SMTL ID : 6fk5.1

Structure of 3' phosphatase NExo (D146N) from Neisseria bound to DNA substrate in presence of magnesium ion

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.02 Å

Oligo State

monomer

Ligands

2 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 5 residues within 4Å: Chain A: N.11, E.36, D.248 Chain B: G.17, A.18 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.36, H2O.4, H2O.6 MG.2: 2 residues within 4Å: Chain A: D.155, H.165 No protein-ligand interaction detected (PLIP)

1 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.3: 3 residues within 4Å: Chain A: H.55, C.56, V.57 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:H.55, A:V.57 Water bridges: A:C.56, A:C.56

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Silhan, J. et al., Structural basis for recognition and repair of the 3'-phosphate by NExo, a base excision DNA repair nuclease from Neisseria meningitidis. Nucleic Acids Res. (2018)

Release Date

2018-10-31

Peptides

NExo D146N: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

NExo D146N

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