SMTL ID : 4f2s.2 (1 other biounit)

DNA Polymerase I Large Fragment complex 4

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.65 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.3 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.331, A:R.331

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

GLC-FRU.2: 15 residues within 4Å: Chain A: E.41, N.42, Y.43, F.87, D.88, K.90, R.91, L.111, D.124, D.125, I.321, N.323, Q.324, A.325, T.335 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.88, A:R.91, A:R.91, A:D.124, A:N.323, A:A.325, A:E.41, A:R.91 Water bridges: A:R.91, A:Q.324, A:A.325, A:E.336

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

CTP.3: 17 residues within 4Å: Chain A: R.331, R.345, S.371, Q.372, E.374, L.375, H.398, R.418, K.422, Y.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.4 16 PLIP interactions: 16 interactions with chain A Hydrogen bonds: A:R.331, A:Q.372, A:Q.372, A:E.374, A:K.422, A:Y.430 Water bridges: A:R.345, A:D.369, A:D.546 Salt bridges: A:H.398, A:H.398, A:R.418, A:K.422, A:K.422, A:K.422 pi-Stacking: A:Y.426

1 x MN: MANGANESE (II) ION(Non-functional Binders)

MN.4: 3 residues within 4Å: Chain A: S.371, Q.372 Ligands: CTP.3 No protein-ligand interaction detected (PLIP)

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

SO4.5: 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

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wang, W. et al., Structures of a High-fidelity DNA Polymerase. to be published

Release Date

2013-07-24

Peptides

DNA polymerase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
D

DNA polymerase

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