SMTL ID : 1pm2.1

CRYSTAL STRUCTURE OF MANGANESE SUBSTITUTED R2-D84E (D84E MUTANT OF THE R2 SUBUNIT OF E. COLI RIBONUCLEOTIDE REDUCTASE)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-dimer

Ligands

4 x MN: MANGANESE (II) ION(Non-covalent)

MN.1: 6 residues within 4Å: Chain A: E.84, E.115, H.118, F.208, E.238 Ligands: MN.2 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:E.84, A:E.84, A:E.115, A:H.118, A:E.238 MN.2: 7 residues within 4Å: Chain A: W.111, E.115, E.204, F.208, E.238, H.241 Ligands: MN.1 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:E.115, A:E.204, A:E.204, A:E.238, A:H.241 MN.9: 6 residues within 4Å: Chain B: E.84, E.115, H.118, F.208, E.238 Ligands: MN.10 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:E.84, B:E.84, B:E.115, B:H.118, B:E.238 MN.10: 7 residues within 4Å: Chain B: W.111, E.115, E.204, F.208, E.238, H.241 Ligands: MN.9 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:E.115, B:E.204, B:E.204, B:E.238, B:H.241

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

HG.3: 6 residues within 4Å: Chain A: Y.194, A.265, K.269, C.272, L.321 Ligands: HG.6 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:Y.194, A:C.272 HG.4: 4 residues within 4Å: Chain A: Y.157, C.196, V.200 Ligands: HG.7 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:C.196 HG.5: 3 residues within 4Å: Chain A: V.210, A.213, C.214 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:V.210, A:C.214 HG.6: 5 residues within 4Å: Chain A: Y.194, L.195, C.268, C.272 Ligands: HG.3 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:C.268, A:C.272 HG.7: 5 residues within 4Å: Chain A: Y.157, C.196, L.197, V.200 Ligands: HG.4 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:C.196 HG.8: 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.11: 5 residues within 4Å: Chain B: Y.156, Y.157, C.196, V.200 Ligands: HG.17 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:C.196, B:C.196 HG.12: 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.13: 3 residues within 4Å: Chain B: Y.194, A.265, L.321 No protein-ligand interaction detected (PLIP) HG.14: 6 residues within 4Å: Chain B: V.210, A.213, C.214, L.299, L.304 Ligands: HG.18 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:V.210 HG.15: 4 residues within 4Å: Chain B: K.284, C.305, E.309 Ligands: HG.16 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:C.305, B:C.305 HG.16: 4 residues within 4Å: Chain B: C.305, Q.306, E.309 Ligands: HG.15 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:C.305 HG.17: 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.18: 5 residues within 4Å: Chain B: N.76, V.210, C.214, L.290 Ligands: HG.14 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:C.214

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Voegtli, W.C. et al., Variable coordination geometries at the diiron(II) active site of ribonucleotide reductase R2. J.Am.Chem.Soc. (2003)

Release Date

2004-01-13

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