SMTL ID : 3de9.1

Crystal Structure of a Trimeric Cytochrome cb562 Assembly Induced by Nickel Coordination

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.04 Å

Oligo State

homo-trimer

Ligands

9 x NI: NICKEL (II) ION(Non-covalent)

NI.1: 8 residues within 4Å: Chain A: H.59, H.63 Chain B: H.59, H.63 Chain C: H.59, H.63 Ligands: NI.5, NI.9 6 PLIP interactions: 2 interactions with chain B, 2 interactions with chain C, 2 interactions with chain A Metal complexes: B:H.59, B:H.63, C:H.59, C:H.63, A:H.59, A:H.63 NI.2: 8 residues within 4Å: Chain A: H.73, H.77 Chain B: H.73, H.77 Chain C: H.73, H.77 Ligands: NI.6, NI.10 6 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B, 2 interactions with chain C Metal complexes: A:H.73, A:H.77, B:H.73, B:H.77, C:H.73, C:H.77 NI.3: 3 residues within 4Å: Chain A: A.1, D.39, K.42 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:A.1, A:D.39 NI.5: 8 residues within 4Å: Chain A: H.59, H.63 Chain B: H.59, H.63 Chain C: H.59, H.63 Ligands: NI.1, NI.9 6 PLIP interactions: 2 interactions with chain B, 2 interactions with chain C, 2 interactions with chain A Metal complexes: B:H.59, B:H.63, C:H.59, C:H.63, A:H.59, A:H.63 NI.6: 8 residues within 4Å: Chain A: H.73, H.77 Chain B: H.73, H.77 Chain C: H.73, H.77 Ligands: NI.2, NI.10 6 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B, 2 interactions with chain C Metal complexes: A:H.73, A:H.77, B:H.73, B:H.77, C:H.73, C:H.77 NI.7: 3 residues within 4Å: Chain B: A.1, D.39, K.42 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:A.1, B:D.39 NI.9: 8 residues within 4Å: Chain A: H.59, H.63 Chain B: H.59, H.63 Chain C: H.59, H.63 Ligands: NI.1, NI.5 6 PLIP interactions: 2 interactions with chain B, 2 interactions with chain C, 2 interactions with chain A Metal complexes: B:H.59, B:H.63, C:H.59, C:H.63, A:H.59, A:H.63 NI.10: 8 residues within 4Å: Chain A: H.73, H.77 Chain B: H.73, H.77 Chain C: H.73, H.77 Ligands: NI.2, NI.6 6 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B, 2 interactions with chain C Metal complexes: A:H.73, A:H.77, B:H.73, B:H.77, C:H.73, C:H.77 NI.11: 3 residues within 4Å: Chain C: A.1, D.39, K.42 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:A.1, C:D.39

3 x HEM: PROTOPORPHYRIN IX CONTAINING FE(Covalent)

HEM.4: 18 residues within 4Å: Chain A: L.3, E.4, M.7, L.10, N.11, L.14, P.45, P.46, F.61, G.64, F.65, L.68, T.97, C.98, C.101, H.102, Y.105, R.106 13 PLIP interactions: 13 interactions with chain A, Hydrophobic interactions: A:M.7, A:L.10, A:L.10, A:N.11, A:L.14, A:P.45, A:F.61, A:F.65, A:F.65, A:F.65, A:L.68, A:R.106 Metal complexes: A:H.102 HEM.8: 18 residues within 4Å: Chain B: L.3, E.4, M.7, L.10, N.11, L.14, P.45, P.46, F.61, G.64, F.65, L.68, 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:L.10, B:L.10, B:N.11, B:L.14, B:P.45, B:F.61, B:F.65, B:F.65, B:F.65, B:L.68, B:R.106 Metal complexes: B:H.102 HEM.12: 18 residues within 4Å: Chain C: L.3, E.4, M.7, L.10, N.11, L.14, P.45, P.46, F.61, G.64, F.65, L.68, 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:N.11, C:L.14, C:P.45, C:F.61, C:F.65, C:F.65, C:F.65, C:L.68, C:R.106 Metal complexes: C:H.102

Links

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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: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

Soluble cytochrome b562

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