SMTL ID : 3taq.1

Crystal Structure of Bacillus DNA Polymerase I Large Fragment Bound to Duplex DNA with Cytosine-Adenine Mismatch at (n-4) Position

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.65 Å

Oligo State

monomer

Ligands

2 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 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.88, A:R.91, A:R.91, A:D.124, A:N.323, A:N.323, A:R.91, A:T.335 Water bridges: A:D.88, A:R.91, A:Q.324, A:E.41, A:D.124 GLC-FRU.2: 7 residues within 4Å: Chain A: E.467, V.470, Q.471, K.474, I.492, R.500, E.504 8 PLIP interactions: 8 interactions with chain A Water bridges: A:E.467, A:E.467, A:E.504, A:E.504, A:R.500, A:E.504, A:E.504, A:S.433, A:R.487 Hydrogen bonds: A:Q.471, A:K.474, A:R.500, A:E.504, A:G.427, A:Y.430 Hydrophobic interactions: A:Y.430 Salt bridges: A:R.505 pi-Stacking: A:Y.430, A:Y.430

1 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 4 residues within 4Å: Chain A: D.369, Y.370, S.371, D.546 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.369, A:Y.370, H2O.19

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

SO4.4: 1 residues within 4Å: Chain A: R.495 3 PLIP interactions: 3 interactions with chain A Water bridges: A:R.495, A:R.495 Salt bridges: A:R.495 SO4.5: 3 residues within 4Å: Chain A: H.398, R.418, K.422 3 PLIP interactions: 3 interactions with chain A Water bridges: A:Q.372 Salt bridges: A:R.418, A:K.422 SO4.6: 1 residues within 4Å: Chain A: S.361 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.361 SO4.7: 2 residues within 4Å: Chain A: R.393, K.400 3 PLIP interactions: 3 interactions with chain A Water bridges: A:R.393, A:R.393 Salt bridges: A:R.393

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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