SMTL ID : 1jpr.1

Mn substituted Ribonucleotide reductase R2 from E. coli oxidized by nitric oxide

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.88 Å

Oligo State

homo-dimer

Ligands

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

MN.1: 5 residues within 4Å: Chain B: D.84, E.115, H.118, E.238 Ligands: MN.2 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.84, B:E.115, B:H.118, B:E.238, H2O.540 MN.2: 6 residues within 4Å: Chain B: W.111, E.115, E.204, E.238, H.241 Ligands: MN.1 6 PLIP interactions: 5 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.115, B:E.204, B:E.238, B:E.238, B:H.241, H2O.447 MN.3: 5 residues within 4Å: Chain A: D.84, E.115, H.118, E.238 Ligands: MN.4 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.84, A:E.115, A:H.118, A:E.238, H2O.116 MN.4: 6 residues within 4Å: Chain A: W.111, E.115, E.204, E.238, H.241 Ligands: MN.3 6 PLIP interactions: 5 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.115, A:E.204, A:E.238, A:E.238, A:H.241, H2O.49

14 x HG: MERCURY (II) ION(Non-covalent)

HG.5: 4 residues within 4Å: Chain A: Y.156, Y.157, C.196, V.200 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:C.196, H2O.35 HG.6: 6 residues within 4Å: Chain B: L.95, Y.157, C.196, L.197, V.200 Ligands: HG.8 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:C.196 HG.7: 4 residues within 4Å: Chain B: Y.194, L.195, C.268, C.272 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:C.268, H2O.383 HG.8: 5 residues within 4Å: Chain B: Y.156, Y.157, C.196, V.200 Ligands: HG.6 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:C.196, B:C.196, H2O.399 HG.9: 4 residues within 4Å: Chain B: I.72, C.214, F.218, M.296 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:C.214 HG.10: 5 residues within 4Å: Chain A: Y.194, M.198, A.265, K.269, C.272 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:Y.194, A:C.272, H2O.43 HG.11: 5 residues within 4Å: Chain A: V.210, A.213, C.214, L.299, L.304 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:V.210, A:C.214 HG.12: 4 residues within 4Å: Chain B: M.198, C.272, L.275, F.276 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:C.272, B:C.272, H2O.717 HG.13: 5 residues within 4Å: Chain B: V.210, A.213, C.214, L.304 Ligands: HG.14 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:V.210 HG.14: 6 residues within 4Å: Chain B: N.76, V.210, C.214, W.286, L.304 Ligands: HG.13 No protein-ligand interaction detected (PLIP) HG.15: 3 residues within 4Å: Chain A: C.305, Q.306, E.309 No protein-ligand interaction detected (PLIP) HG.16: 3 residues within 4Å: Chain B: K.284, C.305, E.309 No protein-ligand interaction detected (PLIP) HG.17: 5 residues within 4Å: Chain B: Y.194, M.198, A.265, C.272, L.321 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:Y.194, H2O.383, H2O.534 HG.18: 4 residues within 4Å: Chain B: K.191, I.264, E.267, C.268 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:I.264, B:C.268

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hogbom, M. et al., Crystal structures of oxidized dinuclear manganese centres in Mn-substituted class I ribonucleotide reductase from Escherichia coli: carboxylate shifts with implications for O2 activation and radical generation. J.Biol.Inorg.Chem. (2001)

Release Date

2001-08-15

Peptides

Protein R2 of Ribonucleotide reductase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Protein R2 of Ribonucleotide reductase

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