SMTL ID : 8h1f.1

Aquifex aeolicus MutL endonuclease domain complexed with zinc ions after soaking

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.22 Å

Oligo State

homo-dimer

Ligands

10 x ZN: ZINC ION(Non-covalent)

ZN.1: 3 residues within 4Å: Chain A: E.61 Ligands: CL.9, CL.10 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:E.61, A:E.61 ZN.2: 1 residues within 4Å: Chain A: D.43 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:D.43, H2O.1, H2O.1, H2O.3, H2O.4 ZN.3: 2 residues within 4Å: Chain A: C.48 Ligands: ZN.5 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:C.48, H2O.4, H2O.4, H2O.5, H2O.5 ZN.4: 5 residues within 4Å: Chain A: L.31, E.34, C.79, H.81 Ligands: ZN.5 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.3 ZN.5: 5 residues within 4Å: Chain A: H.30, E.34, C.48 Ligands: ZN.3, ZN.4 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:E.34, A:C.48, H2O.3, H2O.3, H2O.4 ZN.11: 3 residues within 4Å: Chain B: E.61 Ligands: CL.19, CL.20 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:E.61, B:E.61 ZN.12: 1 residues within 4Å: Chain B: D.43 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:D.43, H2O.5, H2O.6, H2O.8, H2O.9 ZN.13: 2 residues within 4Å: Chain B: C.48 Ligands: ZN.15 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:C.48, H2O.9, H2O.9, H2O.10, H2O.10 ZN.14: 5 residues within 4Å: Chain B: L.31, E.34, C.79, H.81 Ligands: ZN.15 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.8 ZN.15: 5 residues within 4Å: Chain B: H.30, E.34, C.48 Ligands: ZN.13, ZN.14 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:E.34, B:C.48, H2O.8, H2O.8, H2O.9

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

PEG.6: 7 residues within 4Å: Chain A: M.1, Y.25, W.70, R.71, P.76, H.77, Y.86 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:M.1, A:R.71 Water bridges: A:Y.25, A:Y.25 PEG.7: 4 residues within 4Å: Chain A: E.22, Y.23, P.90, R.92 1 PLIP interactions: 1 interactions with chain A Water bridges: A:Y.23 PEG.16: 7 residues within 4Å: Chain B: M.1, Y.25, W.70, R.71, P.76, H.77, Y.86 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:M.1, B:R.71 Water bridges: B:Y.25 PEG.17: 4 residues within 4Å: Chain B: E.22, Y.23, P.90, R.92 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.22 Water bridges: B:Y.23, B:Y.23

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

CL.8: 4 residues within 4Å: Chain A: R.100 Chain B: H.30, K.53, A.54 Ligand excluded by PLIP CL.9: 5 residues within 4Å: Chain A: E.61, R.64, E.65 Ligands: ZN.1, CL.10 Ligand excluded by PLIP CL.10: 4 residues within 4Å: Chain A: E.61, R.64 Ligands: ZN.1, CL.9 Ligand excluded by PLIP CL.18: 4 residues within 4Å: Chain A: H.30, K.53, A.54 Chain B: R.100 Ligand excluded by PLIP CL.19: 5 residues within 4Å: Chain B: E.61, R.64, E.65 Ligands: ZN.11, CL.20 Ligand excluded by PLIP CL.20: 4 residues within 4Å: Chain B: E.61, R.64 Ligands: ZN.11, CL.19 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Fukui, K. et al., Catalytic mechanism of the zinc-dependent MutL endonuclease reaction. Life Sci Alliance (2023)

Release Date

2023-08-16

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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