SMTL ID : 6ykf.1

VcaM4I restriction endonuclease in the presence of 5mC-modified ssDNA

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.48 Å

Oligo State

monomer

Ligands

1 x DC- DA- 5CM- DA- DG: DNA (5'-D(*CP*AP*(5CM)P*AP*G)-3')(Non-covalent)

DC-DA-5CM-DA-DG.1: 24 residues within 4Å: Chain A: S.7, Q.8, K.9, Q.10, T.11, E.15, W.22, N.27, K.28, Y.36, F.51, G.54, F.75, W.82, N.125, G.126, N.127, Q.128, A.129, Y.130 Ligands: SO4.4, GOL.8, GOL.22, SO4.23 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:W.82, A:Y.130, A:Y.130 Hydrogen bonds: A:Q.10, A:T.11, A:T.11, A:E.15, A:W.82, A:A.129 pi-Stacking: A:W.82

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

SO4.2: 4 residues within 4Å: Chain A: P.44, R.63, S.64, H.65 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:H.65 Water bridges: A:H.65 Salt bridges: A:H.65 SO4.3: 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:N.2, A:H.136, A:E.137 Salt bridges: A:H.136 SO4.4: 6 residues within 4Å: Chain A: N.27, Q.32, S.33, H.34, Y.35 Ligands: DC-DA-5CM-DA-DG.1 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.27, A:S.33, A:H.34, A:Y.35 SO4.5: 2 residues within 4Å: Chain A: H.34, N.37 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.37 Water bridges: A:Y.117 Salt bridges: A:H.34 SO4.6: 2 residues within 4Å: Chain A: K.25, W.87 2 PLIP interactions: 2 interactions with chain A Water bridges: A:K.25 Salt bridges: A:K.25 SO4.7: 2 residues within 4Å: Chain A: T.73, N.84 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.84 SO4.18: 3 residues within 4Å: Chain A: S.291, K.292, Q.293 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.292, A:Q.293, A:Q.293 SO4.19: 2 residues within 4Å: Chain A: N.232, N.233 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:N.233 Water bridges: A:S.231, A:N.233, A:N.233, A:N.233, A:N.233, A:Q.234, A:R.236 SO4.20: 3 residues within 4Å: Chain A: E.184, R.201, L.237 5 PLIP interactions: 5 interactions with chain A Water bridges: A:E.184, A:R.201, A:R.201, A:Q.234 Salt bridges: A:R.201 SO4.21: 4 residues within 4Å: Chain A: I.163, T.164, A.167, R.192 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:I.163 Water bridges: A:T.164, A:T.164, A:R.192, A:R.192, A:R.193, A:R.193 Salt bridges: A:R.192 SO4.23: 3 residues within 4Å: Ligands: DC-DA-5CM-DA-DG.1, DC-DA-5CM-DA-DG.1, GOL.22 No protein-ligand interaction detected (PLIP)

10 x GOL: GLYCEROL(Non-functional Binders)

GOL.8: 7 residues within 4Å: Chain A: A.78, G.79, A.80, D.81, W.82 Ligands: DC-DA-5CM-DA-DG.1, GOL.22 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:D.81 Water bridges: A:A.80, A:D.81, A:D.81, A:D.81, A:D.81 GOL.9: 2 residues within 4Å: Chain A: F.16, E.17 1 PLIP interactions: 1 interactions with chain A Water bridges: A:E.17 GOL.10: 2 residues within 4Å: Chain A: Y.69, N.70 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.70 Water bridges: A:S.68, A:Y.69, A:N.70 GOL.11: 5 residues within 4Å: Chain A: K.9, Q.10, N.53, A.78 Ligands: GOL.12 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.53, A:N.53 Water bridges: A:Q.10 GOL.12: 6 residues within 4Å: Chain A: Q.10, T.11, F.12, K.13, Q.14 Ligands: GOL.11 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:K.13, A:K.13, A:Q.14, A:Q.14 Water bridges: A:F.12 GOL.13: 3 residues within 4Å: Chain A: K.103, A.104, I.106 No protein-ligand interaction detected (PLIP) GOL.14: 6 residues within 4Å: Chain A: S.148, E.151, E.152, F.155, K.271, N.273 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.273 Water bridges: A:E.151 GOL.15: 2 residues within 4Å: Chain A: E.97, N.98 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.98 Water bridges: A:E.97, A:K.99 GOL.17: 5 residues within 4Å: Chain A: G.156, F.157, T.160, H.251, K.255 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.156, A:T.160, A:K.255 GOL.22: 7 residues within 4Å: Chain A: Q.10, Q.128 Ligands: DC-DA-5CM-DA-DG.1, DC-DA-5CM-DA-DG.1, DC-DA-5CM-DA-DG.1, GOL.8, SO4.23 1 PLIP interactions: 1 interactions with chain A Water bridges: A:Q.10

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

CL.16: 2 residues within 4Å: Chain A: Y.67, S.68 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

2020-12-23

Peptides

HNH endonuclease: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

HNH endonuclease

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