SMTL ID : 1mxr.1

High resolution structure of Ribonucleotide reductase R2 from E. coli in its oxidised (Met) form

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.42 Å

Oligo State

homo-dimer

Ligands

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

FE.1: 4 residues within 4Å: Chain A: D.84, E.115, H.118 Ligands: FE.2 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.84, A:E.115, A:H.118, H2O.2, H2O.17 FE.2: 6 residues within 4Å: Chain A: W.111, E.115, E.204, E.238, H.241 Ligands: FE.1 6 PLIP interactions: 4 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.115, A:E.204, A:E.238, A:H.241, H2O.2, H2O.17 FE.8: 4 residues within 4Å: Chain B: D.84, E.115, H.118 Ligands: FE.9 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.84, B:E.115, B:H.118, H2O.20, H2O.33 FE.9: 5 residues within 4Å: Chain B: E.115, E.204, E.238, H.241 Ligands: FE.8 6 PLIP interactions: 4 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.115, B:E.204, B:E.238, B:H.241, H2O.19, H2O.33

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

HG.3: 3 residues within 4Å: Chain A: Y.157, C.196, V.200 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:C.196, H2O.3, H2O.15 HG.4: 6 residues within 4Å: Chain A: Y.194, M.198, A.265, K.269, C.272, L.321 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:Y.194, A:C.272, H2O.3 HG.5: 5 residues within 4Å: Chain A: V.210, A.213, C.214, L.299, L.304 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:C.214, H2O.16 HG.6: 3 residues within 4Å: Chain A: C.305, Q.306, E.309 No protein-ligand interaction detected (PLIP) HG.10: 5 residues within 4Å: Chain B: Y.157, C.196, L.197, V.200 Ligands: HG.11 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:C.196 HG.11: 5 residues within 4Å: Chain B: Y.156, Y.157, C.196, V.200 Ligands: HG.10 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:C.196, H2O.22 HG.12: 6 residues within 4Å: Chain B: V.210, A.213, C.214, L.299, L.304 Ligands: HG.13 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:V.210 HG.13: 6 residues within 4Å: Chain B: N.76, V.210, C.214, L.290, L.304 Ligands: HG.12 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:C.214, H2O.24 HG.14: 3 residues within 4Å: Chain B: M.198, C.272, F.276 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:C.272, H2O.26, H2O.27 HG.15: 4 residues within 4Å: Chain B: Y.194, M.198, A.265, L.321 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:Y.194, H2O.19 HG.16: 4 residues within 4Å: Chain B: K.284, C.305, Q.306, E.309 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:E.309

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 7 residues within 4Å: Chain A: A.217, E.220, R.221, I.297, G.298, L.299, W.334 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:E.220, A:E.220, A:R.221, A:R.221, A:I.297, A:G.298

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hogbom, M. et al., Displacement of the tyrosyl radical cofactor in ribonucleotide reductase obtained by single-crystal high-field EPR and 1.4-A x-ray data. Proc.Natl.Acad.Sci.Usa (2003)

Release Date

2003-03-25

Peptides

Ribonucleotide reductase R2: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Ribonucleotide reductase R2

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