SMTL ID : 3fhg.2 (1 other biounit)

Crystal structure of Sulfolobus solfataricus 8-oxoguanine DNA glycosylase (SsOgg)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-dimer

Ligands

10 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 7 residues within 4Å: Chain A: H.132, R.135, I.144, D.194, W.198, V.206, K.207 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.135, A:R.135, A:D.194, A:K.207 Water bridges: A:F.48 GOL.2: 5 residues within 4Å: Chain A: R.35, E.36, Y.52, L.55, K.207 6 PLIP interactions: 5 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:R.35, A:Y.52, A:Y.52, A:K.207 Water bridges: A:E.21, B:N.203 GOL.3: 4 residues within 4Å: Chain A: N.29, E.30, K.101 Ligands: SO4.9 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.30, A:K.101, A:K.101 GOL.4: 4 residues within 4Å: Chain A: N.187, M.188, S.189, I.192 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.189, A:S.189 GOL.5: 5 residues within 4Å: Chain A: E.110, D.111, Q.112, Q.113, D.141 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.110, A:D.111, A:Q.112, A:Q.113 GOL.16: 7 residues within 4Å: Chain B: H.132, R.135, I.144, D.194, W.198, V.206, K.207 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:R.135, B:R.135, B:D.194, B:K.207 Water bridges: B:F.48 GOL.17: 5 residues within 4Å: Chain B: R.35, E.36, Y.52, L.55, K.207 6 PLIP interactions: 5 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:R.35, B:Y.52, B:Y.52, B:K.207 Water bridges: B:E.21, A:N.203 GOL.18: 4 residues within 4Å: Chain B: N.29, E.30, K.101 Ligands: SO4.24 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.30, B:K.101, B:K.101 GOL.19: 4 residues within 4Å: Chain B: N.187, M.188, S.189, I.192 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.189, B:S.189 GOL.20: 5 residues within 4Å: Chain B: E.110, D.111, Q.112, Q.113, D.141 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:E.110, B:D.111, B:Q.112, B:Q.113

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

SO4.6: 3 residues within 4Å: Chain A: K.75, Y.82, N.83 Ligand excluded by PLIP SO4.7: 3 residues within 4Å: Chain A: E.117, R.118, N.121 Ligand excluded by PLIP SO4.8: 9 residues within 4Å: Chain A: R.14, N.203, T.204, I.205 Chain B: R.14, N.203, T.204, I.205 Ligands: SO4.23 Ligand excluded by PLIP SO4.9: 5 residues within 4Å: Chain A: N.26, L.27, K.101, K.105 Ligands: GOL.3 Ligand excluded by PLIP SO4.10: 3 residues within 4Å: Chain A: L.58, G.59, Q.60 Ligand excluded by PLIP SO4.11: 1 residues within 4Å: Chain A: K.61 Ligand excluded by PLIP SO4.12: 1 residues within 4Å: Chain A: G.124 Ligand excluded by PLIP SO4.13: 2 residues within 4Å: Chain A: D.146, R.147 Ligand excluded by PLIP SO4.14: 2 residues within 4Å: Chain A: S.168, K.169 Ligand excluded by PLIP SO4.15: 3 residues within 4Å: Chain A: R.23, F.140, S.189 Ligand excluded by PLIP SO4.21: 3 residues within 4Å: Chain B: K.75, Y.82, N.83 Ligand excluded by PLIP SO4.22: 3 residues within 4Å: Chain B: E.117, R.118, N.121 Ligand excluded by PLIP SO4.23: 9 residues within 4Å: Chain A: R.14, N.203, T.204, I.205 Chain B: R.14, N.203, T.204, I.205 Ligands: SO4.8 Ligand excluded by PLIP SO4.24: 5 residues within 4Å: Chain B: N.26, L.27, K.101, K.105 Ligands: GOL.18 Ligand excluded by PLIP SO4.25: 3 residues within 4Å: Chain B: L.58, G.59, Q.60 Ligand excluded by PLIP SO4.26: 1 residues within 4Å: Chain B: K.61 Ligand excluded by PLIP SO4.27: 1 residues within 4Å: Chain B: G.124 Ligand excluded by PLIP SO4.28: 2 residues within 4Å: Chain B: D.146, R.147 Ligand excluded by PLIP SO4.29: 2 residues within 4Å: Chain B: S.168, K.169 Ligand excluded by PLIP SO4.30: 3 residues within 4Å: Chain B: R.23, F.140, S.189 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Faucher, F. et al., Crystal structures of two archaeal 8-oxoguanine DNA glycosylases provide structural insight into guanine/8-oxoguanine distinction. Structure (2009)

Release Date

2009-05-19

Peptides

N-glycosylase/DNA lyase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

N-glycosylase/DNA lyase

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