SMTL ID : 2bdp.1

CRYSTAL STRUCTURE OF BACILLUS DNA POLYMERASE I FRAGMENT COMPLEXED TO 9 BASE PAIRS OF DUPLEX DNA

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

monomer

Ligands

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

DG-DC-DA-DT-DG-DA-DT-DG-DC.1: 28 residues within 4Å: Chain A: G.2, C.3, A.4, T.5, C.6, A.7, T.8, G.9, C.10 Chain B: T.254, K.255, T.260, S.261, A.262, R.282, Q.283, K.286, Y.291, R.319, Q.328, N.329, I.330, P.331, I.332, R.333, V.532, H.533, D.534 28 PLIP interactions: 28 interactions with chain B Hydrogen bonds: B:N.231, B:S.289, B:Q.316, B:R.319, B:R.319, B:S.321, B:E.324, B:N.326, B:N.329, B:A.411, B:G.415, B:Q.427, B:Q.501 Water bridges: B:K.286, B:Q.316, B:E.362, B:Y.418, B:Y.418, B:N.428, B:R.475, B:N.497, B:N.497 Salt bridges: B:K.236, B:R.475, B:R.493 pi-Stacking: B:Y.418, B:Y.418, B:Y.418

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

SO4.2: 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 SO4.3: 2 residues within 4Å: Chain B: E.521, R.523 3 PLIP interactions: 3 interactions with chain B Water bridges: B:R.523, B:R.523 Salt bridges: B:R.523 SO4.4: 4 residues within 4Å: Chain B: A.2, M.3, A.4, R.47 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:A.4 Salt bridges: B:R.47

1 x MG: MAGNESIUM ION(Non-covalent)

MG.5: 3 residues within 4Å: Chain B: D.357, Y.358, D.534 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.357, B:Y.358, B:D.534, H2O.17

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kiefer, J.R. et al., Visualizing DNA replication in a catalytically active Bacillus DNA polymerase crystal. Nature (1998)

Release Date

1999-01-13

Peptides

PROTEIN (DNA POLYMERASE I): B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

B
A

PROTEIN (DNA POLYMERASE I)

Related Entries With Identical Sequence