SMTL ID : 6ymg.1

VcaM4I restriction endonuclease in complex with 5mC-modified dsDNA

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.14 Å

Oligo State

homo-dimer

Ligands

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

CL.1: 2 residues within 4Å: Chain A: K.292, Q.293 Ligand excluded by PLIP

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

SO4.2: 4 residues within 4Å: Chain A: R.63, S.64, H.65 Chain B: H.186 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:H.65 Salt bridges: A:H.65, B:H.186 SO4.3: 3 residues within 4Å: Chain A: I.163, T.164, R.192 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.192 SO4.4: 3 residues within 4Å: Chain A: A.83, N.84, D.85 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.84, A:D.85 SO4.5: 2 residues within 4Å: Chain A: P.135, H.136 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.136 Salt bridges: A:H.136 SO4.6: 3 residues within 4Å: Chain A: H.34, N.37, Y.117 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.37, A:Y.117 Salt bridges: A:H.34 SO4.7: 4 residues within 4Å: Chain A: H.186 Chain B: R.63, S.64, H.65 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:H.65 Salt bridges: B:H.65, A:H.186 SO4.8: 2 residues within 4Å: Chain B: P.135, H.136 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:H.136 Salt bridges: B:H.136 SO4.9: 3 residues within 4Å: Chain B: T.164, A.167, R.192 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.193 Salt bridges: B:R.192 SO4.10: 3 residues within 4Å: Chain B: S.33, H.34, N.37 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.37 Salt bridges: B:H.34

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

2020-12-23

Peptides

HNH endonuclease: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

HNH endonuclease

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