SMTL ID : 4wrk.2 (1 other biounit)

The 3D structure of D95N mutant DUTPase from phage phi11 of S. aureus reveals the molecular details for the coordination of a structural Mg(II) ion

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.90 Å

Oligo State

homo-trimer

Ligands

3 x DUP: 2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE(Non-covalent)

DUP.1: 14 residues within 4Å: Chain A: R.64, S.65, G.66, Q.136 Chain B: G.78, K.79, I.80, D.81, Y.84, L.88, G.89, N.91 Chain C: F.164 Ligands: MG.3 16 PLIP interactions: 8 interactions with chain B, 8 interactions with chain A Hydrophobic interactions: B:I.80, B:Y.84 Hydrogen bonds: B:K.79, B:D.81, B:G.89, B:G.89, A:R.64, A:R.64, A:S.65, A:S.65, A:S.65, A:G.66, A:Q.136 Water bridges: B:K.79, B:N.91 Salt bridges: A:R.64 DUP.2: 14 residues within 4Å: Chain A: G.78, K.79, I.80, D.81, Y.84, L.88, G.89, N.91 Chain B: F.164 Chain C: R.64, S.65, G.66, Q.136 Ligands: MG.6 12 PLIP interactions: 5 interactions with chain A, 7 interactions with chain C Hydrophobic interactions: A:I.80 Hydrogen bonds: A:K.79, A:D.81, A:G.89, A:G.89, C:R.64, C:R.64, C:S.65, C:S.65, C:S.65, C:G.66, C:Q.136 DUP.5: 13 residues within 4Å: Chain B: R.64, S.65, G.66, Q.136 Chain C: G.78, K.79, I.80, D.81, Y.84, L.88, G.89, N.91 Ligands: MG.4 14 PLIP interactions: 6 interactions with chain B, 8 interactions with chain C Hydrogen bonds: B:R.64, B:S.65, B:S.65, B:S.65, B:G.66, C:K.79, C:D.81, C:D.81, C:G.89, C:G.89 Salt bridges: B:R.64 Hydrophobic interactions: C:I.80, C:Y.84 Water bridges: C:N.91

3 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 3 residues within 4Å: Chain A: D.28, Q.136 Ligands: DUP.1 No protein-ligand interaction detected (PLIP) MG.4: 2 residues within 4Å: Chain B: D.28 Ligands: DUP.5 No protein-ligand interaction detected (PLIP) MG.6: 2 residues within 4Å: Chain C: D.28 Ligands: DUP.2 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bendes, A.A. et al., The 3D structure of D95N mutant DUTPase from phage phi11 of S. aureus reveals the molecular details for the coordination of a structural Mg(II) ion. To Be Published

Release Date

2015-12-23

Peptides

DUTPase: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
D

B
E

C
F

DUTPase

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