SMTL ID : 4dqr.2 (1 other biounit)

Ternary complex of Bacillus DNA Polymerase I Large Fragment E658A, DNA duplex, and rCTP (paired with dG of template) in presence of Mn2+

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.95 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: 35 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, V.544, H.545, D.546 Chain B: G.5, G.6, A.7, G.8, T.9, C.10, A.11, G.12, G.13 Ligands: CTP.2 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:R.331, A:R.331 Water bridges: A:R.345, A:R.345, A:R.345 Salt bridges: A:R.345

1 x CTP: CYTIDINE-5'-TRIPHOSPHATE(Non-covalent)

CTP.2: 14 residues within 4Å: Chain A: R.331, Q.372, A.374, H.398, R.418, K.422, F.426, Y.430, Q.513, D.546 Chain B: G.4, G.5 Ligands: DC-DC-DT-DG-DA-DC-DT-DC-DOC.1, MN.3 18 PLIP interactions: 18 interactions with chain A Hydrophobic interactions: A:F.426 Hydrogen bonds: A:R.331, A:Q.372, A:Q.372 Water bridges: A:D.369, A:D.369, A:D.369, A:A.374, A:L.375, A:K.422, A:K.422, A:Y.430, A:Y.430 Salt bridges: A:H.398, A:R.418, A:K.422, A:K.422, A:K.422

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

MN.3: 3 residues within 4Å: Chain A: Y.370, D.546 Ligands: CTP.2 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.546, H2O.4, H2O.17

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

SO4.4: 4 residues within 4Å: Chain A: K.14, M.15, A.16, R.59 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.16 Salt bridges: A:R.59

2 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.5: 6 residues within 4Å: Chain A: T.213, E.217, L.308, V.311, P.313, K.316 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:T.213, A:P.313, A:K.316 Water bridges: A:E.217 MPD.6: 3 residues within 4Å: Chain A: A.69, D.70, P.71 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:D.70

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wang, W. et al., Structural factors that determine selectivity of a high fidelity DNA polymerase for deoxy-, dideoxy-, and ribonucleotides. J.Biol.Chem. (2012)

Release Date

2012-06-06

Peptides

DNA polymerase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
D

DNA polymerase

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