SMTL ID : 5z42.1

Aquifex aeolicus MutL endonuclease domain with three zinc ions.

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.30 Å

Oligo State

homo-dimer

Ligands

10 x ZN: ZINC ION(Non-covalent)

ZN.1: 5 residues within 4Å: Chain A: H.30, E.34, C.48 Ligands: ZN.2, ZN.3 6 PLIP interactions: 3 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:H.30, A:E.34, A:C.48, H2O.3, H2O.4, H2O.4 ZN.2: 5 residues within 4Å: Chain A: L.31, E.34, C.79, H.81 Ligands: ZN.1 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.34, A:C.79, A:H.81, H2O.3, H2O.4 ZN.3: 2 residues within 4Å: Chain A: C.48 Ligands: ZN.1 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:C.48, H2O.4, H2O.5, H2O.5, H2O.5 ZN.4: 2 residues within 4Å: Chain A: E.93, E.96 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:E.93, A:E.96, H2O.1, H2O.4, H2O.4 ZN.8: 1 residues within 4Å: Chain A: E.61 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.61, A:E.61, H2O.4, H2O.4 ZN.11: 5 residues within 4Å: Chain B: H.30, E.34, C.48 Ligands: ZN.12, ZN.13 6 PLIP interactions: 3 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:H.30, B:E.34, B:C.48, H2O.8, H2O.8, H2O.9 ZN.12: 5 residues within 4Å: Chain B: L.31, E.34, C.79, H.81 Ligands: ZN.11 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.34, B:C.79, B:H.81, H2O.8, H2O.9 ZN.13: 2 residues within 4Å: Chain B: C.48 Ligands: ZN.11 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:C.48, H2O.9, H2O.10, H2O.10, H2O.10 ZN.14: 2 residues within 4Å: Chain B: E.93, E.96 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:E.93, B:E.96, H2O.6, H2O.9, H2O.9 ZN.18: 1 residues within 4Å: Chain B: E.61 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.61, B:E.61, H2O.9, H2O.9

4 x NA: SODIUM ION(Non-functional Binders)

NA.5: 3 residues within 4Å: Chain A: K.2, P.3, T.4 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.4, A:T.4, A:T.4 NA.6: 1 residues within 4Å: Chain B: E.6 2 PLIP interactions: 2 interactions with chain A Water bridges: A:D.12, A:D.12 NA.15: 3 residues within 4Å: Chain B: K.2, P.3, T.4 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:T.4, B:T.4 Water bridges: B:T.4 NA.16: 1 residues within 4Å: Chain A: E.6 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Water bridges: B:D.12 Hydrogen bonds: A:E.6, A:E.6

2 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.7: 4 residues within 4Å: Chain A: M.1, W.70, R.71, P.76 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:M.1 PEG.17: 4 residues within 4Å: Chain B: M.1, W.70, R.71, P.76 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:M.1

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

CL.9: 4 residues within 4Å: Chain A: H.30, K.53, A.54 Chain B: R.100 Ligand excluded by PLIP CL.19: 4 residues within 4Å: Chain A: R.100 Chain B: H.30, K.53, A.54 Ligand excluded by PLIP

2 x MG: MAGNESIUM ION(Non-covalent)

MG.10: 1 residues within 4Å: Chain A: D.43 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.43, A:D.43, H2O.4, H2O.4 MG.20: 1 residues within 4Å: Chain B: D.43 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.43, B:D.43, H2O.9, H2O.9

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Fukui, K. et al., Multiple zinc ions maintain the open conformation of the catalytic site in the DNA mismatch repair endonuclease MutL from Aquifex aeolicus. FEBS Lett. (2018)

Release Date

2018-04-25

Peptides

DNA mismatch repair protein MutL: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

DNA mismatch repair protein MutL

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