SMTL ID : 1rsv.1

azide complex of the diferrous E238A mutant R2 subunit of ribonucleotide reductase

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: D.84, E.115, H.118, F.208 Ligands: FE.2, AZI.9 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.84, A:D.84, A:E.115, A:H.118 FE.2: 6 residues within 4Å: Chain A: W.111, E.115, E.204, H.241 Ligands: FE.1, AZI.9 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:E.115, A:E.204, A:E.204, A:H.241 FE.10: 5 residues within 4Å: Chain B: D.84, E.115, H.118, F.208 Ligands: FE.11 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.84, B:D.84, B:E.115, B:H.118, H2O.13 FE.11: 5 residues within 4Å: Chain B: W.111, E.115, E.204, H.241 Ligands: FE.10 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.115, B:E.115, B:E.204, B:H.241, H2O.13

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

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

1 x AZI: AZIDE ION(Non-covalent)

AZI.9: 10 residues within 4Å: Chain A: D.84, E.115, H.118, E.204, F.208, I.234, A.238, H.241 Ligands: FE.1, FE.2 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.204

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Assarsson, M. et al., Restoring proper radical generation by azide binding to the iron site of the E238A mutant R2 protein of ribonucleotide reductase from Escherichia coli. J.Biol.Chem. (2001)

Release Date

2003-12-23

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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