SMTL ID : 3tan.1

Crystal Structure of Bacillus DNA Polymerase I Large Fragment Bound to Duplex DNA with Cytosine-Adenine Mismatch at (n-1) Position

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.53 Å

Oligo State

monomer

Ligands

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

GLC-FRU.1: 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 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:R.331, A:R.91, A:R.91, A:D.124, A:N.323, A:N.323, A:N.323, A:E.41, A:R.91, A:D.124 Water bridges: A:H.545, A:Y.43, A:D.88, A:R.91, A:Q.324, A:E.41, A:T.335, A:T.335, A:E.336

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

SO4.2: 4 residues within 4Å: Chain A: Q.372, H.398, R.418, K.422 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:H.398 Water bridges: A:Q.372, A:R.418, A:K.422 Salt bridges: A:R.418, A:K.422 SO4.3: 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 SO4.4: 2 residues within 4Å: Chain A: E.533, R.535 5 PLIP interactions: 5 interactions with chain A Water bridges: A:R.535, A:R.535, A:R.535, A:R.535 Salt bridges: A:R.535 SO4.5: 2 residues within 4Å: Chain A: S.444, R.445 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.445 Water bridges: A:K.446

1 x DCP: 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE(Non-covalent)

DCP.6: 9 residues within 4Å: Chain A: R.182, E.185, Q.186, D.187, R.188, L.189, L.482, L.483, H.484 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:E.185 Hydrogen bonds: A:D.187, A:D.187, A:R.188, A:R.188, A:L.189 Water bridges: A:H.484 Salt bridges: A:H.484 pi-Cation interactions: A:R.188

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wang, W. et al., Structural evidence for the rare tautomer hypothesis of spontaneous mutagenesis. Proc.Natl.Acad.Sci.USA (2011)

Release Date

2011-10-19

Peptides

DNA polymerase I: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

DNA polymerase I

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