SMTL ID : 4o0i.1

Crystal structure of fragment DNA polymerase I from Bacillus stearothermophilus with 2'-MeSe-arabino-guanosine derivatized DNA

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

monomer

Ligands

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

SO4.1: 3 residues within 4Å: Chain A: M.3, A.4, R.47 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.4 Salt bridges: A:R.47 SO4.2: 3 residues within 4Å: Chain A: H.386, R.406, K.410 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:R.406, A:K.410 SO4.3: 4 residues within 4Å: Chain A: R.10, V.11, T.12, E.13 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.13 Water bridges: A:E.14 Salt bridges: A:R.10 SO4.4: 5 residues within 4Å: Chain A: E.68, K.71, G.93, V.94, S.95 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.68 Salt bridges: A:K.71 SO4.5: 7 residues within 4Å: Chain A: E.219, Y.223, F.230, N.231, I.232, N.233, Y.281 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:Y.223, A:N.231, A:I.232, A:N.233, A:N.233, A:Y.281, A:Y.281 SO4.6: 5 residues within 4Å: Chain A: E.371, D.372, D.373, G.449, R.452 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.372, A:D.373, A:G.449 Salt bridges: A:R.452

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 9 residues within 4Å: Chain A: E.25, F.75, D.76, R.79, D.113, V.114, D.129, K.154 Ligands: NA.9 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:E.25, A:V.114 Water bridges: A:E.25, A:V.26, A:D.129

2 x NA: SODIUM ION(Non-functional Binders)

NA.8: 3 residues within 4Å: Chain A: T.12, E.14, F.48 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.14, A:E.14 NA.9: 6 residues within 4Å: Chain A: V.24, F.75, D.76, R.79, A.80 Ligands: GOL.7 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:F.75, A:A.80 Water bridges: A:E.25, A:F.75

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Jiang, S. et al., Crystal structure of fragment DNA polymerase I from Bacillus stearothermophilus with 2'-MeSe-arabino-guanosine derivatized DNA. TO BE PUBLISHED

Release Date

2014-12-17

Peptides

DNA polymerase I: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

DNA polymerase I