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Bidentate and tridentate metal-ion coordination states within ternary complexes of RB69 DNA polymerase.

Xia S, Eom SH, Konigsberg WH, Wang J.

Protein Sci. 2012 Mar;21(3):447-51. doi: 10.1002/pro.2026. Epub 2012 Jan 31.


Structural insights into complete metal ion coordination from ternary complexes of B family RB69 DNA polymerase.

Xia S, Wang M, Blaha G, Konigsberg WH, Wang J.

Biochemistry. 2011 Oct 25;50(42):9114-24. doi: 10.1021/bi201260h. Epub 2011 Sep 29.


RB69 DNA polymerase structure, kinetics, and fidelity.

Xia S, Konigsberg WH.

Biochemistry. 2014 May 6;53(17):2752-67. doi: 10.1021/bi4014215. Epub 2014 Apr 23. Review.


Effect of A and B metal ion site occupancy on conformational changes in an RB69 DNA polymerase ternary complex.

Wang M, Lee HR, Konigsberg W.

Biochemistry. 2009 Mar 17;48(10):2075-86. doi: 10.1021/bi801627h. Erratum in: Biochemistry. 2010 Mar 30;49(12):2763.


Effect of Different Divalent Cations on the Kinetics and Fidelity of RB69 DNA Polymerase.

Vashishtha AK, Konigsberg WH.

Biochemistry. 2016 May 10;55(18):2661-70. doi: 10.1021/acs.biochem.5b01350. Epub 2016 Apr 28.


Different Divalent Cations Alter the Kinetics and Fidelity of DNA Polymerases.

Vashishtha AK, Wang J, Konigsberg WH.

J Biol Chem. 2016 Sep 30;291(40):20869-20875. Epub 2016 Jul 26. Review.


The reopening rate of the fingers domain is a determinant of base selectivity for RB69 DNA polymerase.

Lee HR, Wang M, Konigsberg W.

Biochemistry. 2009 Mar 17;48(10):2087-98. doi: 10.1021/bi8016284.


Fidelity of Dpo4: effect of metal ions, nucleotide selection and pyrophosphorolysis.

Vaisman A, Ling H, Woodgate R, Yang W.

EMBO J. 2005 Sep 7;24(17):2957-67. Epub 2005 Aug 18.


DNA mismatch synthesis complexes provide insights into base selectivity of a B family DNA polymerase.

Xia S, Wang J, Konigsberg WH.

J Am Chem Soc. 2013 Jan 9;135(1):193-202. doi: 10.1021/ja3079048. Epub 2012 Dec 21.


Mismatch-induced conformational distortions in polymerase beta support an induced-fit mechanism for fidelity.

Arora K, Beard WA, Wilson SH, Schlick T.

Biochemistry. 2005 Oct 11;44(40):13328-41.


Metal-ion dependence of the active-site conformation of the translesion DNA polymerase Dpo4 from Sulfolobus solfataricus.

Irimia A, Loukachevitch LV, Eoff RL, Guengerich FP, Egli M.

Acta Crystallogr Sect F Struct Biol Cryst Commun. 2010 Sep 1;66(Pt 9):1013-8. doi: 10.1107/S1744309110029374. Epub 2010 Aug 21.


Variation in mutation rates caused by RB69pol fidelity mutants can be rationalized on the basis of their kinetic behavior and crystal structures.

Xia S, Wang M, Lee HR, Sinha A, Blaha G, Christian T, Wang J, Konigsberg W.

J Mol Biol. 2011 Mar 4;406(4):558-70. doi: 10.1016/j.jmb.2010.12.033. Epub 2011 Jan 7.


Contribution of partial charge interactions and base stacking to the efficiency of primer extension at and beyond abasic sites in DNA.

Xia S, Vashishtha A, Bulkley D, Eom SH, Wang J, Konigsberg WH.

Biochemistry. 2012 Jun 19;51(24):4922-31. doi: 10.1021/bi300296q. Epub 2012 Jun 7.


Human DNA polymerase η is pre-aligned for dNTP binding and catalysis.

Ummat A, Silverstein TD, Jain R, Buku A, Johnson RE, Prakash L, Prakash S, Aggarwal AK.

J Mol Biol. 2012 Jan 27;415(4):627-34. doi: 10.1016/j.jmb.2011.11.038. Epub 2011 Nov 29.


Probing minor groove hydrogen bonding interactions between RB69 DNA polymerase and DNA.

Xia S, Christian TD, Wang J, Konigsberg WH.

Biochemistry. 2012 May 29;51(21):4343-53. doi: 10.1021/bi300416z. Epub 2012 May 17.


Crystal structure of a pol alpha family DNA polymerase from the hyperthermophilic archaeon Thermococcus sp. 9 degrees N-7.

Rodriguez AC, Park HW, Mao C, Beese LS.

J Mol Biol. 2000 Jun 2;299(2):447-62.


phi29 DNA polymerase active site: role of residue Val250 as metal-dNTP complex ligand and in protein-primed initiation.

Pérez-Arnaiz P, Lázaro JM, Salas M, de Vega M.

J Mol Biol. 2010 Jan 15;395(2):223-33. doi: 10.1016/j.jmb.2009.10.061. Epub 2009 Oct 31.


Characterization of a replicative DNA polymerase mutant with reduced fidelity and increased translesion synthesis capacity.

Zhong X, Pedersen LC, Kunkel TA.

Nucleic Acids Res. 2008 Jul;36(12):3892-904. doi: 10.1093/nar/gkn312. Epub 2008 May 24.

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