SMTL ID : 1yfd.1

Crystal structure of the Y122H mutant of ribonucleotide reductase R2 protein from E. coli

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-dimer

Ligands

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

HG.1: 3 residues within 4Å: Chain A: Y.157, C.196, V.200 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:C.196, H2O.1 HG.2: 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.7 HG.3: 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.4: 3 residues within 4Å: Chain A: C.305, Q.306, E.309 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:C.305 HG.6: 5 residues within 4Å: Chain B: 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: 6 residues within 4Å: Chain B: Y.194, A.265, C.268, K.269, C.272 Ligands: HG.14 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:A.265, H2O.14 HG.8: 5 residues within 4Å: Chain B: Y.156, Y.157, C.196, V.200 Ligands: HG.6 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:C.196, H2O.10 HG.9: 5 residues within 4Å: Chain B: N.76, V.210, C.214, L.290, L.304 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:C.214 HG.10: 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 HG.11: 4 residues within 4Å: Chain B: C.305, Q.306, E.309 Ligands: HG.12 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:C.305, B:E.309, H2O.16 HG.12: 4 residues within 4Å: Chain B: K.284, C.305, E.309 Ligands: HG.11 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:C.305 HG.13: 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 HG.14: 5 residues within 4Å: Chain B: Y.194, M.198, A.265, L.321 Ligands: HG.7 No protein-ligand interaction detected (PLIP)

2 x FEO: MU-OXO-DIIRON(Non-covalent)(Covalent)

FEO.5: 6 residues within 4Å: Chain A: D.84, E.115, H.118, E.204, E.238, H.241 9 PLIP interactions: 6 interactions with chain A, 3 Ligand-Water interactions, Metal complexes: A:E.115, A:E.115, A:H.118, A:E.204, A:E.238, A:H.241, H2O.1, H2O.1, H2O.1 FEO.15: 6 residues within 4Å: Chain B: D.84, E.115, H.118, E.204, E.238, H.241 10 PLIP interactions: 7 interactions with chain B, 3 Ligand-Water interactions, Metal complexes: B:D.84, B:E.115, B:E.115, B:H.118, B:E.204, B:E.238, B:H.241, H2O.9, H2O.9, H2O.9

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kolberg, M. et al., A new tyrosyl radical on Phe208 as ligand to the diiron center in Escherichia coli ribonucleotide reductase, mutant R2-Y122H. Combined x-ray diffraction and EPR/ENDOR studies. J.Biol.Chem. (2005)

Release Date

2005-02-15

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