SMTL ID : 2xvz.1

COBALT CHELATASE CBIK (PERIPLASMATIC) FROM DESULVOBRIO VULGARIS HILDENBOROUGH (CO-CRYSTALLIZED WITH COBALT)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

homo-tetramer

Ligands

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

HEM.1: 15 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, H.96, L.99, E.100, L.119, P.159 Ligands: HEM.49 12 PLIP interactions: 6 interactions with chain A, 6 interactions with chain D, Hydrophobic interactions: A:P.91, A:L.119, A:P.159, A:P.159, A:I.162, D:P.91, D:L.99, D:L.119, D:P.159 Metal complexes: A:H.96, D:H.96 Salt bridges: D:H.96 HEM.17: 15 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, H.96, L.99, E.100, L.119, P.159 Ligands: HEM.33 13 PLIP interactions: 6 interactions with chain B, 7 interactions with chain C, Hydrophobic interactions: B:P.91, B:L.119, B:P.159, B:P.159, B:I.162, C:P.91, C:L.99, C:L.119, C:P.159 Metal complexes: B:H.96, C:H.96 Hydrogen bonds: C:E.100 Salt bridges: C:H.96 HEM.33: 15 residues within 4Å: Chain B: P.91, H.96, L.99, E.100, L.119, P.159 Chain C: P.91, H.96, L.99, L.119, H.158, P.159, A.160, I.162 Ligands: HEM.17 12 PLIP interactions: 6 interactions with chain C, 6 interactions with chain B, Hydrophobic interactions: C:P.91, C:L.119, C:P.159, C:P.159, C:I.162, B:P.91, B:L.99, B:L.119, B:P.159 Metal complexes: C:H.96, B:H.96 Salt bridges: B:H.96 HEM.49: 15 residues within 4Å: Chain A: P.91, H.96, L.99, E.100, L.119, P.159 Chain D: P.91, H.96, L.99, L.119, H.158, P.159, A.160, I.162 Ligands: HEM.1 13 PLIP interactions: 6 interactions with chain D, 7 interactions with chain A, Hydrophobic interactions: D:P.91, D:L.119, D:P.159, D:P.159, D:I.162, A:P.91, A:L.99, A:L.119, A:P.159 Metal complexes: D:H.96, A:H.96 Hydrogen bonds: A:E.100 Salt bridges: A: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 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.154, A:E.184, A:H.216, H2O.106 CO.18: 4 residues within 4Å: Chain B: H.154, E.184, H.216 Ligands: PER.32 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.154, B:E.184, B:H.216, H2O.218 CO.34: 4 residues within 4Å: Chain C: H.154, E.184, H.216 Ligands: PER.48 4 PLIP interactions: 3 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:H.154, C:E.184, C:H.216, H2O.330 CO.50: 4 residues within 4Å: Chain D: H.154, E.184, H.216 Ligands: PER.64 4 PLIP interactions: 3 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:H.154, D:E.184, D:H.216, H2O.442

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

SO4.3: 5 residues within 4Å: Chain A: G.92, E.93, E.94, T.156, H.158 Ligand excluded by PLIP SO4.4: 7 residues within 4Å: Chain A: F.17, L.87, H.88, T.89, M.210, A.211 Ligands: NA.14 Ligand excluded by PLIP SO4.5: 5 residues within 4Å: Chain A: R.114, V.115, S.116, V.117, R.267 Ligand excluded by PLIP SO4.9: 2 residues within 4Å: Chain A: P.140, A.141 Ligand excluded by PLIP SO4.10: 4 residues within 4Å: Chain A: S.138, S.250, D.251, A.252 Ligand excluded by PLIP SO4.11: 6 residues within 4Å: Chain A: T.19, S.20, V.21, G.214, D.215 Ligands: SO4.12 Ligand excluded by PLIP SO4.12: 5 residues within 4Å: Chain A: F.17, G.214, D.215, H.216 Ligands: SO4.11 Ligand excluded by PLIP SO4.13: 3 residues within 4Å: Chain A: P.43, V.44, R.45 Ligand excluded by PLIP SO4.19: 5 residues within 4Å: Chain B: G.92, E.93, E.94, T.156, H.158 Ligand excluded by PLIP SO4.20: 7 residues within 4Å: Chain B: F.17, L.87, H.88, T.89, M.210, A.211 Ligands: NA.30 Ligand excluded by PLIP SO4.21: 5 residues within 4Å: Chain B: R.114, V.115, S.116, V.117, R.267 Ligand excluded by PLIP SO4.25: 2 residues within 4Å: Chain B: P.140, A.141 Ligand excluded by PLIP SO4.26: 4 residues within 4Å: Chain B: S.138, S.250, D.251, A.252 Ligand excluded by PLIP SO4.27: 6 residues within 4Å: Chain B: T.19, S.20, V.21, G.214, D.215 Ligands: SO4.28 Ligand excluded by PLIP SO4.28: 5 residues within 4Å: Chain B: F.17, G.214, D.215, H.216 Ligands: SO4.27 Ligand excluded by PLIP SO4.29: 3 residues within 4Å: Chain B: P.43, V.44, R.45 Ligand excluded by PLIP SO4.35: 5 residues within 4Å: Chain C: G.92, E.93, E.94, T.156, H.158 Ligand excluded by PLIP SO4.36: 7 residues within 4Å: Chain C: F.17, L.87, H.88, T.89, M.210, A.211 Ligands: NA.46 Ligand excluded by PLIP SO4.37: 5 residues within 4Å: Chain C: R.114, V.115, S.116, V.117, R.267 Ligand excluded by PLIP SO4.41: 2 residues within 4Å: Chain C: P.140, A.141 Ligand excluded by PLIP SO4.42: 4 residues within 4Å: Chain C: S.138, S.250, D.251, A.252 Ligand excluded by PLIP SO4.43: 6 residues within 4Å: Chain C: T.19, S.20, V.21, G.214, D.215 Ligands: SO4.44 Ligand excluded by PLIP SO4.44: 5 residues within 4Å: Chain C: F.17, G.214, D.215, H.216 Ligands: SO4.43 Ligand excluded by PLIP SO4.45: 3 residues within 4Å: Chain C: P.43, V.44, R.45 Ligand excluded by PLIP SO4.51: 5 residues within 4Å: Chain D: G.92, E.93, E.94, T.156, H.158 Ligand excluded by PLIP SO4.52: 7 residues within 4Å: Chain D: F.17, L.87, H.88, T.89, M.210, A.211 Ligands: NA.62 Ligand excluded by PLIP SO4.53: 5 residues within 4Å: Chain D: R.114, V.115, S.116, V.117, R.267 Ligand excluded by PLIP SO4.57: 2 residues within 4Å: Chain D: P.140, A.141 Ligand excluded by PLIP SO4.58: 4 residues within 4Å: Chain D: S.138, S.250, D.251, A.252 Ligand excluded by PLIP SO4.59: 6 residues within 4Å: Chain D: T.19, S.20, V.21, G.214, D.215 Ligands: SO4.60 Ligand excluded by PLIP SO4.60: 5 residues within 4Å: Chain D: F.17, G.214, D.215, H.216 Ligands: SO4.59 Ligand excluded by PLIP SO4.61: 3 residues within 4Å: Chain D: P.43, V.44, R.45 Ligand excluded by PLIP

12 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 4 residues within 4Å: Chain A: V.136, R.143, L.174, D.175 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.143, A:D.175 Water bridges: A:R.143 GOL.7: 4 residues within 4Å: Chain A: W.172, P.176, R.199 Ligands: GOL.55 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:P.176, A:R.199 Water bridges: A:R.199 GOL.8: 6 residues within 4Å: Chain A: T.49, A.50, K.51, M.52, E.94 Chain C: K.110 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.51, A:M.52, A:E.94 GOL.22: 4 residues within 4Å: Chain B: V.136, R.143, L.174, D.175 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.143 Water bridges: B:R.143 GOL.23: 4 residues within 4Å: Chain B: W.172, P.176, R.199 Ligands: GOL.39 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:P.176, B:R.199 Water bridges: B:R.199 GOL.24: 6 residues within 4Å: Chain B: T.49, A.50, K.51, M.52, E.94 Chain D: K.110 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.51, B:M.52, B:E.94 GOL.38: 4 residues within 4Å: Chain C: V.136, R.143, L.174, D.175 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:R.143, C:D.175 Water bridges: C:R.143 GOL.39: 4 residues within 4Å: Chain C: W.172, P.176, R.199 Ligands: GOL.23 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:P.176, C:R.199 Water bridges: C:R.199 GOL.40: 6 residues within 4Å: Chain A: K.110 Chain C: T.49, A.50, K.51, M.52, E.94 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:K.51, C:M.52, C:E.94 GOL.54: 4 residues within 4Å: Chain D: V.136, R.143, L.174, D.175 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:R.143 Water bridges: D:R.143 GOL.55: 4 residues within 4Å: Chain D: W.172, P.176, R.199 Ligands: GOL.7 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:P.176, D:R.199 Water bridges: D:R.199 GOL.56: 6 residues within 4Å: Chain B: K.110 Chain D: T.49, A.50, K.51, M.52, E.94 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:K.51, D:M.52, D:E.94

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

NA.14: 5 residues within 4Å: Chain A: T.89, G.153, H.154, Y.164 Ligands: SO4.4 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.89, A:T.89, A:H.154 NA.30: 5 residues within 4Å: Chain B: T.89, G.153, H.154, Y.164 Ligands: SO4.20 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:T.89, B:H.154, B:Y.164 NA.46: 5 residues within 4Å: Chain C: T.89, G.153, H.154, Y.164 Ligands: SO4.36 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:T.89, C:T.89, C:H.154 NA.62: 5 residues within 4Å: Chain D: T.89, G.153, H.154, Y.164 Ligands: SO4.52 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:T.89, D:H.154, D:Y.164

4 x CL: CHLORIDE ION(Non-functional Binders)

CL.15: 1 residues within 4Å: Chain A: R.203 Ligand excluded by PLIP CL.31: 1 residues within 4Å: Chain B: R.203 Ligand excluded by PLIP CL.47: 1 residues within 4Å: Chain C: R.203 Ligand excluded by PLIP CL.63: 1 residues within 4Å: Chain D: R.203 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 No protein-ligand interaction detected (PLIP) PER.32: 4 residues within 4Å: Chain B: H.154, E.184, H.216 Ligands: CO.18 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:H.216 PER.48: 4 residues within 4Å: Chain C: H.154, E.184, H.216 Ligands: CO.34 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:H.154 PER.64: 4 residues within 4Å: Chain D: H.154, E.184, H.216 Ligands: CO.50 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:H.154

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Romao, C.V. et al., Evolution in a Family of Chelatases Facilitated by the Introduction of Active Site Asymmetry and Protein Oligomerization. Proc.Natl.Acad.Sci.USA (2011)

Release Date

2010-12-22

Peptides

CHELATASE, PUTATIVE: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

CHELATASE, PUTATIVE

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