SMTL ID : 3w2y.1 (1 other biounit)

Crystal structure of DNA uridine endonuclease Mth212 mutant W205S

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

monomer

Ligands

1 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 2 residues within 4Å: Chain A: N.15, E.41 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:E.41, H2O.1, H2O.3, H2O.5, H2O.8

9 x FMT: FORMIC ACID(Non-functional Binders)

FMT.2: 3 residues within 4Å: Chain A: R.86, G.88, F.89 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.86, A:G.88 FMT.3: 3 residues within 4Å: Chain A: N.140, K.186, N.190 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.140, A:K.186 Water bridges: A:E.137 FMT.4: 3 residues within 4Å: Chain A: P.46, F.62, F.63 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:F.63 Water bridges: A:S.61 FMT.5: 2 residues within 4Å: Chain A: E.161, R.181 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.181, A:R.181 Water bridges: A:E.161 FMT.6: 3 residues within 4Å: Chain A: R.239, W.241 Ligands: PEG.7 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.239, A:R.239 FMT.9: 5 residues within 4Å: Chain A: K.23, Y.211, M.247, G.248, S.249 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:K.23, A:K.23, A:G.248, A:S.249 Water bridges: A:R.216 FMT.11: 5 residues within 4Å: Chain A: E.41, K.43, Y.71, S.72, Y.114 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:K.43, A:S.72, A:Y.114, A:Y.114 Water bridges: A:R.99 FMT.12: 5 residues within 4Å: Chain A: R.166, N.170, R.212, V.220, W.222 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.166, A:N.170, A:R.212 FMT.13: 3 residues within 4Å: Chain A: H.159, R.160, I.188 4 PLIP interactions: 4 interactions with chain A Water bridges: A:H.159, A:R.160, A:R.160, A:D.194

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

PEG.7: 4 residues within 4Å: Chain A: F.199, N.200, D.202 Ligands: FMT.6 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.202 Water bridges: A:N.200 PEG.8: 7 residues within 4Å: Chain A: N.117, K.119, N.156, S.174, G.175, S.208, W.222 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.156, A:S.208, A:S.208 Water bridges: A:K.119 PEG.10: 5 residues within 4Å: Chain A: R.197, M.198, F.199, N.200, S.201 2 PLIP interactions: 2 interactions with chain A Water bridges: A:M.198, A:S.201

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tabata, N. et al., Crystal structure of DNA uridine endonuclease Mth212. To be Published

Release Date

2013-12-11

Peptides

Exodeoxyribonuclease: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Exodeoxyribonuclease

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