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Structure paper

TitleMapping Functional Substrate-Enzyme Interactions in the pol beta Active Site through Chemical Biology: Structural Responses to Acidity Modification of Incoming dNTPs.
Journal, issue, pagesBiochemistry, Vol. 57, Page 3934-3944, Year 2018
Publish dateOct 25, 2017 (structure data deposition date)
AuthorsBatra, V.K. / Oertell, K. / Beard, W.A. / Kashemirov, B.A. / McKenna, C.E. / Goodman, M.F. / Wilson, S.H.
External linksBiochemistry / PubMed:29874056
MethodsX-ray diffraction
Resolution1.8 - 2.3 Å
Structure data

PDB-6bel:
Ternary complex crystal structure of DNA polymerase Beta with R-isomer of beta-gamma-CHF-dCTP
Method: X-RAY DIFFRACTION / Resolution: 1.898 Å

PDB-6bem:
Ternary complex crystal structure of DNA polymerase Beta with S-isomer of beta-gamma-CHCL-dCTP
Method: X-RAY DIFFRACTION / Resolution: 1.88 Å

PDB-6cr3:
Ternary complex crystal structure of DNA polymerase Beta with a dideoxy terminated primer with CBr2, beta, gamma dATP analogue
Method: X-RAY DIFFRACTION / Resolution: 1.95 Å

PDB-6cr4:
Ternary complex crystal structure of DNA polymerase Beta with a dideoxy terminated primer with dATP
Method: X-RAY DIFFRACTION / Resolution: 1.8 Å

PDB-6cr5:
Ternary complex crystal structure of DNA polymerase Beta with a dideoxy terminated primer with CH2-beta, gamma dATP analogue
Method: X-RAY DIFFRACTION / Resolution: 1.982 Å

PDB-6cr6:
Ternary complex crystal structure of DNA polymerase Beta with a dideoxy terminated primer with CH-CH3, beta, gamma dATP analogue
Method: X-RAY DIFFRACTION / Resolution: 2.097 Å

PDB-6cr7:
Ternary complex crystal structure of DNA polymerase Beta with a dideoxy terminated primer with CHF, beta, gamma dATP analogue
Method: X-RAY DIFFRACTION / Resolution: 2.29 Å

PDB-6cr8:
Ternary complex crystal structure of DNA polymerase Beta with a dideoxy terminated primer with CHCL (R & S isomers), beta, gamma dATP analogue
Method: X-RAY DIFFRACTION / Resolution: 2.05 Å

PDB-6cr9:
Ternary complex crystal structure of DNA polymerase Beta with a dideoxy terminated primer with CFCL, beta, gamma dATP analogue
Method: X-RAY DIFFRACTION / Resolution: 1.96 Å

PDB-6crb:
Ternary complex crystal structure of DNA polymerase Beta with a dideoxy terminated primer with CF2, beta, gamma dATP analogue
Method: X-RAY DIFFRACTION / Resolution: 2.151 Å

PDB-6crc:
Ternary complex crystal structure of DNA polymerase Beta with a dideoxy terminated primer with CCL2, beta, gamma dATP analogue
Method: X-RAY DIFFRACTION / Resolution: 2.3 Å

PDB-6cti:
Ternary complex crystal structure of DNA polymerase Beta with a dideoxy terminated primer with CCL2, beta, gamma dTTP analogue
Method: X-RAY DIFFRACTION / Resolution: 2.001 Å

PDB-6ctj:
Ternary complex crystal structure of DNA polymerase Beta with a dideoxy terminated primer with CHCH3, beta, gamma dTTP analogue
Method: X-RAY DIFFRACTION / Resolution: 2.1 Å

PDB-6ctk:
Ternary complex crystal structure of DNA polymerase Beta with a dideoxy terminated primer with CHF-R/S isomers, beta, gamma dTTP analogue
Method: X-RAY DIFFRACTION / Resolution: 2.153 Å

PDB-6ctl:
Ternary complex crystal structure of DNA polymerase Beta with a dideoxy terminated primer with CHCL-R/S isomers, beta, gamma dTTP analogue
Method: X-RAY DIFFRACTION / Resolution: 2.0 Å

PDB-6ctm:
Ternary complex crystal structure of DNA polymerase Beta with a dideoxy terminated primer with CHCL(R-isomer), beta, gamma dTTP analogue
Method: X-RAY DIFFRACTION / Resolution: 2.101 Å

PDB-6ctn:
Ternary complex crystal structure of DNA polymerase Beta with a dideoxy terminated primer with CFCL,beta-gamma dTTP analogue
Method: X-RAY DIFFRACTION / Resolution: 1.92 Å

PDB-6cto:
Ternary complex crystal structure of DNA polymerase Beta with a dideoxy terminated primer with CF2, beta, gamma dTTP analogue
Method: X-RAY DIFFRACTION / Resolution: 2.04 Å

PDB-6ctp:
Ternary complex crystal structure of DNA polymerase Beta with a dideoxy terminated primer with CH2, beta, gamma dTTP analogue
Method: X-RAY DIFFRACTION / Resolution: 2.2 Å

PDB-6ctq:
Ternary complex crystal structure of DNA polymerase Beta with a dideoxy terminated primer with dCTP
Method: X-RAY DIFFRACTION / Resolution: 1.87 Å

PDB-6ctr:
Ternary complex crystal structure of DNA polymerase Beta with a dideoxy terminated primer with CHF (R & S isomers), beta, gamma dCTP analogue
Method: X-RAY DIFFRACTION / Resolution: 1.85 Å

PDB-6ctt:
Ternary complex crystal structure of DNA polymerase Beta with a dideoxy terminated primer with CHCL (R & S isomers, beta, gamma dCTP analogue
Method: X-RAY DIFFRACTION / Resolution: 2.0 Å

PDB-6ctu:
Ternary complex crystal structure of DNA polymerase Beta with a dideoxy terminated primer with CFCL, beta, gamma dCTP analogue
Method: X-RAY DIFFRACTION / Resolution: 1.9 Å

PDB-6ctv:
Ternary complex crystal structure of DNA polymerase Beta with a dideoxy terminated primer with CF2, beta, gamma dCTP analogue
Method: X-RAY DIFFRACTION / Resolution: 2.02 Å

PDB-6ctw:
Ternary complex crystal structure of DNA polymerase Beta with a dideoxy terminated primer with CCL2, beta, gamma dCTP analogue
Method: X-RAY DIFFRACTION / Resolution: 1.981 Å

PDB-6ctx:
Ternary complex crystal structure of DNA polymerase Beta with a dideoxy terminated primer with CBr2, beta, gamma dCTP analogue
Method: X-RAY DIFFRACTION / Resolution: 2.02 Å

PDB-6g2q:
Ternary complex crystal structure of DNA polymerase Beta with a dideoxy terminated primer with CHCL (S-isomer), beta, gamma dTTP analogue
Method: X-RAY DIFFRACTION / Resolution: 2.148 Å

Chemicals

ChemComp-MG:
Unknown entry

ChemComp-NA:
Unknown entry

ChemComp-CL:
Unknown entry / Chloride

ChemComp-F3C:
2'-deoxy-5'-O-[(R)-{[(R)-[(R)-fluoro(phosphono)methyl](hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]cytidine

ChemComp-DC:
2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE / dCMP*YM / Deoxycytidine monophosphate

ChemComp-HOH:
WATER / Water

ChemComp-DJJ:
5'-O-[(R)-{[(R)-[(S)-chloro(phosphono)methyl](hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]-2'-deoxycytidine

ChemComp-H84:
2'-deoxy-5'-O-[(R)-{[(R)-[dibromo(phosphono)methyl](hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]adenosine

ChemComp-DTP:
2'-DEOXYADENOSINE 5'-TRIPHOSPHATE / Deoxyadenosine triphosphate

ChemComp-FCJ:
2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonomethyl)phosphoryl]oxy}phosphoryl]adenosine

ChemComp-HGV:
2'-deoxy-5'-O-[(R)-hydroxy({(R)-hydroxy[(1S)-1-phosphonoethyl]phosphoryl}oxy)phosphoryl]adenosine

ChemComp-V3A:
9-{2-deoxy-5-O-[(R)-{[(R)-[(R)-fluoro(phosphono)methyl](hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]-alpha-D-erythro-pentofuranosyl}-9H-purin-6-amine

ChemComp-VA4:
5'-O-[(R)-{[(R)-[(R)-chloro(phosphono)methyl](hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]-2'-deoxyadenosine

ChemComp-VA5:
9-{5-O-[(R)-{[(R)-[(S)-chloro(fluoro)phosphonomethyl](hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]-2-deoxy-alpha-D-threo-pentofuranosyl}-9H-purin-6-amine

ChemComp-VA6:
9-{2-deoxy-5-O-[(S)-{[(S)-[difluoro(phosphono)methyl](hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]-alpha-D-erythro-pentofuranosyl}-9H-purin-6-amine

ChemComp-VA7:
2'-deoxy-5'-O-[(R)-{[(R)-[dichloro(phosphono)methyl](hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]adenosine

ChemComp-VT8:
5'-O-[(R)-{[(R)-[dichloro(phosphono)methyl](hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]thymidine

ChemComp-FDV:
5'-O-[(R)-hydroxy({(R)-hydroxy[(1S)-1-phosphonoethyl]phosphoryl}oxy)phosphoryl]thymidine

ChemComp-FDY:
5'-O-[(R)-{[(R)-[(R)-fluoro(phosphono)methyl](hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]thymidine

ChemComp-FDJ:
5'-O-[(R)-{[(R)-[(R)-chloro(phosphono)methyl](hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]thymidine

ChemComp-VT6:
5'-O-[(R)-{[(R)-[(S)-chloro(fluoro)phosphonomethyl](hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]thymidine

ChemComp-VT7:
5'-O-[(R)-{[(R)-[difluoro(phosphono)methyl](hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]thymidine

ChemComp-TTE:
PHOSPHOMETHYL PHOSPHONIC ACID DEOXYTHYMIDYLATE ESTER

ChemComp-DCP:
2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE / Deoxycytidine triphosphate

ChemComp-FF4:
2'-deoxy-5'-O-[(R)-{[(R)-[(S)-fluoro(phosphono)methyl](hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]cytidine

ChemComp-FF7:
5'-O-[(R)-{[(R)-[(R)-chloro(phosphono)methyl](hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]-2'-deoxycytidine

ChemComp-VC6:
4-amino-1-{5-O-[(R)-{[(R)-[(S)-chloro(fluoro)phosphonomethyl](hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]-2-deoxy-alpha-L-threo-pentofuranosyl}pyrimidin-2(1H)-one

ChemComp-FFJ:
2'-deoxy-5'-O-[(R)-{[(R)-[difluoro(phosphono)methyl](hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]cytidine

ChemComp-VC8:
4-amino-1-{2-deoxy-5-O-[(R)-{[(R)-[dichloro(phosphono)methyl](hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]-alpha-L-threo-pentofuranosyl}pyrimidin-2(1H)-one

ChemComp-VC9:
2'-deoxy-5'-O-[(R)-{[(R)-[dibromo(phosphono)methyl](hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]cytidine

ChemComp-EJH:
[(~{S})-chloranyl-[[[(2~{R},3~{S},5~{R})-5-[5-methyl-2,4-bis(oxidanylidene)pyrimidin-1-yl]-3-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]methyl]phosphonic acid

Source
  • homo sapiens (human)
KeywordsTRANSFERASE/DNA / DNA Polymerase Beta / Conformational Change / enzyme mechanism / LFER / TRANSFERASE-DNA complex / transcription/DNA / transcription-DNA complex / Acidity Modification / REPLICATION

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