SMTL ID : 2hvh.1 (1 other biounit)

ddCTP:O6MeG pair in the polymerase active site (0 position)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.49 Å

Oligo State

monomer

Ligands

1 x DC- DC- DT- DG- DA- DC- DT- DC- DDG: 5'-D(*CP*CP*TP*GP*AP*CP*TP*CP*(DDG))-3'(Non-covalent)

DC-DC-DT-DG-DA-DC-DT-DC-DDG.1: 33 residues within 4Å: Chain A: C.5, G.6, A.7, G.8, T.9, C.10, A.11, G.12, G.13 Chain B: T.254, K.255, T.256, S.259, T.260, S.261, A.262, R.282, Q.283, K.286, Y.291, R.319, Q.328, N.329, I.330, P.331, I.332, R.333, L.334, Q.501, V.532, H.533, D.534 Ligands: DCT.8 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:R.319, B:R.319, B:R.333, B:Q.501 Salt bridges: B:R.333

2 x GLC- FRU: beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose(Non-covalent)

GLC-FRU.2: 9 residues within 4Å: Chain B: E.29, Y.31, D.76, R.79, L.99, V.111, D.112, N.311, A.313 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.79, B:V.111, B:D.112, B:N.311, B:A.313, B:E.29, B:R.79, B:N.311 Water bridges: B:Y.31, B:K.78, B:Q.312 GLC-FRU.3: 6 residues within 4Å: Chain B: E.173, D.175, R.176, L.470, L.471, H.472 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:D.175, B:R.176, B:R.176, B:L.471

1 x MN: MANGANESE (II) ION(Non-covalent)

MN.4: 4 residues within 4Å: Chain B: D.357, Y.358, D.534 Ligands: DCT.8 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:D.357, B:Y.358

3 x SO4: SULFATE ION(Non-functional Binders)

SO4.5: 2 residues within 4Å: Chain B: T.12, E.13 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.13 SO4.6: 2 residues within 4Å: Chain B: R.483, N.484 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.484 Salt bridges: B:R.483 SO4.7: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

1 x DCT: 2',3'-DIDEOXYCYTIDINE 5'-TRIPHOSPHATE(Non-covalent)

DCT.8: 17 residues within 4Å: Chain A: G.4, C.5 Chain B: R.319, D.357, Y.358, S.359, Q.360, I.361, E.362, H.386, R.406, K.410, A.411, Y.414, D.534 Ligands: DC-DC-DT-DG-DA-DC-DT-DC-DDG.1, MN.4 15 PLIP interactions: 15 interactions with chain B Hydrophobic interactions: B:E.362, B:Y.414 Hydrogen bonds: B:R.319, B:S.359, B:Q.360, B:I.361, B:Y.414 Water bridges: B:R.333 Salt bridges: B:H.386, B:H.386, B:R.406, B:K.410, B:K.410, B:K.410 pi-Stacking: B:Y.414

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Warren, J.J. et al., The structural basis for the mutagenicity of O6-methyl-guanine lesions. Proc.Natl.Acad.Sci.Usa (2006)

Release Date

2006-12-12

Peptides

DNA Polymerase I: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

B
A

DNA Polymerase I

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