SMTL ID : 5utd.1

Sperm whale myoglobin V68A/I107Y with nitrite

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.78 Å

Oligo State

monomer

Ligands

1 x HEM: PROTOPORPHYRIN IX CONTAINING FE(Non-covalent)

HEM.1: 17 residues within 4Å: Chain A: T.40, K.43, F.44, R.46, H.65, A.69, A.72, L.90, S.93, H.94, H.98, I.100, Y.104, L.105, Y.108, F.139 Ligands: NO2.3 22 PLIP interactions: 22 interactions with chain A, Hydrophobic interactions: A:T.40, A:F.44, A:F.44, A:F.44, A:F.44, A:A.72, A:L.90, A:L.90, A:H.98, A:I.100, A:I.100, A:Y.104, A:Y.108, A:F.139 Hydrogen bonds: A:S.93 Water bridges: A:R.46 Salt bridges: A:R.46, A:H.94, A:H.98 pi-Stacking: A:H.98, A:Y.108 Metal complexes: A:H.94

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

SO4.2: 3 residues within 4Å: Chain A: K.35, T.52, E.53 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:E.53 Water bridges: A:T.52, A:E.53, A:A.54 Salt bridges: A:K.35

2 x NO2: NITRITE ION(Non-covalent)

NO2.3: 6 residues within 4Å: Chain A: L.30, F.44, H.65, A.69, Y.108 Ligands: HEM.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.108 NO2.4: 4 residues within 4Å: Chain A: R.32, S.36, E.110, A.111 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.32 Water bridges: A:A.111

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wang, B. et al., Nitrosyl Myoglobins and Their Nitrite Precursors: Crystal Structural and Quantum Mechanics and Molecular Mechanics Theoretical Investigations of Preferred Fe -NO Ligand Orientations in Myoglobin Distal Pockets. Biochemistry (2018)

Release Date

2018-02-28

Peptides

Myoglobin: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Myoglobin