SMTL ID : 2v1f.1

Crystal structure of radiation-induced myoglobin compound II - intermediate H at pH 8.7

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.20 Å

Oligo State

monomer

Ligands

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

HEM.1: 20 residues within 4Å: Chain A: T.39, K.42, F.43, K.45, H.64, V.67, V.68, A.71, L.72, L.89, S.92, H.93, H.97, I.99, Y.103, L.104, I.107, F.138 Ligands: OH.2, GOL.5 22 PLIP interactions: 21 interactions with chain A, 1 Ligand-Ligand interactions Hydrophobic interactions: A:F.43, A:F.43, A:F.43, A:F.43, A:V.67, A:V.68, A:A.71, A:L.89, A:I.99, A:Y.103, A:I.107, A:F.138, A:F.138 Hydrogen bonds: A:S.92 Water bridges: A:K.96 Salt bridges: A:K.45, A:H.93, A:H.97 pi-Stacking: A:H.93, A:H.97 Metal complexes: A:H.93, OH.2

1 x OH: HYDROXIDE ION(Non-covalent)

OH.2: 5 residues within 4Å: Chain A: F.43, H.64, V.68, H.93 Ligands: HEM.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.64

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

SO4.3: 3 residues within 4Å: Chain A: K.50, T.51, E.52 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.52 Water bridges: A:T.51, A:A.53 SO4.4: 1 residues within 4Å: Chain A: G.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.1

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 5 residues within 4Å: Chain A: K.45, K.63, H.64, V.67 Ligands: HEM.1 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:K.45, A:K.63, A:H.64 Water bridges: A:K.45, A:K.63 GOL.6: 3 residues within 4Å: Chain A: S.3, D.4, G.5 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:S.3, A:G.5 Water bridges: A:D.4, A:D.4, A:D.4, A:D.4, A:D.4, A:D.4, A:E.6 GOL.7: 3 residues within 4Å: Chain A: D.20, H.24, K.118 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.118, A:K.118 GOL.8: 6 residues within 4Å: Chain A: L.11, N.12, W.14, G.15, E.18, K.77 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.15, A:E.18 Water bridges: A:E.18

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hersleth, H.-P. et al., Crystallographic and Spectroscopic Studies of Peroxide-Derived Myoglobin Compound II and Occurrence of Protonated Fe(Iv)-O. J.Biol.Chem. (2007)

Release Date

2007-06-12

Peptides

MYOGLOBIN: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

MYOGLOBIN

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