SMTL ID : 6yex.1

VcaM4I restriction endonuclease in the absence of DNA

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.50 Å

Oligo State

homo-dimer

Ligands

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

SO4.1: 2 residues within 4Å: Chain A: S.64, H.65 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:H.65 Water bridges: A:H.65, B:H.186 Salt bridges: A:H.65 SO4.2: 2 residues within 4Å: Chain A: P.135, H.136 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:H.136 Water bridges: A:N.2, A:H.136, A:H.136, A:E.137 Salt bridges: A:H.136 SO4.8: 3 residues within 4Å: Chain B: S.291, K.292, Q.293 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:K.292, B:Q.293, B:Q.293 Water bridges: B:S.291, B:S.291 SO4.11: 2 residues within 4Å: Chain B: G.147, S.148 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.148, B:S.148 Water bridges: B:E.149 SO4.12: 5 residues within 4Å: Chain B: N.27, Q.32, S.33, H.34, Y.35 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:N.27, B:H.34, B:Y.35 Water bridges: B:S.33 SO4.13: 2 residues within 4Å: Chain B: S.64, H.65 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:H.65 Water bridges: B:H.65, B:H.65 Salt bridges: B:H.65 SO4.14: 2 residues within 4Å: Chain B: P.135, H.136 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:H.136 Water bridges: B:N.2, B:H.136, B:E.137 Salt bridges: B:H.136

12 x CL: CHLORIDE ION(Non-functional Binders)

CL.3: 2 residues within 4Å: Chain A: S.33, H.34 Ligand excluded by PLIP CL.4: 2 residues within 4Å: Chain A: Q.121, D.122 Ligand excluded by PLIP CL.5: 2 residues within 4Å: Chain A: K.116, Y.117 Ligand excluded by PLIP CL.6: 2 residues within 4Å: Chain A: Y.67, S.68 Ligand excluded by PLIP CL.7: 2 residues within 4Å: Chain A: N.125, G.126 Ligand excluded by PLIP CL.9: 3 residues within 4Å: Chain B: E.261, D.262, R.302 Ligand excluded by PLIP CL.10: 3 residues within 4Å: Chain B: R.201, D.238, G.239 Ligand excluded by PLIP CL.15: 1 residues within 4Å: Chain B: R.101 Ligand excluded by PLIP CL.16: 3 residues within 4Å: Chain B: I.100, R.101, H.105 Ligand excluded by PLIP CL.17: 2 residues within 4Å: Chain B: T.31, Q.32 Ligand excluded by PLIP CL.18: 5 residues within 4Å: Chain B: H.34, N.38, Y.117, F.132, S.133 Ligand excluded by PLIP CL.19: 2 residues within 4Å: Chain B: H.34, N.37 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Pastor, M. et al., Crystal structures of the EVE-HNH endonuclease VcaM4I in the presence and absence of DNA. Nucleic Acids Res. (2021)

Release Date

2020-12-16

Peptides

HNH endonuclease: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

HNH endonuclease

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