SMTL ID : 4hr0.1

R2-like ligand-binding oxidase with aerobically reconstituted metal cofactor

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-dimer

Ligands

2 x MN3: MANGANESE (III) ION(Non-covalent)

MN3.1: 6 residues within 4Å: Chain A: E.83, V.86, E.116, H.119 Ligands: FE.2, PLM.5 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.83, A:E.116, A:H.119, H2O.1, H2O.3 MN3.6: 6 residues within 4Å: Chain B: E.83, V.86, E.116, H.119 Ligands: FE.7, PLM.10 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.83, B:E.116, B:H.119, H2O.4, H2O.7

2 x FE: FE (III) ION(Non-covalent)

FE.2: 8 residues within 4Å: Chain A: F.112, E.116, Y.176, E.181, E.216, H.219 Ligands: MN3.1, PLM.5 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.116, A:E.181, A:E.216, A:H.219, H2O.1 FE.7: 8 residues within 4Å: Chain B: F.112, E.116, Y.176, E.181, E.216, H.219 Ligands: MN3.6, PLM.10 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.116, B:E.181, B:E.216, B:H.219, H2O.4

2 x MN: MANGANESE (II) ION(Non-covalent)

MN.3: 1 residues within 4Å: Chain A: H.144 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:H.144 MN.8: 1 residues within 4Å: Chain B: H.144 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:H.144

2 x NA: SODIUM ION(Non-functional Binders)

NA.4: 8 residues within 4Å: Chain A: Q.127, I.132, G.133, M.135, L.137 Chain B: V.24, K.25, A.26 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:I.132 NA.9: 8 residues within 4Å: Chain A: V.24, K.25, A.26 Chain B: Q.127, I.132, G.133, M.135, L.137 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Q.127

2 x PLM: PALMITIC ACID(Non-covalent)

PLM.5: 28 residues within 4Å: Chain A: L.75, G.78, F.79, G.82, E.83, V.86, E.116, Y.145, F.149, Y.176, V.180, E.181, L.184, A.185, S.187, G.188, Y.189, T.191, E.216, Y.255, V.256, L.259, T.260, Y.279, L.282, V.286 Ligands: MN3.1, FE.2 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:F.79, A:F.79, A:F.149, A:E.181, A:A.185, A:Y.255, A:V.256 Water bridges: A:Y.189 Salt bridges: A:H.119 PLM.10: 28 residues within 4Å: Chain B: L.75, G.78, F.79, G.82, E.83, V.86, E.116, Y.145, F.149, Y.176, V.180, E.181, L.184, A.185, S.187, G.188, Y.189, T.191, E.216, Y.255, V.256, L.259, T.260, Y.279, L.282, V.286 Ligands: MN3.6, FE.7 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:F.79, B:F.79, B:F.149, B:E.181, B:A.185, B:Y.255, B:V.256 Water bridges: B:Y.189 Salt bridges: B:H.119

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Griese, J.J. et al., Direct observation of structurally encoded metal discrimination and ether bond formation in a heterodinuclear metalloprotein. Proc.Natl.Acad.Sci.USA (2013)

Release Date

2013-10-16

Peptides

Ribonuleotide reductase small subunit: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Ribonuleotide reductase small subunit

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