SMTL ID : 5jra.1

Nitric oxide complex of the L16V mutant of cytochrome c prime from Alcaligenes xylosoxidans

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.38 Å

Oligo State

homo-dimer

Ligands

2 x HEC: HEME C(Covalent)

HEC.1: 26 residues within 4Å: Chain A: R.12, Q.13, V.16, M.19, A.20, F.23, W.56, F.59, G.65, G.66, D.67, A.68, I.72, F.79, K.82, Q.83, F.86, S.115, C.116, C.119, H.120, Y.123, R.124 Ligands: ASC.2, SO4.3, NO.4 18 PLIP interactions: 18 interactions with chain A, Hydrophobic interactions: A:V.16, A:F.23, A:W.56, A:W.56, A:F.59, A:I.72, A:F.79, A:K.82, A:Q.83, A:F.86, A:F.86, A:R.124 Hydrogen bonds: A:Q.13, A:D.67, A:A.68 Salt bridges: A:R.12 pi-Cation interactions: A:R.124 Metal complexes: A:H.120 HEC.5: 26 residues within 4Å: Chain B: R.12, Q.13, V.16, M.19, A.20, F.23, W.56, F.59, G.65, G.66, D.67, A.68, I.72, F.79, K.82, Q.83, F.86, S.115, C.116, C.119, H.120, Y.123, R.124 Ligands: ASC.6, SO4.7, NO.8 19 PLIP interactions: 19 interactions with chain B, Hydrophobic interactions: B:V.16, B:F.23, B:W.56, B:W.56, B:F.59, B:I.72, B:F.79, B:K.82, B:Q.83, B:F.86, B:F.86, B:R.124 Hydrogen bonds: B:Q.13, B:D.67, B:D.67, B:A.68 Salt bridges: B:R.12 pi-Cation interactions: B:R.124 Metal complexes: B:H.120

2 x ASC: ASCORBIC ACID(Non-covalent)

ASC.2: 7 residues within 4Å: Chain A: F.23, G.113, C.116, K.117, H.120 Ligands: HEC.1, SO4.3 2 PLIP interactions: 2 interactions with chain A Water bridges: A:G.113, A:R.124 ASC.6: 7 residues within 4Å: Chain B: F.23, G.113, C.116, K.117, H.120 Ligands: HEC.5, SO4.7 2 PLIP interactions: 2 interactions with chain B Water bridges: B:G.113, B:R.124

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

SO4.3: 4 residues within 4Å: Chain A: H.120, R.124 Ligands: HEC.1, ASC.2 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.124 SO4.7: 4 residues within 4Å: Chain B: H.120, R.124 Ligands: HEC.5, ASC.6 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:R.124

2 x NO: NITRIC OXIDE(Non-covalent)

NO.4: 4 residues within 4Å: Chain A: V.16, M.19, W.56 Ligands: HEC.1 No protein-ligand interaction detected (PLIP) NO.8: 4 residues within 4Å: Chain B: V.16, M.19, W.56 Ligands: HEC.5 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kekilli, D. et al., Engineering proximal vs. distal heme-NO coordination via dinitrosyl dynamics: implications for NO sensor design. Chem Sci (2017)

Release Date

2017-03-08

Peptides

Cytochrome c': AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Cytochrome c'

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