SMTL ID : 6cf0.1

Sperm Whale Myoglobin H64V Mutant with Nitrite

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.64 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, T.68, V.69, A.72, L.90, S.93, H.94, H.98, I.100, Y.104, L.105, I.108, F.139 Ligands: NO2.2 23 PLIP interactions: 23 interactions with chain A, Hydrophobic interactions: A:F.44, A:F.44, A:F.44, A:T.68, A:V.69, A:A.72, A:L.90, A:L.90, A:I.100, A:Y.104, A:L.105, A:I.108, A:I.108, A:F.139, A:F.139 Hydrogen bonds: A:S.93 Water bridges: A:H.98 Salt bridges: A:R.46, A:H.94, A:H.98 pi-Stacking: A:H.98 pi-Cation interactions: A:H.94 Metal complexes: A:H.94

4 x NO2: NITRITE ION(Non-covalent)

NO2.2: 4 residues within 4Å: Chain A: F.44, V.65, V.69 Ligands: HEM.1 1 PLIP interactions: 1 interactions with chain A Water bridges: A:V.69 NO2.3: 3 residues within 4Å: Chain A: Q.92, S.93, K.97 2 PLIP interactions: 2 interactions with chain A Water bridges: A:S.93, A:H.98 NO2.4: 2 residues within 4Å: Chain A: E.19, V.22 No protein-ligand interaction detected (PLIP) NO2.5: 5 residues within 4Å: Chain A: R.32, S.36, E.110, A.111, H.114 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.32

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 3 residues within 4Å: Chain A: T.52, E.53, A.54 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:A.54 GOL.7: 6 residues within 4Å: Chain A: N.123, F.124, G.125, A.126, D.127, A.128 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.125, A:A.126, A:D.127, A:A.128 GOL.8: 4 residues within 4Å: Chain A: A.58, S.59, E.60, D.61 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.60, A:D.61, A:D.61

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

SO4.9: 2 residues within 4Å: Chain A: R.32, H.114 2 PLIP interactions: 2 interactions with chain A Water bridges: A:S.36 Salt bridges: A:R.32 SO4.10: 0 residues within 4Å: (No contacts) 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:K.17

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

2018-05-02

Peptides

Myoglobin: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Myoglobin

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