SMTL ID : 8h1e.1

Aquifex aeolicus MutL endonuclease domain complexed with manganese ions

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.22 Å

Oligo State

homo-dimer

Ligands

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

PEG.1: 7 residues within 4Å: Chain A: M.1, Y.25, W.70, R.71, P.76, H.77, Y.86 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:M.1, A:R.71 Water bridges: A:Y.25 PEG.8: 7 residues within 4Å: Chain B: M.1, Y.25, W.70, R.71, P.76, H.77, Y.86 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:M.1, B:Y.25, B:R.71 Water bridges: B:Y.25

12 x MN: MANGANESE (II) ION(Non-covalent)

MN.2: 5 residues within 4Å: Chain A: L.31, E.34, C.79, H.81 Ligands: MN.3 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.34, A:C.79, A:H.81, H2O.2, H2O.2 MN.3: 5 residues within 4Å: Chain A: H.30, E.34, C.48 Ligands: MN.2, MN.4 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.30, A:E.34, A:C.48, H2O.2, H2O.2 MN.4: 2 residues within 4Å: Chain A: C.48 Ligands: MN.3 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:C.48, H2O.2, H2O.3, H2O.3, H2O.3 MN.5: 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.2, H2O.3 MN.6: 1 residues within 4Å: Chain A: D.43 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.43, A:D.43, H2O.3 MN.7: 2 residues within 4Å: Chain A: E.93, E.96 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:E.93, A:E.96 MN.9: 5 residues within 4Å: Chain B: L.31, E.34, C.79, H.81 Ligands: MN.10 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.34, B:C.79, B:H.81, H2O.5, H2O.5 MN.10: 5 residues within 4Å: Chain B: H.30, E.34, C.48 Ligands: MN.9, MN.11 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:H.30, B:E.34, B:C.48, H2O.5, H2O.5 MN.11: 2 residues within 4Å: Chain B: C.48 Ligands: MN.10 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:C.48, H2O.5, H2O.5, H2O.6, H2O.6 MN.12: 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.5, H2O.5 MN.13: 1 residues within 4Å: Chain B: D.43 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.43, B:D.43, H2O.5 MN.14: 2 residues within 4Å: Chain B: E.93, E.96 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:E.93, B:E.96

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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