SMTL ID : 3de8.1 (2 other biounits)

Crystal Structure of a Dimeric Cytochrome cb562 Assembly Induced by Copper Coordination

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.72 Å

Oligo State

homo-tetramer

Ligands

4 x CU: COPPER (II) ION(Non-covalent)

CU.1: 4 residues within 4Å: Chain A: H.59, H.63 Chain D: H.73, H.77 5 PLIP interactions: 2 interactions with chain A, 2 interactions with chain D, 1 Ligand-Water interactions Metal complexes: A:H.59, A:H.63, D:H.73, D:H.77, H2O.18 CU.2: 4 residues within 4Å: Chain A: H.73, H.77 Chain D: H.59, H.63 5 PLIP interactions: 2 interactions with chain D, 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: D:H.59, D:H.63, A:H.73, A:H.77, H2O.18 CU.7: 4 residues within 4Å: Chain B: H.59, H.63 Chain C: H.73, H.77 5 PLIP interactions: 2 interactions with chain B, 2 interactions with chain C, 1 Ligand-Water interactions Metal complexes: B:H.59, B:H.63, C:H.73, C:H.77, H2O.13 CU.8: 4 residues within 4Å: Chain B: H.73, H.77 Chain C: H.59, H.63 5 PLIP interactions: 2 interactions with chain B, 2 interactions with chain C, 1 Ligand-Water interactions Metal complexes: B:H.73, B:H.77, C:H.59, C:H.63, H2O.8

6 x CA: CALCIUM ION(Non-covalent)(Non-functional Binders)

CA.3: 2 residues within 4Å: Chain A: D.74 Chain C: D.74 5 PLIP interactions: 1 interactions with chain A, 1 interactions with chain C, 3 Ligand-Water interactions Metal complexes: A:D.74, C:D.74, H2O.1, H2O.1, H2O.13 CA.4: 2 residues within 4Å: Chain A: E.8, D.12 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:E.8, A:D.12, H2O.1, H2O.1, H2O.1 CA.5: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) CA.9: 3 residues within 4Å: Chain B: E.4, D.5 Ligands: CA.10 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.4, B:E.4, B:D.5, H2O.8, H2O.8 CA.10: 4 residues within 4Å: Chain B: D.2, E.4, D.5 Ligands: CA.9 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.2, B:E.4, B:D.5, H2O.8, H2O.8 CA.12: 2 residues within 4Å: Chain C: K.19, D.21 4 PLIP interactions: 2 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:K.19, C:D.21, H2O.13, H2O.13

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

HEM.6: 15 residues within 4Å: Chain A: L.3, M.7, L.10, N.11, M.33, P.45, P.46, F.61, G.64, F.65, C.98, C.101, H.102, Y.105, R.106 12 PLIP interactions: 12 interactions with chain A, Hydrophobic interactions: A:M.7, A:N.11, A:P.45, A:F.65, A:F.65, A:F.65, A:R.106 Water bridges: A:E.4 Salt bridges: A:R.106 pi-Stacking: A:H.102 pi-Cation interactions: A:R.106 Metal complexes: A:H.102 HEM.11: 19 residues within 4Å: Chain B: L.3, E.4, M.7, E.8, L.10, N.11, L.14, M.33, P.45, P.46, F.61, G.64, F.65, T.97, C.98, C.101, H.102, Y.105, R.106 13 PLIP interactions: 13 interactions with chain B, Hydrophobic interactions: B:M.7, B:N.11, B:P.45, B:F.65, B:F.65, B:F.65, B:R.106 Hydrogen bonds: B:E.8 Water bridges: B:E.4 pi-Stacking: B:H.102, B:H.102 pi-Cation interactions: B:R.106 Metal complexes: B:H.102 HEM.13: 17 residues within 4Å: Chain C: E.4, M.7, L.10, N.11, L.14, M.33, P.45, P.46, F.61, G.64, F.65, T.97, C.98, C.101, H.102, Y.105, R.106 13 PLIP interactions: 13 interactions with chain C, Hydrophobic interactions: C:M.7, C:L.10, C:L.10, C:P.45, C:F.65, C:F.65, C:F.65, C:R.106 Hydrogen bonds: C:E.4 Water bridges: C:R.106, C:R.106 pi-Cation interactions: C:R.106 Metal complexes: C:H.102 HEM.14: 20 residues within 4Å: Chain D: L.3, E.4, M.7, E.8, L.10, N.11, L.14, M.33, P.45, P.46, F.61, G.64, F.65, L.68, T.97, C.98, C.101, H.102, Y.105, R.106 14 PLIP interactions: 14 interactions with chain D, Hydrophobic interactions: D:L.3, D:M.7, D:L.10, D:N.11, D:L.14, D:P.45, D:F.65, D:F.65, D:F.65, D:L.68, D:R.106, D:R.106 Hydrogen bonds: D:E.4 Metal complexes: D:H.102

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Salgado, E.N. et al., Control of protein oligomerization symmetry by metal coordination: C2 and C3 symmetrical assemblies through Cu(II) and Ni(II) coordination. Inorg.Chem. (2009)

Release Date

2009-04-21

Peptides

Soluble cytochrome b562: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Soluble cytochrome b562

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