SMTL ID : 4dwi.1

Crystal structure of fragment DNA polymerase I from Bacillus stearothermophilus with self complementary DNA, Se-dGTP and Calcium

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.85 Å

Oligo State

monomer

Ligands

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 8 residues within 4Å: Chain A: E.26, F.76, D.77, R.80, D.114, V.115, D.130, K.155 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:E.26, A:V.115 Water bridges: A:V.27, A:F.76, A:D.77, A:D.130 GOL.2: 8 residues within 4Å: Chain A: T.291, Y.292, L.296, P.326, N.327, N.330, I.331 Chain B: T.7 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.327, A:N.330, A:N.330 GOL.3: 5 residues within 4Å: Chain A: W.87, F.195, A.196, T.304, K.306 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.306 Water bridges: A:D.303 GOL.4: 7 residues within 4Å: Chain A: Y.32, D.77, K.79, R.80, F.311, N.312, Q.313 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:Y.32, A:D.77, A:K.79, A:R.80, A:N.312, A:Q.313 Water bridges: A:Q.313, A:A.314

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

SO4.5: 4 residues within 4Å: Chain A: K.3, M.4, A.5, R.48 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.5 Salt bridges: A:R.48 SO4.6: 3 residues within 4Å: Chain A: H.387, R.407, K.411 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:H.387 Water bridges: A:Q.361 Salt bridges: A:R.407, A:K.411 SO4.7: 2 residues within 4Å: Chain A: S.360, Q.361 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.361, A:Q.361 SO4.8: 3 residues within 4Å: Chain A: R.11, T.13, E.14 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.14 Water bridges: A:E.15 Salt bridges: A:R.11 SO4.9: 1 residues within 4Å: Chain A: R.524 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.524 SO4.10: 4 residues within 4Å: Chain A: S.235, K.237, Q.238 Chain B: A.10 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.235, A:S.235, A:Q.238 Salt bridges: A:K.237

1 x 9MG: 9-METHYLGUANINE(Non-functional Binders)

9MG.11: 4 residues within 4Å: Chain B: A.10 Chain C: C.2, T.3 Ligands: CA.12 No protein-ligand interaction detected (PLIP)

1 x CA: CALCIUM ION(Non-functional Binders)

CA.12: 2 residues within 4Å: Chain C: C.2 Ligands: 9MG.11 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gan, J.H. et al., Biochemical and structural insights into the fidelity of bacillus stearothermophilus DNA polymerase. To be Published

Release Date

2013-03-27

Peptides

DNA polymerase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

DNA polymerase

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