SMTL ID : 4m08.1

Crystal Structure of Mutant Chlorite Dismutase from Candidatus Nitrospira defluvii W145V

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

homo-pentamer

Ligands

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

HEM.1: 22 residues within 4Å: Chain A: P.111, T.112, Y.113, V.114, F.117, L.125, I.142, 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.220 Ligands: IMD.7, EDO.11 20 PLIP interactions: 20 interactions with chain A, Hydrophobic interactions: A:V.114, A:F.117, A:L.125, A:L.125, A:A.167, A:L.171, A:L.178, A:F.189, A:F.189, A:T.191, A:F.193, A:F.193, A:L.208, A:F.220 Hydrogen bonds: A:T.112, A:Y.113, A:Y.113, A:V.114 Water bridges: A:H.180 Metal complexes: A:H.163 HEM.12: 24 residues within 4Å: Chain B: P.111, T.112, Y.113, V.114, F.117, L.125, I.140, I.142, W.149, 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: IMD.18 21 PLIP interactions: 21 interactions with chain B, Hydrophobic interactions: B:F.117, B:L.125, B:I.140, B:T.164, B:A.167, B:Y.170, B:L.171, B:L.178, B:F.189, 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:Y.113, B:V.114 Metal complexes: B:H.163 HEM.22: 24 residues within 4Å: Chain C: P.111, T.112, Y.113, V.114, F.117, L.125, I.140, I.142, K.144, W.149, 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: IMD.25 26 PLIP interactions: 26 interactions with chain C, Hydrophobic interactions: C:V.114, C:F.117, C:L.125, C:L.125, C:I.140, C:I.142, C:A.167, C:L.171, C:L.178, C:F.189, C:F.189, C:F.189, C:T.191, C:F.193, C:F.193, C:L.204, C:L.204, C:L.208, C:F.220 Hydrogen bonds: C:T.112, C:Y.113, C:Y.113, C:V.114 Water bridges: C:H.180 Salt bridges: C:K.144 Metal complexes: C:H.163 HEM.33: 23 residues within 4Å: Chain D: P.111, T.112, Y.113, V.114, L.125, I.140, I.142, W.149, 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: IMD.36 19 PLIP interactions: 19 interactions with chain D, Hydrophobic interactions: D:V.114, D:L.125, 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:F.193, D:F.193, D:L.204, D:L.208, D:F.220 Hydrogen bonds: D:T.112, D:Y.113, D:V.114 Metal complexes: D:H.163 HEM.39: 24 residues within 4Å: Chain E: P.111, T.112, Y.113, V.114, F.117, L.125, I.140, I.142, W.149, 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: IMD.42 20 PLIP interactions: 20 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:F.189, E:T.191, E:F.193, E:F.193, E:L.204, E:L.208, E:F.220 Hydrogen bonds: E:T.112, E:Y.113, E:Y.113, E:V.114 Metal complexes: E:H.163

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

SO4.2: 4 residues within 4Å: Chain A: H.202, R.206 Chain E: K.109, H.180 Ligand excluded by PLIP SO4.3: 4 residues within 4Å: Chain A: P.32, G.33, R.36, Q.241 Ligand excluded by PLIP SO4.4: 2 residues within 4Å: Chain A: P.231, L.232 Ligand excluded by PLIP SO4.5: 2 residues within 4Å: Chain A: R.93, R.96 Ligand excluded by PLIP SO4.6: 5 residues within 4Å: Chain A: E.196, R.197, L.198, E.199 Chain E: Y.16 Ligand excluded by PLIP SO4.9: 4 residues within 4Å: Chain A: K.109, H.180 Chain C: H.202, R.206 Ligand excluded by PLIP SO4.10: 5 residues within 4Å: Chain A: R.176, K.177, L.178 Ligands: IMD.7, EDO.11 Ligand excluded by PLIP SO4.13: 4 residues within 4Å: Chain B: H.202, R.206 Chain C: K.109, H.180 Ligand excluded by PLIP SO4.14: 5 residues within 4Å: Chain B: E.196, R.197, L.198, E.199 Chain C: Y.16 Ligand excluded by PLIP SO4.15: 4 residues within 4Å: Chain B: R.176, K.177, L.178 Ligands: IMD.18 Ligand excluded by PLIP SO4.21: 4 residues within 4Å: Chain B: D.152, Q.153, R.156 Chain D: Q.210 Ligand excluded by PLIP SO4.23: 4 residues within 4Å: Chain B: Q.210 Chain C: D.152, Q.153, R.156 Ligand excluded by PLIP SO4.24: 2 residues within 4Å: Chain C: P.32, G.33 Ligand excluded by PLIP SO4.26: 5 residues within 4Å: Chain C: N.128, R.176, K.177, L.178 Ligands: IMD.25 Ligand excluded by PLIP SO4.27: 5 residues within 4Å: Chain A: Y.16 Chain C: E.196, R.197, L.198, E.199 Ligand excluded by PLIP SO4.28: 5 residues within 4Å: Chain C: E.42, G.91, T.92, R.93, R.96 Ligand excluded by PLIP SO4.29: 3 residues within 4Å: Chain C: P.118, E.119, S.120 Ligand excluded by PLIP SO4.32: 5 residues within 4Å: Chain D: Y.16, R.77 Chain E: R.197, L.198, E.199 Ligand excluded by PLIP SO4.34: 3 residues within 4Å: Chain D: K.177, L.178 Ligands: IMD.36 Ligand excluded by PLIP SO4.35: 7 residues within 4Å: Chain B: Y.16, R.77, T.78 Chain D: E.196, R.197, L.198, E.199 Ligand excluded by PLIP SO4.40: 5 residues within 4Å: Chain E: N.128, R.176, K.177, L.178 Ligands: IMD.42 Ligand excluded by PLIP SO4.41: 3 residues within 4Å: Chain E: V.56, P.231, L.232 Ligand excluded by PLIP

5 x IMD: IMIDAZOLE(Non-covalent)

IMD.7: 8 residues within 4Å: Chain A: R.176, K.177, L.178, T.191, F.193 Ligands: HEM.1, SO4.10, EDO.11 No protein-ligand interaction detected (PLIP) IMD.18: 5 residues within 4Å: Chain B: R.176, K.177, L.178 Ligands: HEM.12, SO4.15 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.177 pi-Cation interactions: B:R.176 IMD.25: 6 residues within 4Å: Chain C: R.176, K.177, L.178, F.193 Ligands: HEM.22, SO4.26 1 PLIP interactions: 1 interactions with chain C Water bridges: C:R.176 IMD.36: 5 residues within 4Å: Chain D: R.176, K.177, F.193 Ligands: HEM.33, SO4.34 No protein-ligand interaction detected (PLIP) IMD.42: 7 residues within 4Å: Chain E: R.176, K.177, L.178, T.191, F.193 Ligands: HEM.39, SO4.40 No protein-ligand interaction detected (PLIP)

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

EDO.8: 2 residues within 4Å: Chain A: D.152, Q.153 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.153 EDO.11: 4 residues within 4Å: Chain A: R.176 Ligands: HEM.1, IMD.7, SO4.10 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.176 EDO.16: 5 residues within 4Å: Chain B: E.162, Q.210, K.212, R.215 Chain C: A.150 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.215 EDO.17: 5 residues within 4Å: Chain B: K.143, R.218 Chain D: N.217, F.220, H.222 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.143, B:K.143, B:R.218 EDO.19: 3 residues within 4Å: Chain B: P.118, E.119, S.120 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.119, B:S.120 EDO.20: 2 residues within 4Å: Chain B: H.26, D.27 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:H.26 EDO.30: 4 residues within 4Å: Chain B: F.220, H.222 Chain C: K.143, R.218 4 PLIP interactions: 2 interactions with chain C, 2 interactions with chain B Hydrogen bonds: C:K.143, C:R.218, B:F.220, B:H.222 EDO.31: 2 residues within 4Å: Chain C: Q.165, A.166 1 PLIP interactions: 1 interactions with chain C Water bridges: C:A.166 EDO.37: 6 residues within 4Å: Chain D: K.143, R.218 Chain E: R.218, R.219, F.220, H.222 3 PLIP interactions: 2 interactions with chain E, 1 interactions with chain D Hydrogen bonds: E:R.218, E:F.220, D:K.143 EDO.38: 5 residues within 4Å: Chain A: R.218, R.219, F.220, H.222 Chain E: K.143 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain E Hydrogen bonds: A:F.220, E:K.143

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