SMTL ID : 5ngx.1

The 1.06 A resolution structure of the L16G mutant of ferric cytochrome c prime from Alcaligenes xylosoxidans, complexed with nitrite

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.06 Å

Oligo State

monomer

Ligands

1 x HEC: HEME C(Non-covalent)

HEC.1: 22 residues within 4Å: Chain A: R.12, Q.13, G.16, M.19, A.20, W.56, F.59, G.65, G.66, D.67, A.68, I.72, F.79, K.82, Q.83, F.86, C.116, C.119, H.120, Y.123, R.124 Ligands: NO2.2 23 PLIP interactions: 22 interactions with chain A, 1 Ligand-Water interactions Hydrophobic interactions: A:A.20, 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:T.17, A:T.17, A:D.67, A:A.68 Salt bridges: A:R.12 pi-Stacking: A:H.120, A:H.120 pi-Cation interactions: A:R.124, A:R.124 Metal complexes: A:H.120, H2O.4

1 x NO2: NITRITE ION(Non-covalent)

NO2.2: 5 residues within 4Å: Chain A: G.16, M.19, P.55, W.56 Ligands: HEC.1 No protein-ligand interaction detected (PLIP)

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 4 residues within 4Å: Chain A: R.69, P.70, K.125, K.126 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.69, A:K.126 Water bridges: A:K.125, A:K.125

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nilsson, Z.N. et al., Distinguishing Nitro vs Nitrito Coordination in Cytochrome c' Using Vibrational Spectroscopy and Density Functional Theory. Inorg.Chem. (2017)

Release Date

2018-05-16

Peptides

Cytochrome c': A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Cytochrome c'