SMTL ID : 2xvy.1

Cobalt chelatase CbiK (periplasmic) from Desulvobrio vulgaris Hildenborough (co-crystallised with cobalt and SHC)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

homo-tetramer

Ligands

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

HEM.1: 19 residues within 4Å: Chain A: P.91, H.96, L.99, L.119, H.158, P.159, A.160, I.162 Chain D: P.91, E.93, F.95, H.96, L.99, E.100, L.119, H.158, P.159, A.160 Ligands: HEM.55 17 PLIP interactions: 7 interactions with chain A, 10 interactions with chain D, Hydrophobic interactions: A:P.91, A:P.91, A:L.99, A:L.119, A:P.159, A:I.162, D:P.91, D:F.95, D:L.99, D:L.119, D:P.159, D:P.159 Metal complexes: A:H.96, D:H.96 Hydrogen bonds: D:E.100 Salt bridges: D:H.96, D:H.158 HEM.19: 19 residues within 4Å: Chain B: P.91, H.96, L.99, L.119, H.158, P.159, A.160, I.162 Chain C: P.91, E.93, F.95, H.96, L.99, E.100, L.119, H.158, P.159, A.160 Ligands: HEM.37 16 PLIP interactions: 9 interactions with chain C, 7 interactions with chain B, Hydrophobic interactions: C:P.91, C:F.95, C:L.99, C:L.119, C:P.159, C:P.159, B:P.91, B:P.91, B:L.99, B:L.119, B:P.159, B:I.162 Salt bridges: C:H.96, C:H.158 Metal complexes: C:H.96, B:H.96 HEM.37: 19 residues within 4Å: Chain B: P.91, E.93, F.95, H.96, L.99, E.100, L.119, H.158, P.159, A.160 Chain C: P.91, H.96, L.99, L.119, H.158, P.159, A.160, I.162 Ligands: HEM.19 17 PLIP interactions: 10 interactions with chain B, 7 interactions with chain C, Hydrophobic interactions: B:P.91, B:F.95, B:L.99, B:L.119, B:P.159, B:P.159, C:P.91, C:P.91, C:L.99, C:L.119, C:P.159, C:I.162 Hydrogen bonds: B:E.100 Salt bridges: B:H.96, B:H.158 Metal complexes: B:H.96, C:H.96 HEM.55: 19 residues within 4Å: Chain A: P.91, E.93, F.95, H.96, L.99, E.100, L.119, H.158, P.159, A.160 Chain D: P.91, H.96, L.99, L.119, H.158, P.159, A.160, I.162 Ligands: HEM.1 16 PLIP interactions: 9 interactions with chain A, 7 interactions with chain D, Hydrophobic interactions: A:P.91, A:F.95, A:L.99, A:L.119, A:P.159, A:P.159, D:P.91, D:P.91, D:L.99, D:L.119, D:P.159, D:I.162 Salt bridges: A:H.96, A:H.158 Metal complexes: A:H.96, D:H.96

4 x CO: COBALT (II) ION(Non-covalent)

CO.2: 4 residues within 4Å: Chain A: H.154, E.184, H.216 Ligands: PER.16 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.154, A:E.184, A:H.216, H2O.9, H2O.9 CO.20: 4 residues within 4Å: Chain B: H.154, E.184, H.216 Ligands: PER.34 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:H.154, B:E.184, B:H.216, H2O.18, H2O.18 CO.38: 4 residues within 4Å: Chain C: H.154, E.184, H.216 Ligands: PER.52 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:H.154, C:E.184, C:H.216, H2O.27, H2O.27 CO.56: 4 residues within 4Å: Chain D: H.154, E.184, H.216 Ligands: PER.70 5 PLIP interactions: 3 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:H.154, D:E.184, D:H.216, H2O.36, H2O.36

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

SO4.3: 7 residues within 4Å: Chain A: F.17, L.87, H.88, T.89, M.210, A.211 Ligands: NA.17 Ligand excluded by PLIP SO4.4: 6 residues within 4Å: Chain A: I.90, G.92, E.93, E.94, T.156, H.158 Ligand excluded by PLIP SO4.5: 6 residues within 4Å: Chain A: H.103, R.114, V.115, S.116, V.117, R.267 Ligand excluded by PLIP SO4.6: 3 residues within 4Å: Chain A: L.139, P.140, A.141 Ligand excluded by PLIP SO4.7: 2 residues within 4Å: Chain A: K.144, R.203 Ligand excluded by PLIP SO4.8: 2 residues within 4Å: Chain A: P.43, R.45 Ligand excluded by PLIP SO4.21: 7 residues within 4Å: Chain B: F.17, L.87, H.88, T.89, M.210, A.211 Ligands: NA.35 Ligand excluded by PLIP SO4.22: 6 residues within 4Å: Chain B: I.90, G.92, E.93, E.94, T.156, H.158 Ligand excluded by PLIP SO4.23: 6 residues within 4Å: Chain B: H.103, R.114, V.115, S.116, V.117, R.267 Ligand excluded by PLIP SO4.24: 3 residues within 4Å: Chain B: L.139, P.140, A.141 Ligand excluded by PLIP SO4.25: 2 residues within 4Å: Chain B: K.144, R.203 Ligand excluded by PLIP SO4.26: 2 residues within 4Å: Chain B: P.43, R.45 Ligand excluded by PLIP SO4.39: 7 residues within 4Å: Chain C: F.17, L.87, H.88, T.89, M.210, A.211 Ligands: NA.53 Ligand excluded by PLIP SO4.40: 6 residues within 4Å: Chain C: I.90, G.92, E.93, E.94, T.156, H.158 Ligand excluded by PLIP SO4.41: 6 residues within 4Å: Chain C: H.103, R.114, V.115, S.116, V.117, R.267 Ligand excluded by PLIP SO4.42: 3 residues within 4Å: Chain C: L.139, P.140, A.141 Ligand excluded by PLIP SO4.43: 2 residues within 4Å: Chain C: K.144, R.203 Ligand excluded by PLIP SO4.44: 2 residues within 4Å: Chain C: P.43, R.45 Ligand excluded by PLIP SO4.57: 7 residues within 4Å: Chain D: F.17, L.87, H.88, T.89, M.210, A.211 Ligands: NA.71 Ligand excluded by PLIP SO4.58: 6 residues within 4Å: Chain D: I.90, G.92, E.93, E.94, T.156, H.158 Ligand excluded by PLIP SO4.59: 6 residues within 4Å: Chain D: H.103, R.114, V.115, S.116, V.117, R.267 Ligand excluded by PLIP SO4.60: 3 residues within 4Å: Chain D: L.139, P.140, A.141 Ligand excluded by PLIP SO4.61: 2 residues within 4Å: Chain D: K.144, R.203 Ligand excluded by PLIP SO4.62: 2 residues within 4Å: Chain D: P.43, R.45 Ligand excluded by PLIP

28 x GOL: GLYCEROL(Non-functional Binders)

GOL.9: 5 residues within 4Å: Chain A: S.138, E.249, S.250, D.251, A.252 Ligand excluded by PLIP GOL.10: 4 residues within 4Å: Chain A: T.49, A.50, K.51, M.52 Ligand excluded by PLIP GOL.11: 4 residues within 4Å: Chain A: W.172, P.176, R.199 Ligands: GOL.65 Ligand excluded by PLIP GOL.12: 4 residues within 4Å: Chain A: V.136, R.143, L.174, D.175 Ligand excluded by PLIP GOL.13: 8 residues within 4Å: Chain A: T.19, S.20, V.21, I.53, K.56, G.214, D.215 Ligands: NA.18 Ligand excluded by PLIP GOL.14: 5 residues within 4Å: Chain A: Q.8, K.9, T.10, D.41, P.43 Ligand excluded by PLIP GOL.15: 3 residues within 4Å: Chain A: D.197, V.198, K.200 Ligand excluded by PLIP GOL.27: 5 residues within 4Å: Chain B: S.138, E.249, S.250, D.251, A.252 Ligand excluded by PLIP GOL.28: 4 residues within 4Å: Chain B: T.49, A.50, K.51, M.52 Ligand excluded by PLIP GOL.29: 4 residues within 4Å: Chain B: W.172, P.176, R.199 Ligands: GOL.47 Ligand excluded by PLIP GOL.30: 4 residues within 4Å: Chain B: V.136, R.143, L.174, D.175 Ligand excluded by PLIP GOL.31: 8 residues within 4Å: Chain B: T.19, S.20, V.21, I.53, K.56, G.214, D.215 Ligands: NA.36 Ligand excluded by PLIP GOL.32: 5 residues within 4Å: Chain B: Q.8, K.9, T.10, D.41, P.43 Ligand excluded by PLIP GOL.33: 3 residues within 4Å: Chain B: D.197, V.198, K.200 Ligand excluded by PLIP GOL.45: 5 residues within 4Å: Chain C: S.138, E.249, S.250, D.251, A.252 Ligand excluded by PLIP GOL.46: 4 residues within 4Å: Chain C: T.49, A.50, K.51, M.52 Ligand excluded by PLIP GOL.47: 4 residues within 4Å: Chain C: W.172, P.176, R.199 Ligands: GOL.29 Ligand excluded by PLIP GOL.48: 4 residues within 4Å: Chain C: V.136, R.143, L.174, D.175 Ligand excluded by PLIP GOL.49: 8 residues within 4Å: Chain C: T.19, S.20, V.21, I.53, K.56, G.214, D.215 Ligands: NA.54 Ligand excluded by PLIP GOL.50: 5 residues within 4Å: Chain C: Q.8, K.9, T.10, D.41, P.43 Ligand excluded by PLIP GOL.51: 3 residues within 4Å: Chain C: D.197, V.198, K.200 Ligand excluded by PLIP GOL.63: 5 residues within 4Å: Chain D: S.138, E.249, S.250, D.251, A.252 Ligand excluded by PLIP GOL.64: 4 residues within 4Å: Chain D: T.49, A.50, K.51, M.52 Ligand excluded by PLIP GOL.65: 4 residues within 4Å: Chain D: W.172, P.176, R.199 Ligands: GOL.11 Ligand excluded by PLIP GOL.66: 4 residues within 4Å: Chain D: V.136, R.143, L.174, D.175 Ligand excluded by PLIP GOL.67: 8 residues within 4Å: Chain D: T.19, S.20, V.21, I.53, K.56, G.214, D.215 Ligands: NA.72 Ligand excluded by PLIP GOL.68: 5 residues within 4Å: Chain D: Q.8, K.9, T.10, D.41, P.43 Ligand excluded by PLIP GOL.69: 3 residues within 4Å: Chain D: D.197, V.198, K.200 Ligand excluded by PLIP

4 x PER: PEROXIDE ION(Non-covalent)

PER.16: 4 residues within 4Å: Chain A: H.154, E.184, H.216 Ligands: CO.2 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.154 Water bridges: A:E.184 PER.34: 4 residues within 4Å: Chain B: H.154, E.184, H.216 Ligands: CO.20 No protein-ligand interaction detected (PLIP) PER.52: 4 residues within 4Å: Chain C: H.154, E.184, H.216 Ligands: CO.38 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:H.154 Water bridges: C:E.184 PER.70: 4 residues within 4Å: Chain D: H.154, E.184, H.216 Ligands: CO.56 No protein-ligand interaction detected (PLIP)

8 x NA: SODIUM ION(Non-functional Binders)

NA.17: 6 residues within 4Å: Chain A: T.89, G.153, H.154, Y.164, L.209 Ligands: SO4.3 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.89, A:H.154, A:Y.164 NA.18: 4 residues within 4Å: Chain A: M.210, D.215, H.216 Ligands: GOL.13 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.215, A:H.216 Water bridges: A:V.212, A:G.214 NA.35: 6 residues within 4Å: Chain B: T.89, G.153, H.154, Y.164, L.209 Ligands: SO4.21 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:T.89, B:H.154, B:Y.164 NA.36: 4 residues within 4Å: Chain B: M.210, D.215, H.216 Ligands: GOL.31 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:D.215, B:H.216 Water bridges: B:V.212, B:G.214 NA.53: 6 residues within 4Å: Chain C: T.89, G.153, H.154, Y.164, L.209 Ligands: SO4.39 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:T.89, C:H.154, C:L.209 NA.54: 4 residues within 4Å: Chain C: M.210, D.215, H.216 Ligands: GOL.49 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:D.215, C:H.216 Water bridges: C:G.214, C:G.214 NA.71: 6 residues within 4Å: Chain D: T.89, G.153, H.154, Y.164, L.209 Ligands: SO4.57 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:T.89, D:H.154, D:Y.164 NA.72: 4 residues within 4Å: Chain D: M.210, D.215, H.216 Ligands: GOL.67 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:D.215, D:H.216 Water bridges: D:G.214, D:G.214

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lobo, S.A. et al., Desulfovibrio vulgaris CbiK(P) cobaltochelatase: evolution of a haem binding protein orchestrated by the incorporation of two histidine residues. Environ. Microbiol. (2017)

Release Date

2011-11-16

Peptides

CHELATASE, PUTATIVE: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

CHELATASE, PUTATIVE

Related Entries With Identical Sequence