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Structure paper

TitleAmino Acid templating mechanisms in selection of nucleotides opposite abasic sites by a family a DNA polymerase.
Journal, issue, pagesJ. Biol. Chem., Vol. 287, Page 14099-14108, Year 2012
Publish dateApr 29, 2011 (structure data deposition date)
AuthorsObeid, S. / Welte, W. / Diederichs, K. / Marx, A.
External linksJ. Biol. Chem. / PubMed:22318723
MethodsX-ray diffraction
Resolution1.8 - 2.4 Å
Structure data

PDB-3rr7:
Binary Structure of the large fragment of Taq DNA polymerase bound to an abasic site
Method: X-RAY DIFFRACTION / Resolution: 1.95 Å

PDB-3rr8:
Ternary Structure of the large fragment of Taq DNA polymerase bound to an abasic site and a ddGTP
Method: X-RAY DIFFRACTION / Resolution: 2.4 Å

PDB-3rrg:
Ternary Structure of the large fragment of Taq DNA polymerase bound to an abasic site and a ddGTP
Method: X-RAY DIFFRACTION / Resolution: 2.3 Å

PDB-3rrh:
Ternary Structure of the large fragment of Taq DNA polymerase bound to an abasic site and a ddTTP
Method: X-RAY DIFFRACTION / Resolution: 1.8 Å

PDB-3t3f:
Ternary Structure of the large fragment of Taq DNA polymerase bound to an abasic site and dNITP
Method: X-RAY DIFFRACTION / Resolution: 1.9 Å

Chemicals

ChemComp-FMT:
FORMIC ACID

ChemComp-GOL:
GLYCEROL

ChemComp-MG:
Unknown entry

ChemComp-HOH:
WATER

ChemComp-DG3:
2'-3'-DIDEOXYGUANOSINE-5'-TRIPHOSPHATE

ChemComp-NA:
Unknown entry

ChemComp-ACT:
ACETATE ION

ChemComp-TTP:
THYMIDINE-5'-TRIPHOSPHATE

ChemComp-PGE:
TRIETHYLENE GLYCOL

ChemComp-N5P:
1-{2-DEOXY-5-O-[(R)-HYDROXY{[(R)-HYDROXY(PHOSPHONOOXY)PHOSPHORYL]OXY}PHOSPHORYL]-BETA-D-ERYTHRO-PENTOFURANOSYL}-5-NITRO

Source
  • thermus aquaticus (bacteria)
KeywordsTRANSFERASE/DNA / DNA polymerase / Abasic site / Translesion synthesis / TRANSFERASE-DNA complex / A-rule / base stacking / dNITP / Nitroindol triphosphate / base analogue

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