SMTL ID : 4cx9.1

The 5-coordinate proximal NO complex of cytochrome c prime from Shewanella frigidimarina

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.43 Å

Oligo State

homo-dimer

Ligands

2 x NO: NITRIC OXIDE(Non-covalent)

NO.1: 4 residues within 4Å: Chain A: C.118, H.122, K.126 Ligands: HEC.2 No protein-ligand interaction detected (PLIP) NO.9: 5 residues within 4Å: Chain B: C.118, H.122, K.126 Ligands: HEC.8, GOL.10 No protein-ligand interaction detected (PLIP)

2 x HEC: HEME C(Covalent)(Non-covalent)

HEC.2: 21 residues within 4Å: Chain A: R.12, Q.13, F.16, I.19, A.20, F.23, F.59, T.68, E.69, A.70, I.74, F.81, K.84, M.85, F.88, S.117, C.118, C.121, Y.125, K.126 Ligands: NO.1 20 PLIP interactions: 19 interactions with chain A, 1 Ligand-Ligand interactions Hydrophobic interactions: A:F.16, A:F.16, A:F.16, A:I.19, A:A.20, A:F.23, A:F.59, A:I.74, A:F.81, A:K.84, A:M.85, A:F.88, A:F.88 Hydrogen bonds: A:Q.13, A:E.69, A:A.70 Salt bridges: A:R.12 pi-Stacking: A:F.16, A:F.16 Metal complexes: NO.1 HEC.8: 24 residues within 4Å: Chain B: I.9, R.12, Q.13, F.16, G.17, I.19, A.20, F.23, F.59, T.68, E.69, A.70, I.74, F.81, K.84, M.85, F.88, S.117, C.118, C.121, Y.125, K.126 Ligands: NO.9, GOL.10 19 PLIP interactions: 18 interactions with chain B, 1 Ligand-Ligand interactions Hydrophobic interactions: B:F.16, B:F.16, B:F.16, B:I.19, B:A.20, B:F.23, B:F.59, B:I.74, B:F.81, B:K.84, B:M.85, B:F.88, B:F.88 Hydrogen bonds: B:Q.13, B:T.68, B:E.69, B:A.70 Salt bridges: B:R.12 Metal complexes: NO.9

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

SO4.3: 3 residues within 4Å: Chain A: A.6, G.66, D.67 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.67 SO4.4: 3 residues within 4Å: Chain A: I.60, A.61 Ligands: GOL.6 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:A.61

5 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 3 residues within 4Å: Chain A: E.57 Chain B: V.40, T.43 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.57 Water bridges: A:E.57 GOL.6: 6 residues within 4Å: Chain A: H.56, E.57, F.59, I.60, K.78 Ligands: SO4.4 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:H.56, A:F.59, A:K.78, A:K.78 GOL.7: 3 residues within 4Å: Chain A: A.87, D.90, N.91 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.90, A:D.90 Water bridges: A:N.91, A:N.91 GOL.10: 5 residues within 4Å: Chain B: C.118, H.122, K.126 Ligands: HEC.8, NO.9 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:C.118, B:K.126 GOL.11: 3 residues within 4Å: Chain A: T.43 Chain B: K.53, Q.89 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:Q.89, B:Q.89, A:T.43 Water bridges: A:T.43

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Manole, A. et al., Conformational Control of the Binding of Diatomic Gases to Cytochrome C'. J.Biol.Inorg.Chem. (2015)

Release Date

2015-04-08

Peptides

CYTOCHROME C, CLASS II: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

CYTOCHROME C, CLASS II

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