SMTL ID : 6uke.1

HhaI endonuclease in Complex with Iodine-Labelled DNA

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.62 Å

Oligo State

monomer

Ligands

1 x CA: CALCIUM ION(Non-covalent)

CA.1: 5 residues within 4Å: Chain A: S.151, C.152, T.153, S.233 Ligands: EDO.15 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:S.151, A:T.153, H2O.2

19 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.2: 3 residues within 4Å: Chain A: T.101 Chain C: T.4, G.5 Ligand excluded by PLIP EDO.3: 4 residues within 4Å: Chain A: M.49, P.50, H.51 Chain B: A.11 Ligand excluded by PLIP EDO.4: 5 residues within 4Å: Chain A: N.149, V.150, S.151, S.233, S.235 Ligand excluded by PLIP EDO.5: 4 residues within 4Å: Chain A: N.149, K.237, N.238, N.239 Ligand excluded by PLIP EDO.6: 5 residues within 4Å: Chain A: H.163, L.164, L.188, H.218, V.219 Ligand excluded by PLIP EDO.7: 7 residues within 4Å: Chain A: A.23, K.24, K.25, S.33, D.34, L.36, Y.44 Ligand excluded by PLIP EDO.8: 3 residues within 4Å: Chain A: P.42, F.43, S.125 Ligand excluded by PLIP EDO.9: 2 residues within 4Å: Chain A: K.250, E.253 Ligand excluded by PLIP EDO.10: 6 residues within 4Å: Chain A: N.20, K.21, F.22, A.23, K.25, T.38 Ligand excluded by PLIP EDO.11: 4 residues within 4Å: Chain A: E.91, N.92, F.93, S.94 Ligand excluded by PLIP EDO.12: 4 residues within 4Å: Chain A: Y.18, K.21, F.37, I.256 Ligand excluded by PLIP EDO.13: 4 residues within 4Å: Chain A: Y.13, D.135, F.136, R.249 Ligand excluded by PLIP EDO.14: 6 residues within 4Å: Chain A: E.7, K.24, D.34, E.46 Chain B: G.8, C.9 Ligand excluded by PLIP EDO.15: 6 residues within 4Å: Chain A: K.102, G.103, K.104, T.153 Chain C: U.3 Ligands: CA.1 Ligand excluded by PLIP EDO.16: 5 residues within 4Å: Chain A: K.158, R.200, F.226 Chain C: G.5, C.6 Ligand excluded by PLIP EDO.19: 4 residues within 4Å: Chain A: W.3 Chain B: G.8, C.9 Chain C: G.7 Ligand excluded by PLIP EDO.20: 5 residues within 4Å: Chain B: A.10, A.11, C.12 Chain C: T.4, G.5 Ligand excluded by PLIP EDO.21: 3 residues within 4Å: Chain A: N.2 Chain B: A.11, C.12 Ligand excluded by PLIP EDO.23: 9 residues within 4Å: Chain A: D.29, S.30, T.31 Chain B: G.6, C.7, G.8 Chain C: G.7, C.8, T.9 Ligand excluded by PLIP

2 x ACT: ACETATE ION(Non-functional Binders)

ACT.17: 4 residues within 4Å: Chain A: F.68, M.86, Q.87, S.90 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:M.86 Hydrogen bonds: A:F.68, A:M.86, A:S.90 Water bridges: A:D.69 ACT.22: 6 residues within 4Å: Chain A: K.73, K.75 Chain B: A.5, G.6 Chain C: U.10, G.11 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:K.75

1 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.18: 3 residues within 4Å: Chain A: E.145, H.146, K.237 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:H.146, A:K.237

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Horton, J.R. et al., Structure of HhaI endonuclease with cognate DNA at an atomic resolution of 1.0 angstrom. Nucleic Acids Res. (2020)

Release Date

2019-12-18

Peptides

HhaI Restriction Endonuclease: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
X

HhaI Restriction Endonuclease

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