SMTL ID : 1nke.1

A BACILLUS DNA POLYMERASE I PRODUCT COMPLEX BOUND TO A CYTOSINE-THYMINE MISMATCH AFTER A SINGLE ROUND OF PRIMER EXTENSION, FOLLOWING INCORPORATION OF DCTP.

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

monomer

Ligands

2 x SUC: SUGAR (SUCROSE)(Non-covalent)

SUC.1: 9 residues within 4Å: Chain C: E.29, N.30, Y.31, D.76, R.79, L.99, D.112, I.309, N.311 9 PLIP interactions: 9 interactions with chain C Hydrogen bonds: C:E.29, C:R.79, C:D.112, C:N.311, C:N.311 Salt bridges: C:R.79 Water bridges: C:D.76, C:R.79, C:Q.312 SUC.2: 9 residues within 4Å: Chain C: E.219, Y.223, F.230, N.231, I.232, N.233, Y.281 Chain B: A.11, T.12 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:Y.223, C:N.231, C:N.231, C:I.232, C:N.233, C:N.233

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

SO4.3: 3 residues within 4Å: Chain C: H.386, R.406, K.410 2 PLIP interactions: 2 interactions with chain C Salt bridges: C:R.406, C:K.410 SO4.4: 1 residues within 4Å: Chain C: R.523 2 PLIP interactions: 2 interactions with chain C Salt bridges: C:R.523 Water bridges: C:R.523 SO4.5: 3 residues within 4Å: Chain C: M.3, A.4, R.47 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:A.4 Salt bridges: C:R.47 SO4.6: 2 residues within 4Å: Chain C: S.432, R.433 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:R.433 SO4.7: 1 residues within 4Å: Chain C: I.440 No protein-ligand interaction detected (PLIP)

1 x MG: MAGNESIUM ION(Non-covalent)

MG.8: 3 residues within 4Å: Chain C: D.357, Y.358, D.534 4 PLIP interactions: 3 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.357, C:Y.358, C:D.534, H2O.4096

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

DCP.9: 7 residues within 4Å: Chain C: E.173, Q.174, D.175, R.176, L.177, L.471, H.472 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:D.175, C:R.176, C:L.177 Salt bridges: C:R.176, C:R.176 pi-Cation interactions: C:R.176

Links

RCSB   PDBe   PDBj   PDBsum   CATH   PLIP

Citation

Johnson, S.J. et al., Structures of mismatch replication errors observed in a DNA polymerase. Cell(Cambridge,Mass.) (2004)

Release Date

2004-03-30

Peptides

DNA POLYMERASE I: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

C
A

DNA POLYMERASE I

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