.145
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Human XPG nuclease structure, assembly, and activities with insights for neurodegeneration and cancer from pathogenic mutations. Proc Natl Acad Sci U S A. 2020 06 23; 117(25):14127-14138.
Score: 0.136
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Phosphate steering by Flap Endonuclease 1 promotes 5'-flap specificity and incision to prevent genome instability. Nat Commun. 2017 06 27; 8:15855.
Score: 0.111
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Double strand binding-single strand incision mechanism for human flap endonuclease: implications for the superfamily. Mech Ageing Dev. 2012 Apr; 133(4):195-202.
Score: 0.076
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ABC ATPase signature helices in Rad50 link nucleotide state to Mre11 interface for DNA repair. Nat Struct Mol Biol. 2011 Apr; 18(4):423-31.
Score: 0.072
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Flipping of alkylated DNA damage bridges base and nucleotide excision repair. Nature. 2009 Jun 11; 459(7248):808-13.
Score: 0.063
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p38alpha MAP kinase C-terminal domain binding pocket characterized by crystallographic and computational analyses. J Mol Biol. 2009 Aug 07; 391(1):1-11.
Score: 0.063
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Developing master keys to brain pathology, cancer and aging from the structural biology of proteins controlling reactive oxygen species and DNA repair. Neuroscience. 2007 Apr 14; 145(4):1280-99.
Score: 0.053
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WRN exonuclease structure and molecular mechanism imply an editing role in DNA end processing. Nat Struct Mol Biol. 2006 May; 13(5):414-22.
Score: 0.051
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DNA binding and nucleotide flipping by the human DNA repair protein AGT. Nat Struct Mol Biol. 2004 Aug; 11(8):714-20.
Score: 0.045
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Structural basis for FEN-1 substrate specificity and PCNA-mediated activation in DNA replication and repair. Cell. 2004 Jan 09; 116(1):39-50.
Score: 0.043
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ALS mutants of human superoxide dismutase form fibrous aggregates via framework destabilization. J Mol Biol. 2003 Sep 19; 332(3):601-15.
Score: 0.043
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Full-length archaeal Rad51 structure and mutants: mechanisms for RAD51 assembly and control by BRCA2. EMBO J. 2003 Sep 01; 22(17):4566-76.
Score: 0.042
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Structural basis for recognition and catalysis by the bifunctional dCTP deaminase and dUTPase from Methanococcus jannaschii. J Mol Biol. 2003 Aug 22; 331(4):885-96.
Score: 0.042
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Characterization of the electrophile binding site and substrate binding mode of the 26-kDa glutathione S-transferase from Schistosoma japonicum. Proteins. 2003 Apr 01; 51(1):137-46.
Score: 0.041
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Rad50/SMC proteins and ABC transporters: unifying concepts from high-resolution structures. Curr Opin Struct Biol. 2003 Apr; 13(2):249-55.
Score: 0.041
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The Rad50 zinc-hook is a structure joining Mre11 complexes in DNA recombination and repair. Nature. 2002 Aug 01; 418(6897):562-6.
Score: 0.039
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The ARTT motif and a unified structural understanding of substrate recognition in ADP-ribosylating bacterial toxins and eukaryotic ADP-ribosyltransferases. Int J Med Microbiol. 2002 Feb; 291(6-7):523-9.
Score: 0.038
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Structure and activity of a thermostable thymine-DNA glycosylase: evidence for base twisting to remove mismatched normal DNA bases. J Mol Biol. 2002 Jan 18; 315(3):373-84.
Score: 0.038
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Structural biochemistry and interaction architecture of the DNA double-strand break repair Mre11 nuclease and Rad50-ATPase. Cell. 2001 May 18; 105(4):473-85.
Score: 0.036
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Crystal structure and novel recognition motif of rho ADP-ribosylating C3 exoenzyme from Clostridium botulinum: structural insights for recognition specificity and catalysis. J Mol Biol. 2001 Jan 05; 305(1):95-107.
Score: 0.035
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Conserved structural motifs governing the stoichiometric repair of alkylated DNA by O(6)-alkylguanine-DNA alkyltransferase. Mutat Res. 2000 Aug 30; 460(3-4):151-63.
Score: 0.034
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Abasic site recognition by two apurinic/apyrimidinic endonuclease families in DNA base excision repair: the 3' ends justify the means. Mutat Res. 2000 Aug 30; 460(3-4):211-29.
Score: 0.034
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Uracil-DNA glycosylase-DNA substrate and product structures: conformational strain promotes catalytic efficiency by coupled stereoelectronic effects. Proc Natl Acad Sci U S A. 2000 May 09; 97(10):5083-8.
Score: 0.034
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Structures of the N(omega)-hydroxy-L-arginine complex of inducible nitric oxide synthase oxygenase dimer with active and inactive pterins. Biochemistry. 2000 Apr 25; 39(16):4608-21.
Score: 0.034
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Active and alkylated human AGT structures: a novel zinc site, inhibitor and extrahelical base binding. EMBO J. 2000 Apr 03; 19(7):1719-30.
Score: 0.033
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Active and inhibited human catalase structures: ligand and NADPH binding and catalytic mechanism. J Mol Biol. 2000 Feb 11; 296(1):295-309.
Score: 0.033
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Evolution and mechanism from structures of an ADP-ribosylating toxin and NAD complex. Nat Struct Biol. 1999 Oct; 6(10):932-6.
Score: 0.032
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Flexible Tethering of ASPP Proteins Facilitates PP-1c Catalysis. Structure. 2019 10 01; 27(10):1485-1496.e4.
Score: 0.032
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Structure of the DNA repair enzyme endonuclease IV and its DNA complex: double-nucleotide flipping at abasic sites and three-metal-ion catalysis. Cell. 1999 Aug 06; 98(3):397-408.
Score: 0.032
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Protein mimicry of DNA from crystal structures of the uracil-DNA glycosylase inhibitor protein and its complex with Escherichia coli uracil-DNA glycosylase. J Mol Biol. 1999 Mar 26; 287(2):331-46.
Score: 0.031
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Structure of the DNA repair and replication endonuclease and exonuclease FEN-1: coupling DNA and PCNA binding to FEN-1 activity. Cell. 1998 Oct 02; 95(1):135-46.
Score: 0.030
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Base excision repair initiation revealed by crystal structures and binding kinetics of human uracil-DNA glycosylase with DNA. EMBO J. 1998 Sep 01; 17(17):5214-26.
Score: 0.030
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Crystal structure of Y34F mutant human mitochondrial manganese superoxide dismutase and the functional role of tyrosine 34. Biochemistry. 1998 Apr 07; 37(14):4722-30.
Score: 0.029
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Structure of nitric oxide synthase oxygenase dimer with pterin and substrate. Science. 1998 Mar 27; 279(5359):2121-6.
Score: 0.029
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The structure of nitric oxide synthase oxygenase domain and inhibitor complexes. Science. 1997 Oct 17; 278(5337):425-31.
Score: 0.028
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Computational, pulse-radiolytic, and structural investigations of lysine-136 and its role in the electrostatic triad of human Cu,Zn superoxide dismutase. Proteins. 1997 Sep; 29(1):103-12.
Score: 0.028
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Hybrid Methods Reveal Multiple Flexibly Linked DNA Polymerases within the Bacteriophage T7 Replisome. Structure. 2017 01 03; 25(1):157-166.
Score: 0.027
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Mechanism and Regulation of DNA-Protein Crosslink Repair by the DNA-Dependent Metalloprotease SPRTN. Mol Cell. 2016 11 17; 64(4):688-703.
Score: 0.026
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Human dUTP pyrophosphatase: uracil recognition by a beta hairpin and active sites formed by three separate subunits. Structure. 1996 Sep 15; 4(9):1077-92.
Score: 0.026
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Human mitochondrial manganese superoxide dismutase polymorphic variant Ile58Thr reduces activity by destabilizing the tetrameric interface. Biochemistry. 1996 Apr 09; 35(14):4287-97.
Score: 0.025
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Crystal structure of human uracil-DNA glycosylase in complex with a protein inhibitor: protein mimicry of DNA. Cell. 1995 Sep 08; 82(5):701-8.
Score: 0.024
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Novel DNA binding motifs in the DNA repair enzyme endonuclease III crystal structure. EMBO J. 1995 Aug 15; 14(16):4108-20.
Score: 0.024
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Crystal structure of the human cell cycle protein CksHs1: single domain fold with similarity to kinase N-lobe domain. J Mol Biol. 1995 Jun 23; 249(5):835-42.
Score: 0.024
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FlaF Is a ?-Sandwich Protein that Anchors the Archaellum in the Archaeal Cell Envelope by Binding the S-Layer Protein. Structure. 2015 May 05; 23(5):863-872.
Score: 0.024
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Crystal structure and mutational analysis of human uracil-DNA glycosylase: structural basis for specificity and catalysis. Cell. 1995 Mar 24; 80(6):869-78.
Score: 0.024
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Crystal structures of a schistosomal drug and vaccine target: glutathione S-transferase from Schistosoma japonica and its complex with the leading antischistosomal drug praziquantel. J Mol Biol. 1995 Feb 10; 246(1):21-7.
Score: 0.023
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Enzyme structure. Cracking tyrosine phosphatases. Nature. 1994 Aug 18; 370(6490):506-7.
Score: 0.023
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Mechanistic insights into the role of Hop2-Mnd1 in meiotic homologous DNA pairing. Nucleic Acids Res. 2014 Jan; 42(2):906-17.
Score: 0.021
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Human CksHs2 atomic structure: a role for its hexameric assembly in cell cycle control. Science. 1993 Oct 15; 262(5132):387-95.
Score: 0.021
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Rational design and expression of a heparin-targeted human superoxide dismutase. Biochem Biophys Res Commun. 1993 Jan 15; 190(1):250-6.
Score: 0.020
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Sculpting of DNA at abasic sites by DNA glycosylase homolog mag2. Structure. 2013 Jan 08; 21(1):154-166.
Score: 0.020
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Protein metal-binding sites. Curr Opin Biotechnol. 1992 Aug; 3(4):378-87.
Score: 0.020
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Structure of mammalian poly(ADP-ribose) glycohydrolase reveals a flexible tyrosine clasp as a substrate-binding element. Nat Struct Mol Biol. 2012 May 20; 19(6):653-6.
Score: 0.019
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Repair complexes of FEN1 endonuclease, DNA, and Rad9-Hus1-Rad1 are distinguished from their PCNA counterparts by functionally important stability. Proc Natl Acad Sci U S A. 2012 May 29; 109(22):8528-33.
Score: 0.019
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Kinetic and stoichiometric characterisation of streptavidin-binding aptamers. Chembiochem. 2012 Apr 16; 13(6):829-36.
Score: 0.019
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Eukaryotic class II cyclobutane pyrimidine dimer photolyase structure reveals basis for improved ultraviolet tolerance in plants. J Biol Chem. 2012 Apr 06; 287(15):12060-9.
Score: 0.019
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Metal-binding sites in proteins. Curr Opin Biotechnol. 1991 Aug; 2(4):582-91.
Score: 0.018
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Neutralizing mutations of carboxylates that bind metal 2 in T5 flap endonuclease result in an enzyme that still requires two metal ions. J Biol Chem. 2011 Sep 02; 286(35):30878-30887.
Score: 0.018
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Archaeal flagellar ATPase motor shows ATP-dependent hexameric assembly and activity stimulation by specific lipid binding. Biochem J. 2011 Jul 01; 437(1):43-52.
Score: 0.018
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The DNA repair endonuclease XPG interacts directly and functionally with the WRN helicase defective in Werner syndrome. Cell Cycle. 2011 Jun 15; 10(12):1998-2007.
Score: 0.018
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Solution structure of RNase P RNA. RNA. 2011 Jun; 17(6):1159-71.
Score: 0.018
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Mapping interactions between the RNA chaperone FinO and its RNA targets. Nucleic Acids Res. 2011 May; 39(10):4450-63.
Score: 0.018
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Mechanism and atomic structure of superoxide dismutase. Free Radic Res Commun. 1991; 12-13 Pt 1:269-78.
Score: 0.018
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ATP induces conformational changes in the carboxyl-terminal region of ClC-5. J Biol Chem. 2011 Feb 25; 286(8):6733-41.
Score: 0.018
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Enzyme motifs in antibodies. Nature. 1990 Dec 13; 348(6302):589.
Score: 0.018
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The structure of the CRISPR-associated protein Csa3 provides insight into the regulation of the CRISPR/Cas system. J Mol Biol. 2011 Jan 28; 405(4):939-55.
Score: 0.017
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Substrate recognition and catalysis by flap endonucleases and related enzymes. Biochem Soc Trans. 2010 Apr; 38(2):433-7.
Score: 0.017
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Functional motifs in the (6-4) photolyase crystal structure make a comparative framework for DNA repair photolyases and clock cryptochromes. Proc Natl Acad Sci U S A. 2009 Apr 28; 106(17):6962-7.
Score: 0.016
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The BARD1 C-terminal domain structure and interactions with polyadenylation factor CstF-50. Biochemistry. 2008 Nov 04; 47(44):11446-56.
Score: 0.015
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DNA apurinic-apyrimidinic site binding and excision by endonuclease IV. Nat Struct Mol Biol. 2008 May; 15(5):515-22.
Score: 0.015
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Probing enzyme-substrate recognition and catalytic mechanism in Cu,Zn superoxide dismutase. Basic Life Sci. 1988; 49:635-40.
Score: 0.014
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Structural characterization of zinc-deficient human superoxide dismutase and implications for ALS. J Mol Biol. 2007 Nov 02; 373(4):877-90.
Score: 0.014
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Comparison of the catalytic parameters and reaction specificities of a phage and an archaeal flap endonuclease. J Mol Biol. 2007 Aug 03; 371(1):34-48.
Score: 0.014
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The C-terminal domain of yeast PCNA is required for physical and functional interactions with Cdc9 DNA ligase. Nucleic Acids Res. 2007; 35(5):1624-37.
Score: 0.013
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Unraveling the three-metal-ion catalytic mechanism of the DNA repair enzyme endonuclease IV. Proc Natl Acad Sci U S A. 2007 Jan 30; 104(5):1465-70.
Score: 0.013
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A flexible interface between DNA ligase and PCNA supports conformational switching and efficient ligation of DNA. Mol Cell. 2006 Oct 20; 24(2):279-91.
Score: 0.013
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Hydrogen bonding in human manganese superoxide dismutase containing 3-fluorotyrosine. Biophys J. 2005 Dec; 89(6):4171-9.
Score: 0.012
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Reaction intermediates in the catalytic mechanism of Escherichia coli MutY DNA glycosylase. J Biol Chem. 2004 Nov 05; 279(45):46930-9.
Score: 0.011
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Nickel superoxide dismutase structure and mechanism. Biochemistry. 2004 Jun 29; 43(25):8038-47.
Score: 0.011
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Structural basis for isozyme-specific regulation of electron transfer in nitric-oxide synthase. J Biol Chem. 2004 Sep 03; 279(36):37918-27.
Score: 0.011
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Role of hydrogen bonding in the active site of human manganese superoxide dismutase. Biochemistry. 2004 Jun 08; 43(22):7038-45.
Score: 0.011
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Interaction interface of human flap endonuclease-1 with its DNA substrates. J Biol Chem. 2004 Jun 04; 279(23):24394-402.
Score: 0.011
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The rad50 signature motif: essential to ATP binding and biological function. J Mol Biol. 2004 Jan 23; 335(4):937-51.
Score: 0.011
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Amino acid substitution at the dimeric interface of human manganese superoxide dismutase. J Biol Chem. 2004 Feb 13; 279(7):5861-6.
Score: 0.011
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Structure and mechanism of copper, zinc superoxide dismutase. Nature. 1983 Nov 17-23; 306(5940):284-7.
Score: 0.011
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Catalytic and structural effects of amino acid substitution at histidine 30 in human manganese superoxide dismutase: insertion of valine C gamma into the substrate access channel. Biochemistry. 2003 Mar 18; 42(10):2781-9.
Score: 0.010
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Structural basis for endothelial nitric oxide synthase binding to calmodulin. EMBO J. 2003 Feb 17; 22(4):766-75.
Score: 0.010
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Identification of a new cryptochrome class. Structure, function, and evolution. Mol Cell. 2003 Jan; 11(1):59-67.
Score: 0.010
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Determination and analysis of the 2 A-structure of copper, zinc superoxide dismutase. J Mol Biol. 1982 Sep 15; 160(2):181-217.
Score: 0.010
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MDB: the Metalloprotein Database and Browser at The Scripps Research Institute. Nucleic Acids Res. 2002 Jan 01; 30(1):379-82.
Score: 0.009
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Structures of tetrahydrobiopterin binding-site mutants of inducible nitric oxide synthase oxygenase dimer and implicated roles of Trp457. Biochemistry. 2001 Oct 30; 40(43):12826-32.
Score: 0.009
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Multiple replacements of glutamine 143 in human manganese superoxide dismutase: effects on structure, stability, and catalysis. Biochemistry. 2000 Jun 20; 39(24):7131-7.
Score: 0.008
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Inducible nitric oxide synthase: role of the N-terminal beta-hairpin hook and pterin-binding segment in dimerization and tetrahydrobiopterin interaction. EMBO J. 1999 Nov 15; 18(22):6260-70.
Score: 0.008
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N-terminal domain swapping and metal ion binding in nitric oxide synthase dimerization. EMBO J. 1999 Nov 15; 18(22):6271-81.
Score: 0.008
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Interrupting the hydrogen bond network at the active site of human manganese superoxide dismutase. J Biol Chem. 1999 Sep 24; 274(39):27711-6.
Score: 0.008
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Role of tryptophan 161 in catalysis by human manganese superoxide dismutase. Biochemistry. 1999 Sep 07; 38(36):11686-92.
Score: 0.008
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Mutational analysis of the tetrahydrobiopterin-binding site in inducible nitric-oxide synthase. J Biol Chem. 1999 Aug 20; 274(34):24100-12.
Score: 0.008
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Human glutathione transferase A4-4 crystal structures and mutagenesis reveal the basis of high catalytic efficiency with toxic lipid peroxidation products. J Mol Biol. 1999 May 07; 288(3):427-39.
Score: 0.008
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Mutation of an active site residue in Escherichia coli uracil-DNA glycosylase: effect on DNA binding, uracil inhibition and catalysis. Biochemistry. 1999 Apr 13; 38(15):4834-45.
Score: 0.008
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Newly discovered archaebacterial flap endonucleases show a structure-specific mechanism for DNA substrate binding and catalysis resembling human flap endonuclease-1. J Biol Chem. 1998 Oct 16; 273(42):27154-61.
Score: 0.008
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Screening a peptidyl database for potential ligands to proteins with side-chain flexibility. Proteins. 1998 Oct 01; 33(1):74-87.
Score: 0.008
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Probing the active site of human manganese superoxide dismutase: the role of glutamine 143. Biochemistry. 1998 Apr 07; 37(14):4731-9.
Score: 0.007
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The crystal structure of the human DNA repair endonuclease HAP1 suggests the recognition of extra-helical deoxyribose at DNA abasic sites. EMBO J. 1997 Nov 03; 16(21):6548-58.
Score: 0.007
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Exon 5 encoded domain is not required for the toxic function of mutant SOD1 but essential for the dismutase activity: identification and characterization of two new SOD1 mutations associated with familial amyotrophic lateral sclerosis. Neurogenetics. 1997 May; 1(1):65-71.
Score: 0.007
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Novel dimeric interface and electrostatic recognition in bacterial Cu,Zn superoxide dismutase. Proc Natl Acad Sci U S A. 1996 Nov 12; 93(23):12774-9.
Score: 0.007
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A mutation in the human cyclin-dependent kinase interacting protein, CksHs2, interferes with cyclin-dependent kinase binding and biological function, but preserves protein structure and assembly. J Mol Biol. 1996 Sep 06; 261(5):646-57.
Score: 0.007
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Excision of cytosine and thymine from DNA by mutants of human uracil-DNA glycosylase. EMBO J. 1996 Jul 01; 15(13):3442-7.
Score: 0.006
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Atomic and residue hydrophilicity in the context of folded protein structures. Proteins. 1995 Dec; 23(4):536-47.
Score: 0.006
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Identification of critical active-site residues in the multifunctional human DNA repair enzyme HAP1. Nat Struct Biol. 1995 Jul; 2(7):561-8.
Score: 0.006
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The role of arginine 143 in the electrostatics and mechanism of Cu,Zn superoxide dismutase: computational and experimental evaluation by mutational analysis. Proteins. 1994 May; 19(1):24-34.
Score: 0.006
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Amyotrophic lateral sclerosis and structural defects in Cu,Zn superoxide dismutase. Science. 1993 Aug 20; 261(5124):1047-51.
Score: 0.005
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Electrostatic orientation of the electron-transfer complex between plastocyanin and cytochrome c. J Biol Chem. 1991 Jul 15; 266(20):13431-41.
Score: 0.005
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Probing the structural basis for enzyme-substrate recognition in Cu,Zn superoxide dismutase. Free Radic Res Commun. 1991; 12-13 Pt 1:287-96.
Score: 0.004
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Electrostatic recognition between superoxide and copper, zinc superoxide dismutase. Nature. 1983 Nov 17-23; 306(5940):287-90.
Score: 0.003