SMTL ID : 1rsr.1

azide complex of the diferrous F208A mutant R2 subunit of ribonucleotide reductase

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-dimer

Ligands

4 x FE2: FE (II) ION(Non-covalent)

FE2.1: 5 residues within 4Å: Chain A: D.84, E.115, H.118, E.238 Ligands: FE2.2 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.84, A:E.115, A:H.118, A:E.238 FE2.2: 6 residues within 4Å: Chain A: W.111, E.115, E.204, E.238, H.241 Ligands: FE2.1 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:E.115, A:E.204, A:E.238, A:H.241 FE2.9: 6 residues within 4Å: Chain B: D.84, E.115, H.118, E.238 Ligands: FE2.10, AZI.17 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.84, B:E.115, B:H.118, B:E.238 FE2.10: 7 residues within 4Å: Chain B: W.111, E.115, E.204, E.238, H.241 Ligands: FE2.9, AZI.17 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:E.115, B:E.115, B:E.204, B:E.238, B:H.241

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

HG.3: 6 residues within 4Å: Chain A: Y.156, Y.157, C.196, V.200 Ligands: HG.6, HG.8 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:C.196, H2O.5 HG.4: 5 residues within 4Å: Chain A: Y.194, M.198, C.268, C.272 Ligands: HG.5 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:C.272, H2O.6 HG.5: 6 residues within 4Å: Chain A: Y.194, M.198, A.265, K.269, C.272 Ligands: HG.4 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:Y.194, A:C.272, H2O.5, H2O.6, H2O.6 HG.6: 5 residues within 4Å: Chain A: Y.157, C.196, L.197, V.200 Ligands: HG.3 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:C.196, H2O.5 HG.7: 4 residues within 4Å: Chain A: V.210, A.213, C.214, L.299 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:V.210, A:C.214, H2O.5, H2O.5 HG.8: 5 residues within 4Å: Chain A: I.153, Y.157, S.199, V.200 Ligands: HG.3 No protein-ligand interaction detected (PLIP) HG.11: 5 residues within 4Å: Chain B: Y.157, C.196, L.197, V.200 Ligands: HG.13 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:C.196 HG.12: 5 residues within 4Å: Chain B: Y.194, L.195, C.268, K.269, C.272 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:C.268, B:C.268, B:C.272, H2O.7 HG.13: 5 residues within 4Å: Chain B: Y.156, Y.157, C.196, V.200 Ligands: HG.11 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:C.196, B:C.196, H2O.11 HG.14: 5 residues within 4Å: Chain B: I.72, C.214, F.218, M.296, L.299 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:C.214 HG.15: 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.16: 3 residues within 4Å: Chain B: F.73, N.76, S.215 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:S.215, H2O.7, H2O.12

1 x AZI: AZIDE ION(Non-covalent)

AZI.17: 9 residues within 4Å: Chain B: D.84, Q.87, E.115, L.203, E.204, A.208, E.238 Ligands: FE2.9, FE2.10 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.238, B:E.238

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Andersson, M.E. et al., The Crystal Structure of an Azide Complex of the Diferrous R2 Subunit of Ribonucleotide Reductase Displays a Novel Carboxylate Shift with Important Mechanistic Implications for Diiron-Catalyzed Oxygen Activation. J.Am.Chem.Soc. (1999)

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