SMTL ID : 4dsi.1

Crystal structure of fragment DNA polymerase I from Bacillus stearothermophilus with duplex DNA, Se-dGTP and Calcium

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.05 Å

Oligo State

monomer

Ligands

1 x DC- DC- DT- DG- DA- DC- DT- DC- DG: Se-dGTP(Non-covalent)

DC-DC-DT-DG-DA-DC-DT-DC-DG.1: 40 residues within 4Å: Chain A: N.232, N.234, S.235, K.237, Q.238, K.287, S.290, T.291, G.295, N.312, L.315, T.316, Q.317, T.318, R.320, S.322, S.323, T.324, E.325, N.327, Y.419, R.476, F.491, R.494, M.495, N.498, Q.502 Chain B: C.4, G.5, A.6, G.7, T.8, C.9, A.10, G.11, G.12 Ligands: GOL.3, SO4.8, DGP.10, CA.11 Protein-ligand interaction information (PLIP) not available

5 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 8 residues within 4Å: Chain A: E.26, F.76, D.77, R.80, D.114, V.115, D.130, K.155 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:E.26, A:V.115 Water bridges: A:V.27, A:F.76, A:D.77, A:D.130 GOL.3: 8 residues within 4Å: Chain A: T.291, Y.292, G.295, L.296, P.326, N.327, N.330 Ligands: DC-DC-DT-DG-DA-DC-DT-DC-DG.1 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.327, A:N.330, A:N.330 GOL.4: 6 residues within 4Å: Chain A: W.87, F.195, A.196, T.304, K.306, H.308 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.306, A:K.306 GOL.5: 7 residues within 4Å: Chain A: Y.32, D.77, K.79, R.80, F.311, N.312, Q.313 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:Y.32, A:Y.32, A:K.79, A:R.80, A:F.311, A:Q.313 Water bridges: A:N.312, A:A.314 GOL.6: 7 residues within 4Å: Chain A: I.417, G.420, I.421, S.422, I.441, F.445, M.455 1 PLIP interactions: 1 interactions with chain A Water bridges: A:D.423

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

SO4.7: 3 residues within 4Å: Chain A: M.4, A.5, R.48 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.5 Salt bridges: A:R.48 SO4.8: 4 residues within 4Å: Chain A: Y.419, F.491, R.494 Ligands: DC-DC-DT-DG-DA-DC-DT-DC-DG.1 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.494 SO4.9: 3 residues within 4Å: Chain A: H.387, R.407, K.411 5 PLIP interactions: 5 interactions with chain A Water bridges: A:Q.361, A:H.387 Salt bridges: A:H.387, A:R.407, A:K.411

1 x DGP: 2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE(Non-functional Binders)

DGP.10: 2 residues within 4Å: Chain B: C.4 Ligands: DC-DC-DT-DG-DA-DC-DT-DC-DG.1 No protein-ligand interaction detected (PLIP)

1 x CA: CALCIUM ION(Non-covalent)

CA.11: 4 residues within 4Å: Chain A: N.232, N.234 Ligands: DC-DC-DT-DG-DA-DC-DT-DC-DG.1, DC-DC-DT-DG-DA-DC-DT-DC-DG.1 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gan, J.H. et al., Biochemical and structural insights into the fidelity of bacillus stearothermophilus DNA polymerase. To be Published

Release Date

2013-03-27

Peptides

DNA polymerase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

DNA polymerase

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