SMTL ID : 3nn2.1

Structure of chlorite dismutase from Candidatus Nitrospira defluvii in complex with cyanide

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.94 Å

Oligo State

homo-pentamer

Ligands

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

HEM.1: 26 residues within 4Å: Chain A: P.111, T.112, Y.113, V.114, F.117, L.125, I.140, I.142, W.148, M.160, H.163, T.164, A.167, L.171, R.176, L.178, F.189, T.191, F.193, L.204, L.208, F.214, F.220 Ligands: PO4.2, CYN.7, GOL.8 26 PLIP interactions: 26 interactions with chain A, Hydrophobic interactions: A:V.114, A:F.117, A:L.125, A:I.140, A:A.167, A:L.171, A:L.178, A:F.189, A:F.189, A:F.189, A:T.191, A:F.193, A:F.193, A:F.193, A:L.208, A:F.214, A:F.220, A:F.220 Hydrogen bonds: A:T.112, A:T.112, A:Y.113, A:V.114, A:W.148 Water bridges: A:T.112, A:H.180 Metal complexes: A:H.163 HEM.11: 27 residues within 4Å: Chain B: P.111, T.112, Y.113, V.114, F.117, L.125, I.140, I.142, W.148, M.160, H.163, T.164, A.167, Y.170, L.171, R.176, L.178, F.189, T.191, F.193, L.204, L.208, F.214, F.220 Ligands: PO4.15, CYN.16, GOL.17 25 PLIP interactions: 25 interactions with chain B, Hydrophobic interactions: B:V.114, B:F.117, B:L.125, B:L.125, B:I.140, B:A.167, B:Y.170, B:L.171, B:L.178, B:F.189, B:F.189, B:F.189, B:F.193, B:F.193, B:L.208, B:F.214, B:F.220, B:F.220 Hydrogen bonds: B:T.112, B:Y.113, B:V.114, B:W.148 Water bridges: B:T.112, B:T.112 Metal complexes: B:H.163 HEM.21: 27 residues within 4Å: Chain C: P.111, T.112, Y.113, V.114, F.117, L.125, I.140, I.142, W.148, M.160, H.163, T.164, A.167, L.171, R.176, L.178, F.189, T.191, F.193, L.204, L.208, F.214, F.220 Ligands: PO4.23, CYN.25, GOL.26, GOL.28 22 PLIP interactions: 22 interactions with chain C, Hydrophobic interactions: C:F.117, C:L.125, C:L.125, C:I.140, C:A.167, C:L.171, C:L.178, C:F.189, C:F.189, C:F.193, C:F.193, C:L.208, C:F.214, C:F.220, C:F.220 Hydrogen bonds: C:T.112, C:T.112, C:Y.113, C:V.114 Water bridges: C:T.112, C:H.180 Metal complexes: C:H.163 HEM.29: 26 residues within 4Å: Chain D: P.111, T.112, Y.113, V.114, F.117, L.125, I.140, I.142, W.148, M.160, H.163, T.164, A.167, L.171, R.176, L.178, F.189, T.191, F.193, L.204, L.208, F.214, F.220 Ligands: PO4.32, CYN.34, GOL.35 24 PLIP interactions: 24 interactions with chain D, Hydrophobic interactions: D:V.114, D:F.117, D:L.125, D:I.140, D:A.167, D:L.171, D:L.178, D:F.189, D:F.189, D:F.189, D:T.191, D:F.193, D:F.193, D:F.193, D:L.208, D:F.214, D:F.220 Hydrogen bonds: D:T.112, D:Y.113, D:V.114, D:W.148 Water bridges: D:T.112, D:T.112 Metal complexes: D:H.163 HEM.37: 26 residues within 4Å: Chain E: P.111, T.112, Y.113, V.114, F.117, L.125, I.140, I.142, W.148, M.160, H.163, T.164, A.167, Y.170, L.171, R.176, L.178, F.189, T.191, F.193, L.204, L.208, F.220 Ligands: PO4.38, CYN.40, GOL.41 21 PLIP interactions: 21 interactions with chain E, Hydrophobic interactions: E:F.117, E:L.125, E:I.140, E:A.167, E:L.171, E:L.178, E:F.189, E:F.189, E:T.191, E:F.193, E:F.193, E:F.193, E:L.208, E:F.220 Hydrogen bonds: E:T.112, E:Y.113, E:V.114, E:W.148 Water bridges: E:T.112, E:T.112 Metal complexes: E:H.163

18 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.2: 8 residues within 4Å: Chain A: T.112, Y.113, W.148, W.149, F.189 Chain C: R.206 Ligands: HEM.1, PO4.24 Ligand excluded by PLIP PO4.3: 4 residues within 4Å: Chain A: K.143, R.218, R.219 Chain C: H.222 Ligand excluded by PLIP PO4.4: 4 residues within 4Å: Chain A: H.222 Chain E: K.143, R.218, R.219 Ligand excluded by PLIP PO4.5: 5 residues within 4Å: Chain A: R.197, L.198, E.199, D.200 Chain E: Y.16 Ligand excluded by PLIP PO4.6: 6 residues within 4Å: Chain A: H.202, R.206 Chain E: K.109, H.180, F.189 Ligands: PO4.38 Ligand excluded by PLIP PO4.12: 4 residues within 4Å: Chain B: K.143, R.218, R.219 Chain D: H.222 Ligand excluded by PLIP PO4.13: 4 residues within 4Å: Chain B: R.197, L.198, E.199 Chain C: Y.16 Ligand excluded by PLIP PO4.14: 6 residues within 4Å: Chain B: H.202, R.206 Chain C: K.109, H.180, F.189 Ligands: PO4.23 Ligand excluded by PLIP PO4.15: 9 residues within 4Å: Chain B: T.112, Y.113, W.148, W.149, R.156, F.189 Chain D: R.206 Ligands: HEM.11, PO4.30 Ligand excluded by PLIP PO4.22: 4 residues within 4Å: Chain B: H.222 Chain C: K.143, R.218, R.219 Ligand excluded by PLIP PO4.23: 9 residues within 4Å: Chain B: R.206 Chain C: T.112, Y.113, W.148, W.149, R.156, F.189 Ligands: PO4.14, HEM.21 Ligand excluded by PLIP PO4.24: 6 residues within 4Å: Chain A: K.109, H.180, F.189 Chain C: H.202, R.206 Ligands: PO4.2 Ligand excluded by PLIP PO4.30: 6 residues within 4Å: Chain B: K.109, H.180, F.189 Chain D: H.202, R.206 Ligands: PO4.15 Ligand excluded by PLIP PO4.31: 4 residues within 4Å: Chain D: K.143, R.218, R.219 Chain E: H.222 Ligand excluded by PLIP PO4.32: 8 residues within 4Å: Chain D: T.112, Y.113, W.148, W.149, F.189 Chain E: R.206 Ligands: HEM.29, PO4.33 Ligand excluded by PLIP PO4.33: 6 residues within 4Å: Chain D: K.109, H.180, F.189 Chain E: H.202, R.206 Ligands: PO4.32 Ligand excluded by PLIP PO4.38: 8 residues within 4Å: Chain A: R.206 Chain E: T.112, Y.113, W.148, W.149, F.189 Ligands: PO4.6, HEM.37 Ligand excluded by PLIP PO4.39: 4 residues within 4Å: Chain D: Y.16 Chain E: R.197, L.198, E.199 Ligand excluded by PLIP

5 x CYN: CYANIDE ION(Non-covalent)(Non-functional Binders)

CYN.7: 3 residues within 4Å: Chain A: L.178 Ligands: HEM.1, GOL.8 No protein-ligand interaction detected (PLIP) CYN.16: 3 residues within 4Å: Chain B: L.178 Ligands: HEM.11, GOL.17 No protein-ligand interaction detected (PLIP) CYN.25: 3 residues within 4Å: Chain C: L.178 Ligands: HEM.21, GOL.26 No protein-ligand interaction detected (PLIP) CYN.34: 2 residues within 4Å: Ligands: HEM.29, GOL.35 No protein-ligand interaction detected (PLIP) CYN.40: 2 residues within 4Å: Ligands: HEM.37, GOL.41 No protein-ligand interaction detected (PLIP)

13 x GOL: GLYCEROL(Non-functional Binders)

GOL.8: 4 residues within 4Å: Chain A: R.176, L.178 Ligands: HEM.1, CYN.7 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.176 Water bridges: A:L.178, A:L.178 GOL.9: 3 residues within 4Å: Chain A: Q.49, W.50, K.53 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.53 Water bridges: A:Q.49, A:Q.49, A:W.50 GOL.10: 4 residues within 4Å: Chain A: K.44, P.231, L.232, D.233 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:L.232, A:D.233, A:D.233 Water bridges: A:K.44, A:V.56, A:S.230 GOL.17: 5 residues within 4Å: Chain B: P.111, R.176, L.178 Ligands: HEM.11, CYN.16 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.176 GOL.18: 10 residues within 4Å: Chain B: G.129, E.130, P.135, K.172, T.173, K.175, E.194, T.195, E.196, R.197 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:E.130, B:K.172, B:K.175, B:E.194, B:E.196, B:R.197 GOL.19: 5 residues within 4Å: Chain B: S.120, M.121, E.124, Q.165, L.168 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.124, B:Q.165 Water bridges: B:S.120 GOL.20: 4 residues within 4Å: Chain B: H.222, P.223 Chain C: D.186, R.219 5 PLIP interactions: 3 interactions with chain C, 2 interactions with chain B Hydrogen bonds: C:D.186, C:R.219, B:H.222, B:H.222 Water bridges: C:D.186 GOL.26: 5 residues within 4Å: Chain C: P.111, R.176 Ligands: HEM.21, CYN.25, GOL.28 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:R.176, C:R.176 Water bridges: C:L.178 GOL.27: 4 residues within 4Å: Chain A: D.186, R.219 Chain C: H.222, P.223 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:D.186, A:R.219, C:H.222 GOL.28: 8 residues within 4Å: Chain C: S.108, K.109, K.110, P.111, L.178, H.180 Ligands: HEM.21, GOL.26 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:K.109, C:L.178 Water bridges: C:K.110, C:T.112, C:H.180, C:H.180 GOL.35: 5 residues within 4Å: Chain D: P.111, R.176, L.178 Ligands: HEM.29, CYN.34 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:R.176, D:L.178 GOL.36: 8 residues within 4Å: Chain B: Y.16, T.78, L.79 Chain D: Y.136, E.196, R.197, L.198, E.199 6 PLIP interactions: 5 interactions with chain D, 1 interactions with chain B Hydrogen bonds: D:Y.136, D:L.198, D:E.199, B:L.79 Water bridges: D:R.197, D:D.200 GOL.41: 6 residues within 4Å: Chain E: P.111, V.114, R.176, L.178 Ligands: HEM.37, CYN.40 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:R.176 Water bridges: E:L.178

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

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