SMTL ID : 4m07.1

Crystal Structure of Mutant Chlorite Dismutase from Candidatus Nitrospira defluvii W145F

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-pentamer

Ligands

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

HEM.1: 21 residues within 4Å: Chain A: 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, R.195, L.197, F.208, T.210, F.212, L.223, L.227, F.239 18 PLIP interactions: 18 interactions with chain A, Hydrophobic interactions: A:F.136, A:L.144, A:L.144, A:A.186, A:L.197, A:L.197, A:F.208, A:F.208, A:T.210, A:F.212, A:F.212, A:L.223, A:L.227, A:F.239 Hydrogen bonds: A:T.131, A:Y.132, A:V.133 Metal complexes: A:H.182 HEM.6: 22 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, L.190, R.195, L.197, F.208, T.210, F.212, L.223, L.227, F.239 24 PLIP interactions: 23 interactions with chain B, 1 interactions with chain D, Hydrophobic interactions: B:V.133, B:F.136, B:L.144, B:L.144, B:I.159, B:I.161, B:T.183, 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:V.133 Metal complexes: B:H.182 Salt bridges: D:R.225 HEM.11: 21 residues within 4Å: Chain C: P.130, T.131, Y.132, V.133, F.136, L.144, I.159, I.161, 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 21 PLIP interactions: 20 interactions with chain C, 1 interactions with chain B, Hydrophobic interactions: C:V.133, C:F.136, C:L.144, C:L.144, C:I.159, C:A.186, C:L.197, C:F.208, C:F.208, C:T.210, C:F.212, C:F.212, C:L.227, C:F.239, C:F.239 Hydrogen bonds: C:T.131, C:T.131, C:Y.132, C:V.133 Metal complexes: C:H.182 Water bridges: B:R.225 HEM.15: 20 residues within 4Å: Chain D: P.130, T.131, Y.132, V.133, I.159, I.161, F.167, M.179, H.182, T.183, A.186, Y.189, R.195, L.197, F.208, T.210, F.212, L.223, L.227, F.239 17 PLIP interactions: 17 interactions with chain D, Hydrophobic interactions: D:I.159, D:T.183, D:A.186, D:L.197, D:F.208, D:F.208, D:F.208, D:T.210, D:F.212, D:F.212, D:L.223, D:L.227, D:F.239 Hydrogen bonds: D:T.131, D:Y.132, D:V.133 Metal complexes: D:H.182 HEM.20: 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, Y.189, L.190, R.195, L.197, F.208, T.210, F.212, L.223, L.227, F.239 18 PLIP interactions: 18 interactions with chain E, Hydrophobic interactions: E:F.136, E:L.144, E:L.144, E:I.159, E:A.186, E:L.197, E:F.208, E:F.208, E:T.210, E:F.212, E:F.212, E:L.227, E:F.239, E:F.239 Hydrogen bonds: E:T.131, E:Y.132, E:V.133 Metal complexes: E:H.182

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

EDO.2: 5 residues within 4Å: Chain A: Y.35, T.97 Chain C: E.215, R.216, L.217 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:L.217, A:Y.35 EDO.5: 7 residues within 4Å: Chain A: F.38, T.40, G.121, L.122, L.123, P.242, L.244 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:F.38, A:T.40, A:G.121 EDO.7: 6 residues within 4Å: Chain B: E.149, G.151, P.154, T.192, T.214, E.215 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.215, B:E.215 EDO.9: 5 residues within 4Å: Chain B: Y.35 Chain D: Y.155, E.215, R.216, L.217 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:E.215, D:L.217 EDO.10: 5 residues within 4Å: Chain B: G.121, L.122, L.123, P.242, L.244 No protein-ligand interaction detected (PLIP) EDO.14: 4 residues within 4Å: Chain C: G.121, L.122, L.123, P.242 No protein-ligand interaction detected (PLIP) EDO.17: 7 residues within 4Å: Chain D: Y.35, T.97 Chain E: Y.155, E.215, R.216, L.217, E.218 4 PLIP interactions: 4 interactions with chain E Hydrogen bonds: E:Y.155, E:Y.155, E:L.217, E:E.218 EDO.18: 3 residues within 4Å: Chain D: D.205, R.238 Chain E: H.241 2 PLIP interactions: 1 interactions with chain E, 1 interactions with chain D Hydrogen bonds: E:H.241, D:D.205 EDO.19: 4 residues within 4Å: Chain D: G.121, L.122, L.123, P.242 No protein-ligand interaction detected (PLIP) EDO.21: 5 residues within 4Å: Chain E: G.121, L.122, L.123, P.242, L.244 No protein-ligand interaction detected (PLIP)

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 5 residues within 4Å: Chain A: R.237, R.238, F.239, H.241 Chain E: K.162 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain E Hydrogen bonds: A:F.239, E:K.162, E:K.162 GOL.4: 3 residues within 4Å: Chain A: K.162, R.237 Chain C: H.241 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.162, A:R.237 GOL.8: 6 residues within 4Å: Chain B: K.162, R.237 Chain D: R.237, R.238, F.239, H.241 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:F.239 GOL.12: 6 residues within 4Å: Chain B: Y.155, E.215, L.217, E.218 Chain C: Y.35, T.97 7 PLIP interactions: 6 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:Y.155, B:Y.155, B:L.217, B:E.218, B:E.218, B:E.218, C:Y.35 GOL.13: 5 residues within 4Å: Chain B: R.237, F.239, H.241 Chain C: K.162, R.237 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain B Hydrogen bonds: C:K.162, B:R.237 GOL.16: 6 residues within 4Å: Chain D: K.162, R.237 Chain E: R.237, R.238, F.239, H.241 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:K.162, D:R.237

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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