SMTL ID : 1l3s.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 1.70 Å

Oligo State

monomer

Ligands

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

DG-DC-DG-DA-DT-DC-DA-DC-DG.1: 31 residues within 4Å: Chain A: C.7, G.8, T.9, G.10, A.11, T.12, C.13, G.14, C.15, A.16 Chain B: T.254, K.255, 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

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

GLC-FRU.2: 10 residues within 4Å: Chain B: E.29, N.30, Y.31, D.76, R.79, L.99, D.112, I.309, N.311, T.323 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.79, B:D.112, B:N.311, B:N.311, B:A.313, B:R.79 Water bridges: B:D.76, B:R.79, B:Q.312 GLC-FRU.3: 5 residues within 4Å: Chain B: E.455, V.458, K.462, R.488, E.492 17 PLIP interactions: 17 interactions with chain B Hydrogen bonds: B:E.455, B:E.492, B:K.462, B:K.462, B:E.492, B:G.415, B:S.421, B:S.421, B:G.424, B:R.433, B:N.486, B:R.493, B:R.493 Water bridges: B:E.455, B:E.492, B:R.488, B:R.488 Hydrophobic interactions: B:Y.423, B:Y.423, B:F.485 Salt bridges: B:D.422, B:R.493 pi-Stacking: B:Y.418, B:Y.418, B:Y.423 pi-Cation interactions: B:R.493

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

SO4.4: 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 SO4.5: 1 residues within 4Å: Chain B: R.523 3 PLIP interactions: 3 interactions with chain B Water bridges: B:R.523, B:R.523 Salt bridges: B:R.523 SO4.6: 4 residues within 4Å: Chain B: K.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 SO4.7: 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:S.432, B:K.434 Salt bridges: B:R.433 SO4.8: 3 residues within 4Å: Chain B: S.421, D.422, I.440 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.422

1 x MG: MAGNESIUM ION(Non-covalent)

MG.9: 3 residues within 4Å: Chain B: D.357, Y.358, D.534 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:D.357, B:Y.358

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Johnson, S.J. et al., Processive DNA synthesis observed in a polymerase crystal suggests a mechanism for the prevention of frameshift mutations. Proc.Natl.Acad.Sci.USA (2003)

Release Date

2003-03-25

Peptides

DNA Polymerase I: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

B
A

DNA Polymerase I

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