SMTL ID : 4m06.1

Crystal Structure of Mutant Chlorite Dismutase from Candidatus Nitrospira defluvii W145F in Complex with Cyanide

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.60 Å

Oligo State

homo-pentamer

Ligands

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

HEM.1: 23 residues within 4Å: Chain A: P.130, T.131, Y.132, V.133, L.144, I.159, I.161, F.167, M.179, H.182, T.183, A.186, Y.189, L.190, R.195, L.197, F.208, T.210, F.212, L.223, L.227, F.239 Ligands: CYN.3 21 PLIP interactions: 20 interactions with chain A, 1 interactions with chain C, Hydrophobic interactions: A:V.133, A:L.144, A:I.159, A:A.186, A:L.190, A:L.197, A:F.208, A:F.208, A:F.208, A:T.210, A:F.212, A:F.212, A:L.227, A:F.239 Hydrogen bonds: A:T.131, A:T.131, A:Y.132, A:Y.132, A:V.133 Metal complexes: A:H.182 Salt bridges: C:R.225 HEM.4: 24 residues within 4Å: Chain B: P.130, T.131, Y.132, V.133, F.136, L.144, I.159, I.161, F.167, M.179, H.182, T.183, A.186, Y.189, L.190, R.195, L.197, F.208, T.210, F.212, L.223, L.227, F.239 Ligands: CYN.5 22 PLIP interactions: 21 interactions with chain B, 1 interactions with chain D, Hydrophobic interactions: B:F.136, B:L.144, B:L.144, B:I.159, B:A.186, B:L.190, B:L.197, B:L.197, B:F.208, B:F.208, B:F.208, B:T.210, B:F.212, B:F.212, B:L.227, B:F.239 Hydrogen bonds: B:T.131, B:Y.132, B:Y.132, B:V.133 Metal complexes: B:H.182 Salt bridges: D:R.225 HEM.6: 23 residues within 4Å: Chain C: P.130, T.131, Y.132, V.133, F.136, L.144, I.161, F.167, M.179, H.182, T.183, A.186, Y.189, L.190, R.195, L.197, F.208, T.210, F.212, L.223, L.227, F.239 Ligands: CYN.7 18 PLIP interactions: 18 interactions with chain C, Hydrophobic interactions: C:F.136, C:L.144, C:A.186, C:L.190, C:L.197, C:F.208, C:F.208, C:F.208, C:T.210, C:F.212, C:L.227, C:F.239 Hydrogen bonds: C:T.131, C:Y.132, C:Y.132, C:V.133 Water bridges: C:T.131 Metal complexes: C:H.182 HEM.9: 23 residues within 4Å: Chain D: P.130, T.131, Y.132, V.133, F.136, L.144, I.159, I.161, F.167, M.179, H.182, T.183, A.186, L.190, R.195, L.197, F.208, T.210, F.212, L.223, L.227, F.239 Ligands: CYN.10 21 PLIP interactions: 21 interactions with chain D, Hydrophobic interactions: D:F.136, D:L.144, D:L.144, D:I.159, D:A.186, D:L.190, D:L.197, D:F.208, D:F.208, D:F.208, D:T.210, D:F.212, D:F.212, D:L.227, D:F.239 Hydrogen bonds: D:T.131, D:T.131, D:Y.132, D:Y.132, D:V.133 Metal complexes: D:H.182 HEM.11: 23 residues within 4Å: Chain E: P.130, T.131, Y.132, V.133, F.136, L.144, I.159, I.161, F.167, M.179, H.182, T.183, A.186, L.190, R.195, L.197, F.208, T.210, F.212, L.223, L.227, F.239 Ligands: CYN.12 22 PLIP interactions: 22 interactions with chain E, Hydrophobic interactions: E:V.133, E:F.136, E:L.144, E:L.144, E:I.159, E:A.186, E:L.197, E:L.197, E:F.208, E:F.208, E:F.208, E:T.210, E:F.212, E:F.212, E:L.227, E:F.239 Hydrogen bonds: E:T.131, E:T.131, E:Y.132, E:Y.132, E:V.133 Metal complexes: E:H.182

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 6 residues within 4Å: Chain A: K.162, R.237 Chain C: R.237, R.238, F.239, H.241 5 PLIP interactions: 3 interactions with chain C, 2 interactions with chain A Hydrogen bonds: C:R.237, C:F.239, C:F.239, A:K.162, A:R.237

5 x CYN: CYANIDE ION(Non-covalent)

CYN.3: 2 residues within 4Å: Chain A: L.197 Ligands: HEM.1 No protein-ligand interaction detected (PLIP) CYN.5: 2 residues within 4Å: Chain B: L.197 Ligands: HEM.4 No protein-ligand interaction detected (PLIP) CYN.7: 3 residues within 4Å: Chain C: R.195, L.197 Ligands: HEM.6 No protein-ligand interaction detected (PLIP) CYN.10: 2 residues within 4Å: Chain D: L.197 Ligands: HEM.9 No protein-ligand interaction detected (PLIP) CYN.12: 3 residues within 4Å: Chain E: R.195, L.197 Ligands: HEM.11 No protein-ligand interaction detected (PLIP)

2 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.8: 1 residues within 4Å: Chain C: R.195 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:R.195, C:L.197 EDO.13: 7 residues within 4Å: Chain D: L.122, L.203, D.204 Chain E: L.83, S.84, D.85, T.243 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:L.83, E:D.85

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hofbauer, S. et al., Manipulating conserved heme cavity residues of chlorite dismutase: effect on structure, redox chemistry, and reactivity. Biochemistry (2014)

Release Date

2014-01-15

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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