SMTL ID : 3px6.1 (1 other biounit)

Crystal Structure of Bacillus DNA Polymerase I Large Fragment Bound to DNA and ddCTP-dA Mismatch (tautomer) in Closed Conformation

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.59 Å

Oligo State

monomer

Ligands

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

DC-DC-DT-DG-DA-DC-DT-DC-DOC.1: 37 residues within 4Å: Chain A: P.247, T.266, K.267, T.268, S.271, T.272, S.273, A.274, L.291, R.294, Q.295, K.298, Y.303, R.331, Q.340, N.341, I.342, P.343, I.344, R.345, L.346, R.353, R.419, V.544, H.545, D.546, E.547 Chain B: G.5, G.6, A.7, G.8, T.9, C.10, A.11, G.12, G.13 Ligands: DCT.2 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:H.545 Hydrogen bonds: A:R.331, A:R.331 Water bridges: A:R.419, A:R.419, A:R.419, A:R.419, A:K.422, A:H.545 Salt bridges: A:R.419

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

DCT.2: 18 residues within 4Å: Chain A: R.331, D.369, Y.370, S.371, Q.372, I.373, E.374, H.398, R.418, K.422, A.423, Y.426, Y.430, D.546 Chain B: A.4, G.5 Ligands: DC-DC-DT-DG-DA-DC-DT-DC-DOC.1, MN.4 17 PLIP interactions: 17 interactions with chain A Hydrophobic interactions: A:I.373, A:Y.426 Hydrogen bonds: A:R.331, A:S.371, A:Q.372, A:I.373, A:Y.426 Water bridges: A:K.422, A:K.422, A:K.422, A:K.422 Salt bridges: A:H.398, A:R.418, A:K.422, A:K.422, A:K.422 pi-Stacking: A:Y.426 DCT.3: 9 residues within 4Å: Chain A: R.182, E.185, Q.186, D.187, R.188, L.189, L.482, L.483, H.484 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:E.185 Hydrogen bonds: A:D.187, A:D.187, A:R.188, A:R.188, A:L.189 Salt bridges: A:H.484 pi-Cation interactions: A:R.188

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

MN.4: 6 residues within 4Å: Chain A: D.369, Y.370, S.371, I.373, D.546 Ligands: DCT.2 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.369, A:Y.370, A:D.546

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

SO4.5: 2 residues within 4Å: Chain A: R.495, N.496 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.496 Salt bridges: A:R.495 SO4.6: 2 residues within 4Å: Chain A: A.69, D.70 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:A.69

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wang, W. et al., Structural evidence for the rare tautomer hypothesis of spontaneous mutagenesis. Proc.Natl.Acad.Sci.USA (2011)

Release Date

2011-10-19

Peptides

DNA polymerase I: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

DNA polymerase I

Related Entries With Identical Sequence