SMTL ID : 2bc5.5 (9 other biounits)

Crystal structure of E. coli cytochrome b562 with engineered c-type heme linkages

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.25 Å

Oligo State

homo-tetramer

Ligands

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

SO4.1: 6 residues within 4Å: Chain A: G.82, K.83, V.84, K.85, E.86 Chain C: K.85 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:K.85, A:E.86 Salt bridges: C:K.85 SO4.3: 2 residues within 4Å: Chain B: R.106 Chain C: Q.103 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain C Water bridges: B:R.106, B:R.106 Salt bridges: B:R.106 Hydrogen bonds: C:Q.103 SO4.4: 4 residues within 4Å: Chain B: K.51, S.55, P.56, E.57 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.57, B:E.57 Salt bridges: B:K.51 SO4.5: 3 residues within 4Å: Chain B: H.102, R.106 Chain C: Q.103 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain C Salt bridges: B:R.106 Hydrogen bonds: C:Q.103 SO4.7: 1 residues within 4Å: Chain C: K.42 1 PLIP interactions: 1 interactions with chain C Salt bridges: C:K.42 SO4.8: 1 residues within 4Å: Chain C: K.32 1 PLIP interactions: 1 interactions with chain C Salt bridges: C:K.32 SO4.9: 1 residues within 4Å: Chain C: K.19 1 PLIP interactions: 1 interactions with chain C Salt bridges: C:K.19 SO4.10: 4 residues within 4Å: Chain C: G.82, K.83, V.84, K.85 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:V.84, C:K.85 Water bridges: C:K.83, C:E.86 SO4.12: 4 residues within 4Å: Chain D: G.82, K.83, V.84, K.85 5 PLIP interactions: 1 interactions with chain B, 4 interactions with chain D Salt bridges: B:K.85 Hydrogen bonds: D:G.82, D:V.84, D:K.85 Water bridges: D:E.86

4 x HEC: HEME C(Covalent)

HEC.2: 19 residues within 4Å: Chain A: 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, C.98, C.101, H.102, Y.105, R.106 14 PLIP interactions: 14 interactions with chain A, Hydrophobic interactions: A:L.3, A:M.7, A:N.11, A:L.14, A:P.45, A:F.61, A:F.65, A:F.65, A:F.65, A:L.68 Hydrogen bonds: A:E.4, A:E.4 pi-Cation interactions: A:R.106 Metal complexes: A:H.102 HEC.6: 18 residues within 4Å: Chain B: L.3, E.4, M.7, E.8, 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:L.3, B:M.7, B:L.14, B:P.45, B:F.61, B:F.61, B:F.65, B:F.65, B:F.65 Hydrogen bonds: B:E.4, B:E.8 pi-Cation interactions: B:R.106 Metal complexes: B:H.102 HEC.11: 16 residues within 4Å: Chain C: E.4, M.7, E.8, N.11, M.33, P.45, 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 C, Hydrophobic interactions: C:M.7, C:N.11, C:P.45, C:F.61, C:F.65, C:F.65, C:F.65, C:L.68, C:R.106 Hydrogen bonds: C:E.8 Water bridges: C:E.4, C:E.4 pi-Cation interactions: C:R.106 Metal complexes: C:H.102 HEC.13: 17 residues within 4Å: Chain D: L.3, E.4, M.7, E.8, N.11, M.33, P.45, P.46, F.61, G.64, F.65, L.68, C.98, C.101, H.102, Y.105, R.106 12 PLIP interactions: 12 interactions with chain D, Hydrophobic interactions: D:M.7, D:N.11, D:P.45, D:F.61, D:F.65, D:F.65, D:F.65, D:L.68 pi-Stacking: D:H.102, D:H.102 pi-Cation interactions: D:R.106 Metal complexes: D:H.102

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Faraone-Mennella, J. et al., Stability and Folding Kinetics of Structurally Characterized Cytochrome c-b(562). Biochemistry (2006)

Release Date

2006-09-26

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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