SMTL ID : 6dsw.1

Bst DNA polymerase I pre-chemistry (n) structure

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.59 Å

Oligo State

monomer

Ligands

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

DG-DC-DG-DA-DT-DC-DA-DC-DG.1: 30 residues within 4Å: Chain A: C.6, G.7, T.8, G.9, A.10, T.11, C.12, G.13, C.14, A.15 Chain B: T.256, S.259, T.260, S.261, A.262, R.282, K.286, Y.291, R.319, Q.328, N.329, I.330, P.331, I.332, R.333, Y.418, Q.501, V.532, H.533, D.534 Protein-ligand interaction information (PLIP) not available

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

MPD.2: 5 residues within 4Å: Chain B: A.4, F.5, R.47, R.153, A.156 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:R.153, B:A.156

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

SO4.3: 3 residues within 4Å: Chain B: H.386, R.406, K.410 3 PLIP interactions: 3 interactions with chain B Water bridges: B:Q.360 Salt bridges: B:R.406, B:K.410 SO4.4: 2 residues within 4Å: Chain B: S.432, R.433 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.433 Water bridges: B:R.433, B:K.434 Salt bridges: B:R.433

1 x MG: MAGNESIUM ION(Non-covalent)

MG.5: 3 residues within 4Å: Chain B: D.357, Y.358, D.534 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.357, B:Y.358, H2O.17, H2O.25

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chim, N. et al., Crystal structures of DNA polymerase I capture novel intermediates in the DNA synthesis pathway. Elife (2018)

Release Date

2018-10-31

Peptides

DNA polymerase I: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

B
A

DNA polymerase I

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