SMTL ID : 8bt4.1

Ribonucleotide Reductase class Ie R2 from Mesoplasma florum, radical-lost ground state

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.35 Å

Oligo State

homo-dimer

Ligands

2 x CA: CALCIUM ION(Non-covalent)

CA.1: 4 residues within 4Å: Chain A: G.271, D.274, D.275 Ligands: GOL.2 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:G.271, A:D.274, A:D.275, H2O.1 CA.7: 4 residues within 4Å: Chain B: G.271, D.274, D.275 Ligands: GOL.8 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:G.271, B:D.274, B:D.275

7 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 3 residues within 4Å: Chain A: D.274, D.275 Ligands: CA.1 No protein-ligand interaction detected (PLIP) GOL.3: 5 residues within 4Å: Chain A: Y.282, T.302, R.303, I.304, F.309 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.302, A:T.302, A:I.304 Water bridges: A:I.304 GOL.4: 2 residues within 4Å: Chain A: K.245, F.249 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.245, A:Y.253, A:Y.253 GOL.5: 5 residues within 4Å: Chain A: L.74, W.78, L.198, R.201, K.203 1 PLIP interactions: 1 interactions with chain A Water bridges: A:T.73 GOL.6: 9 residues within 4Å: Chain A: Y.14, S.19, E.22, R.33, S.108, L.109, T.110, D.111, Q.114 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:S.19, A:E.22, A:E.22, A:R.33, A:T.110 Water bridges: A:Q.25, A:R.33, A:D.111 GOL.8: 4 residues within 4Å: Chain B: G.271, D.274, D.275 Ligands: CA.7 No protein-ligand interaction detected (PLIP) GOL.9: 8 residues within 4Å: Chain B: Y.14, S.19, E.22, R.33, L.109, T.110, D.111, Q.114 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:Y.14, B:S.19, B:S.19, B:E.22, B:R.33, B:T.110, B:D.111 Water bridges: B:R.33, B:D.111

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lebrette, H. et al., Structure of a ribonucleotide reductase R2 protein radical. Science (2023)

Release Date

2023-11-01

Peptides

Ribonucleoside-diphosphate reductase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Ribonucleoside-diphosphate reductase

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