SMTL ID : 4ep5.1

Thermus thermophilus RuvC structure

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.08 Å

Oligo State

homo-dimer

Ligands

8 x SO4: SULFATE ION(Non-functional Binders)

SO4.1: 12 residues within 4Å: Chain A: V.35, V.36, K.37, R.50, R.54 Chain B: V.35, V.36, K.37, R.50 Ligands: SO4.2, SO4.6, SO4.7 13 PLIP interactions: 7 interactions with chain A, 6 interactions with chain B Hydrogen bonds: A:K.37, B:K.37 Water bridges: A:K.37, A:K.37, A:R.50, A:R.50, B:K.37, B:K.37, B:R.50 Salt bridges: A:K.37, A:R.50, B:K.37, B:R.50 SO4.2: 9 residues within 4Å: Chain A: E.34, V.35, K.37 Chain B: E.34, V.35, K.37 Ligands: SO4.1, SO4.6, SO4.7 8 PLIP interactions: 4 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:V.35, A:V.35, B:E.34, B:V.35 Water bridges: A:K.37, B:K.37 Salt bridges: A:K.37, B:K.37 SO4.3: 4 residues within 4Å: Chain A: K.111, A.121, K.122, E.123 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.122 Salt bridges: A:K.111 SO4.4: 4 residues within 4Å: Chain A: G.106, P.107, M.108, Q.109 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.106, A:M.108, A:Q.109 SO4.6: 12 residues within 4Å: Chain A: V.35, V.36, K.37, R.50 Chain B: V.35, V.36, K.37, R.50, R.54 Ligands: SO4.1, SO4.2, SO4.7 13 PLIP interactions: 6 interactions with chain A, 7 interactions with chain B Hydrogen bonds: A:K.37, B:K.37 Water bridges: A:K.37, A:K.37, A:R.50, B:K.37, B:K.37, B:R.50, B:R.50 Salt bridges: A:K.37, A:R.50, B:K.37, B:R.50 SO4.7: 9 residues within 4Å: Chain A: E.34, V.35, K.37 Chain B: E.34, V.35, K.37 Ligands: SO4.1, SO4.2, SO4.6 8 PLIP interactions: 4 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:E.34, A:V.35, B:V.35, B:V.35 Water bridges: A:K.37, B:K.37 Salt bridges: A:K.37, B:K.37 SO4.8: 4 residues within 4Å: Chain B: K.111, A.121, K.122, E.123 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.122 Salt bridges: B:K.111 SO4.9: 4 residues within 4Å: Chain B: G.106, P.107, M.108, Q.109 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:G.106, B:M.108, B:Q.109

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 6 residues within 4Å: Chain A: H.12, K.37, R.140, P.141 Chain B: R.54, R.61 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:R.54, B:R.61, A:H.12, A:R.140 GOL.10: 6 residues within 4Å: Chain A: R.54, R.61 Chain B: H.12, K.37, R.140, P.141 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:H.12, B:R.140, A:R.54, A:R.61

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chen, L. et al., Structural asymmetry in the Thermus thermophilus RuvC dimer suggests a basis for sequential strand cleavages during Holliday junction resolution. Nucleic Acids Res. (2013)

Release Date

2012-11-14

Peptides

Crossover junction endodeoxyribonuclease RuvC: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Crossover junction endodeoxyribonuclease RuvC