SMTL ID : 1piu.1

OXIDIZED RIBONUCLEOTIDE REDUCTASE R2-D84E MUTANT CONTAINING OXO-BRIDGED DIFERRIC CLUSTER

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-dimer

Ligands

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

FE.1: 6 residues within 4Å: Chain A: E.84, E.115, H.118, E.238 Ligands: FE.2, O.16 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.84, A:E.84, A:E.115, A:H.118, H2O.75 FE.2: 7 residues within 4Å: Chain A: W.111, E.115, E.204, E.238, H.241 Ligands: FE.1, O.16 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.115, A:E.204, A:E.238, A:H.241, H2O.75 FE.3: 6 residues within 4Å: Chain B: E.84, E.115, H.118, E.238 Ligands: FE.4, O.15 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.84, B:E.115, B:H.118, H2O.198, H2O.199 FE.4: 7 residues within 4Å: Chain B: W.111, E.115, E.204, E.238, H.241 Ligands: FE.3, O.15 6 PLIP interactions: 4 interactions with chain B, 1 Ligand-Ligand interactions, 1 Ligand-Water interactions Metal complexes: B:E.115, B:E.204, B:E.238, B:H.241, O.15, H2O.199

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

HG.5: 5 residues within 4Å: Chain A: Y.194, M.198, A.265, K.269, C.272 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:Y.194, A:C.272 HG.6: 2 residues within 4Å: Chain A: Y.157, C.196 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:C.196 HG.7: 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.8: 4 residues within 4Å: Chain B: Y.156, Y.157, C.196, V.200 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:C.196 HG.9: 4 residues within 4Å: Chain B: Y.194, L.195, C.268, C.272 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:C.268, B:C.268, B:C.272 HG.10: 5 residues within 4Å: Chain B: V.210, A.213, C.214, L.299, L.304 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:V.210, B:C.214 HG.11: 4 residues within 4Å: Chain A: K.284, C.305, Q.306, E.309 No protein-ligand interaction detected (PLIP) HG.12: 4 residues within 4Å: Chain B: M.198, C.272, L.275, F.276 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:C.272 HG.13: 4 residues within 4Å: Chain A: K.191, I.264, E.267, C.268 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:C.268, H2O.54 HG.14: 3 residues within 4Å: Chain B: K.284, C.305, E.309 No protein-ligand interaction detected (PLIP)

2 x O: OXYGEN ATOM(Non-covalent)

O.15: 6 residues within 4Å: Chain B: E.115, H.118, E.238, H.241 Ligands: FE.3, FE.4 No protein-ligand interaction detected (PLIP) O.16: 6 residues within 4Å: Chain A: E.115, H.118, E.238, H.241 Ligands: FE.1, FE.2 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.118, A:E.238

Links

RCSB   PDBe   PDBj   PDBsum   CATH   PLIP

Citation

Voegtli, W.C. et al., Crystal Structure of the Ribonucleotide Reductase R2 Mutant that Accumulates a u-1,2-Peroxodiiron(III)Intermediate during Oxygen Activation. J.Am.Chem.Soc. (2000)

Release Date

2003-06-17

Peptides

Ribonucleoside-diphosphate reductase 1 beta chain: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Ribonucleoside-diphosphate reductase 1 beta chain

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