SMTL ID : 5azr.1

Crystal structure of aqua-cobalt(III) tetradehydrocorrin in the heme pocket of horse heart myoglobin

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.20 Å

Oligo State

monomer

Ligands

1 x J1R: (1R,19R) cobalt tetradehydrocorrin(Non-covalent)

J1R.1: 15 residues within 4Å: Chain A: K.42, F.43, K.45, V.67, V.68, A.71, S.92, H.93, H.97, I.99, Y.103, L.104, I.107, F.138 Ligands: J1S.2 20 PLIP interactions: 19 interactions with chain A, 1 Ligand-Water interactions, Hydrophobic interactions: A:F.43, A:F.43, A:V.67, A:V.68, A:A.71, A:I.99, A:I.99, A:Y.103, A:L.104, A:I.107, A:I.107, A:F.138 Hydrogen bonds: A:S.92 Water bridges: A:D.44 Salt bridges: A:K.45, A:H.93, A:H.97 pi-Stacking: A:H.97 Metal complexes: A:H.93, H2O.1

1 x J1S: (1S,19S) cobalt tetradehydrocorrin(Non-covalent)

J1S.2: 14 residues within 4Å: Chain A: K.42, F.43, K.45, V.67, V.68, A.71, S.92, H.93, H.97, I.99, Y.103, L.104, I.107 Ligands: J1R.1 18 PLIP interactions: 17 interactions with chain A, 1 Ligand-Water interactions, Hydrophobic interactions: A:F.43, A:F.43, A:V.67, A:V.68, A:A.71, A:I.99, A:I.99, A:Y.103, A:L.104, A:I.107 Hydrogen bonds: A:S.92 Water bridges: A:D.44 Salt bridges: A:K.45, A:H.64, A:H.93, A:H.97 Metal complexes: A:H.93, H2O.1

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:K.50, A:E.52 Water bridges: A:A.53 SO4.4: 3 residues within 4Å: Chain A: H.81, H.82, E.83 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:H.81, A:E.83 Water bridges: A:H.82, A:H.82, A:A.84

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 2 residues within 4Å: Chain A: K.79, H.81 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.79, A:H.81 GOL.6: 4 residues within 4Å: Chain A: S.3, D.4, G.5, E.6 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.3, A:G.5 Water bridges: A:D.4, A:E.6

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Morita, Y. et al., Crystal Structures and Coordination Behavior of Aqua- and Cyano-Co(III) Tetradehydrocorrins in the Heme Pocket of Myoglobin. Inorg.Chem. (2016)

Release Date

2016-01-20

Peptides

Myoglobin: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Myoglobin

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