SMTL ID : 3nn4.1

Structure of chlorite dismutase from Candidatus Nitrospira defluvii R173K mutant

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

homo-pentamer

Ligands

5 x HEM: PROTOPORPHYRIN IX CONTAINING FE(Non-covalent)

HEM.1: 24 residues within 4Å: Chain A: P.111, T.112, Y.113, V.114, F.117, L.125, I.140, I.142, K.144, W.148, M.160, H.163, T.164, A.167, L.171, K.176, L.178, F.189, T.191, F.193, L.204, L.208, E.213, F.220 27 PLIP interactions: 26 interactions with chain A, 1 Ligand-Water interactions, Hydrophobic interactions: A:V.114, A:F.117, A:L.125, A:L.125, A:I.140, A:A.167, A:L.171, A:K.176, A:L.178, A:L.178, A:F.189, A:T.191, A:F.193, A:F.193, A:L.204, A:L.204, A:L.204, A:L.208, A:F.220, A:F.220 Hydrogen bonds: A:T.112, A:Y.113, A:V.114 Salt bridges: A:K.144 pi-Cation interactions: A:K.176 Metal complexes: A:H.163, H2O.1 HEM.6: 23 residues within 4Å: Chain B: P.111, T.112, Y.113, V.114, L.125, I.140, I.142, K.144, W.148, M.160, H.163, T.164, A.167, L.171, K.176, L.178, F.189, T.191, F.193, L.204, L.208, E.213, F.220 20 PLIP interactions: 20 interactions with chain B, Hydrophobic interactions: B:V.114, B:I.140, B:A.167, B:L.171, B:K.176, B:F.189, B:F.189, B:T.191, B:F.193, B:F.193, B:L.208, B:F.220 Hydrogen bonds: B:T.112, B:Y.113, B:V.114, B:E.213 Salt bridges: B:K.144 pi-Stacking: B:H.163 pi-Cation interactions: B:K.176 Metal complexes: B:H.163 HEM.11: 25 residues within 4Å: Chain C: P.111, T.112, Y.113, V.114, F.117, L.125, I.140, I.142, K.144, W.148, M.160, H.163, T.164, A.167, L.168, L.171, K.176, L.178, F.189, T.191, F.193, L.204, L.208, E.213, F.220 26 PLIP interactions: 25 interactions with chain C, 1 Ligand-Water interactions, Hydrophobic interactions: C:V.114, C:F.117, C:L.125, C:L.125, C:I.140, C:A.167, C:L.168, C:L.171, C:K.176, C:L.178, C:F.189, C:F.189, C:F.189, C:F.193, C:F.193, C:F.193, C:L.204, C:L.208, C:F.220, C:F.220 Hydrogen bonds: C:T.112, C:Y.113, C:V.114 Salt bridges: C:K.144 Metal complexes: C:H.163, H2O.4 HEM.17: 24 residues within 4Å: Chain D: P.111, T.112, Y.113, V.114, F.117, L.125, I.140, I.142, K.144, W.148, M.160, H.163, T.164, A.167, L.171, K.176, L.178, F.189, T.191, F.193, L.204, L.208, E.213, F.220 20 PLIP interactions: 20 interactions with chain D, Hydrophobic interactions: D:F.117, D:L.125, D:L.125, D:I.140, D:A.167, D:L.171, D:K.176, D:L.178, D:L.178, D:F.189, D:F.193, D:F.193, D:L.208, D:F.220, D:F.220 Hydrogen bonds: D:T.112, D:Y.113, D:V.114 Salt bridges: D:K.144 Metal complexes: D:H.163 HEM.20: 25 residues within 4Å: Chain E: P.111, T.112, Y.113, V.114, F.117, L.125, I.140, I.142, K.144, W.148, M.160, H.163, T.164, A.167, L.168, L.171, K.176, L.178, F.189, T.191, F.193, L.204, L.208, E.213, F.220 24 PLIP interactions: 24 interactions with chain E, Hydrophobic interactions: E:V.114, E:F.117, E:L.125, E:I.140, E:T.164, E:A.167, E:L.168, E:L.171, E:K.176, E:F.189, E:F.189, E:T.191, E:F.193, E:F.193, E:L.208, E:F.220, E:F.220 Hydrogen bonds: E:T.112, E:Y.113, E:Y.113, E:V.114, E:E.213 Salt bridges: E:K.144 Metal complexes: E:H.163

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

SO4.2: 3 residues within 4Å: Chain A: K.176, K.177, L.178 Ligand excluded by PLIP SO4.3: 4 residues within 4Å: Chain A: K.143, R.218, R.219 Chain C: H.222 Ligand excluded by PLIP SO4.4: 6 residues within 4Å: Chain A: K.109, T.112, H.180, F.189 Chain C: H.202, R.206 Ligand excluded by PLIP SO4.5: 5 residues within 4Å: Chain A: E.196, R.197, L.198, E.199 Chain E: Y.16 Ligand excluded by PLIP SO4.7: 3 residues within 4Å: Chain B: K.176, K.177, L.178 Ligand excluded by PLIP SO4.8: 4 residues within 4Å: Chain B: K.143, R.218, R.219 Chain D: H.222 Ligand excluded by PLIP SO4.9: 5 residues within 4Å: Chain B: K.109, T.112, H.180 Chain D: H.202, R.206 Ligand excluded by PLIP SO4.10: 5 residues within 4Å: Chain B: E.196, R.197, L.198, E.199 Chain C: Y.16 Ligand excluded by PLIP SO4.12: 3 residues within 4Å: Chain C: K.176, K.177, L.178 Ligand excluded by PLIP SO4.13: 5 residues within 4Å: Chain B: H.222 Chain C: K.143, D.186, R.218, R.219 Ligand excluded by PLIP SO4.14: 5 residues within 4Å: Chain B: H.202, R.206 Chain C: K.109, T.112, H.180 Ligand excluded by PLIP SO4.15: 4 residues within 4Å: Chain B: D.30 Chain C: R.93, R.96, H.97 Ligand excluded by PLIP SO4.16: 5 residues within 4Å: Chain A: Y.16 Chain C: E.196, R.197, L.198, E.199 Ligand excluded by PLIP SO4.18: 3 residues within 4Å: Chain D: K.176, K.177, L.178 Ligand excluded by PLIP SO4.19: 4 residues within 4Å: Chain B: Y.16 Chain D: E.196, R.197, L.198 Ligand excluded by PLIP SO4.21: 3 residues within 4Å: Chain E: K.176, K.177, L.178 Ligand excluded by PLIP SO4.22: 4 residues within 4Å: Chain A: H.222 Chain E: K.143, R.218, R.219 Ligand excluded by PLIP SO4.23: 4 residues within 4Å: Chain D: K.143, R.218, R.219 Chain E: H.222 Ligand excluded by PLIP SO4.24: 6 residues within 4Å: Chain D: K.109, T.112, H.180 Chain E: H.202, N.203, R.206 Ligand excluded by PLIP SO4.25: 5 residues within 4Å: Chain A: H.202, R.206 Chain E: K.109, T.112, H.180 Ligand excluded by PLIP SO4.26: 5 residues within 4Å: Chain D: Y.16 Chain E: E.196, R.197, L.198, E.199 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kostan, J. et al., Structural and functional characterisation of the chlorite dismutase from the nitrite-oxidizing bacterium "Candidatus Nitrospira defluvii": Identification of a catalytically important amino acid residue. J.Struct.Biol. (2010)

Release Date

2010-07-28

Peptides

Chlorite dismutase: ABCDE

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

Chlorite dismutase