SMTL ID : 5a13.2 (1 other biounit)

Crystal structure of Chlorite Dismutase from Magnetospirillum sp. in complex with thiocyanate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.75 Å

Oligo State

homo-pentamer

Ligands

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

HEM.1: 24 residues within 4Å: Chain A: L.112, N.113, Y.114, I.115, L.127, I.143, V.145, K.147, W.151, I.163, H.166, T.167, T.170, L.174, R.179, L.181, F.192, T.194, F.196, L.207, L.208, L.211, W.223 Ligands: SCN.2 24 PLIP interactions: 24 interactions with chain A, Hydrophobic interactions: A:L.112, A:L.127, A:I.143, A:V.145, A:I.163, A:I.163, A:T.170, A:L.181, A:F.192, A:F.192, A:F.196, A:F.196, A:L.208, A:L.208, A:L.211 Hydrogen bonds: A:N.113, A:Y.114, A:I.115 Water bridges: A:Y.114, A:Y.114, A:Y.114 Salt bridges: A:K.147 pi-Cation interactions: A:R.179 Metal complexes: A:H.166 HEM.4: 26 residues within 4Å: Chain B: L.112, N.113, Y.114, I.115, L.127, I.143, V.145, K.147, W.151, I.163, H.166, T.167, T.170, L.171, L.174, V.177, R.179, L.181, F.192, T.194, F.196, L.207, L.208, L.211, W.223 Ligands: SCN.5 27 PLIP interactions: 27 interactions with chain B, Hydrophobic interactions: B:L.112, B:I.115, B:L.127, B:I.143, B:V.145, B:I.163, B:I.163, B:L.174, B:V.177, B:L.181, B:F.192, B:F.192, B:T.194, B:F.196, B:F.196, B:L.207, B:L.208, B:L.208, B:L.211 Hydrogen bonds: B:N.113, B:N.113, B:Y.114, B:I.115 Water bridges: B:Y.114 Salt bridges: B:K.147 pi-Cation interactions: B:R.179 Metal complexes: B:H.166 HEM.7: 24 residues within 4Å: Chain C: L.112, N.113, Y.114, I.115, L.127, I.143, V.145, K.147, W.151, I.163, H.166, T.167, T.170, L.174, R.179, L.181, F.192, T.194, F.196, L.207, L.208, L.211, W.223 Ligands: SCN.8 27 PLIP interactions: 27 interactions with chain C, Hydrophobic interactions: C:L.112, C:L.127, C:I.143, C:V.145, C:I.163, C:I.163, C:T.170, C:L.174, C:L.181, C:L.181, C:F.192, C:F.192, C:F.192, C:F.196, C:F.196, C:L.207, C:L.208, C:L.208, C:L.211 Hydrogen bonds: C:N.113, C:Y.114, C:I.115 Water bridges: C:N.113, C:N.113, C:Y.114 Salt bridges: C:K.147 Metal complexes: C:H.166 HEM.11: 25 residues within 4Å: Chain D: L.112, N.113, Y.114, I.115, L.127, I.143, V.145, K.147, W.151, I.163, H.166, T.167, T.170, L.171, L.174, R.179, L.181, F.192, T.194, F.196, L.207, L.208, L.211, W.223 Ligands: SCN.12 28 PLIP interactions: 28 interactions with chain D, Hydrophobic interactions: D:L.112, D:I.115, D:L.127, D:I.143, D:V.145, D:I.163, D:I.163, D:T.167, D:L.174, D:L.181, D:L.181, D:F.192, D:F.192, D:F.192, D:F.196, D:F.196, D:L.207, D:L.208, D:L.208, D:L.211 Hydrogen bonds: D:N.113, D:Y.114, D:I.115 Water bridges: D:Y.114, D:H.183 Salt bridges: D:K.147 pi-Cation interactions: D:R.179 Metal complexes: D:H.166 HEM.15: 25 residues within 4Å: Chain E: L.112, N.113, Y.114, I.115, L.127, I.143, V.145, K.147, W.151, I.163, H.166, T.167, T.170, L.171, L.174, R.179, L.181, F.192, T.194, F.196, L.207, L.208, L.211, W.223 Ligands: SCN.16 31 PLIP interactions: 31 interactions with chain E, Hydrophobic interactions: E:L.112, E:I.115, E:L.127, E:I.143, E:V.145, E:I.163, E:I.163, E:L.171, E:L.174, E:L.181, E:L.181, E:F.192, E:F.192, E:F.192, E:F.196, E:F.196, E:L.207, E:L.208, E:L.208, E:L.211 Hydrogen bonds: E:N.113, E:Y.114, E:I.115 Water bridges: E:N.113, E:N.113, E:Y.114, E:H.183, E:H.183 Salt bridges: E:K.147 pi-Cation interactions: E:R.179 Metal complexes: E:H.166

5 x SCN: THIOCYANATE ION(Non-functional Binders)

SCN.2: 6 residues within 4Å: Chain A: R.179, K.180, L.181, T.194, F.196 Ligands: HEM.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.179 SCN.5: 6 residues within 4Å: Chain B: R.179, K.180, L.181, T.194, F.196 Ligands: HEM.4 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.179 SCN.8: 6 residues within 4Å: Chain C: R.179, K.180, L.181, T.194, F.196 Ligands: HEM.7 No protein-ligand interaction detected (PLIP) SCN.12: 6 residues within 4Å: Chain D: R.179, K.180, L.181, T.194, F.196 Ligands: HEM.11 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:R.179 SCN.16: 6 residues within 4Å: Chain E: R.179, K.180, L.181, T.194, F.196 Ligands: HEM.15 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:R.179

7 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 7 residues within 4Å: Chain A: T.12, T.13, P.14, T.109, K.110, L.112, K.180 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.12, A:K.110 Water bridges: A:K.180, A:K.180 GOL.6: 6 residues within 4Å: Chain B: T.12, T.13, T.109, K.110, L.112, K.180 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:T.12, B:K.110, B:K.110, B:L.112 Water bridges: B:K.180 GOL.9: 6 residues within 4Å: Chain C: T.12, T.13, P.14, T.109, K.110, K.180 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:T.12, C:K.110, C:K.110 Water bridges: C:K.180, C:K.180 GOL.10: 7 residues within 4Å: Chain C: M.30, R.63, T.241, G.244 Chain E: V.88, R.91, A.92 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:R.63 Water bridges: C:R.63 GOL.13: 6 residues within 4Å: Chain D: T.12, T.13, P.14, T.109, K.110, K.180 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:T.12, D:K.110, D:K.110 Water bridges: D:K.180, D:K.180 GOL.14: 7 residues within 4Å: Chain A: M.30, R.63, T.241, G.244 Chain D: V.88, R.91, A.92 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.63 Water bridges: A:R.63 GOL.17: 7 residues within 4Å: Chain E: T.12, T.13, P.14, T.109, K.110, L.112, K.180 5 PLIP interactions: 5 interactions with chain E Hydrogen bonds: E:T.12, E:K.110, E:K.110 Water bridges: E:K.180, E:K.180

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

De Schutter, A. et al., Ligand Binding to Chlorite Dismutase from Magnetospirillum Sp. J.Phys.Chem.B (2015)

Release Date

2015-09-02

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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