SMTL ID : 6ufq.1

Crystal structure of D678N GoxA bound to glycine

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.51 Å

Oligo State

homo-tetramer

Ligands

4 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 5 residues within 4Å: Chain A: D.360, A.362, I.365, A.699, N.700 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.360, A:A.362, A:I.365, A:A.699, H2O.1 MG.3: 5 residues within 4Å: Chain B: D.360, A.362, I.365, A.699, N.700 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:D.360, B:D.360, B:A.362, B:I.365, B:A.699 MG.5: 6 residues within 4Å: Chain C: D.360, A.362, P.363, I.365, A.699, N.700 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:D.360, C:A.362, C:I.365, C:A.699 MG.7: 6 residues within 4Å: Chain D: D.360, A.362, P.363, I.365, A.699, N.700 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:D.360, D:A.362, D:I.365, D:A.699

4 x GLY: GLYCINE(Non-covalent)

GLY.2: 10 residues within 4Å: Chain A: Y.766, H.767 Chain B: F.316, H.583, P.584, N.678, S.681, C.682, W.696, W.697 6 PLIP interactions: 2 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:Y.766, B:H.583, B:H.583, B:S.681 Salt bridges: A:H.767, B:H.583 GLY.4: 10 residues within 4Å: Chain A: F.316, H.583, P.584, S.681, C.682, W.696, W.697, Y.772 Chain B: Y.766, H.767 7 PLIP interactions: 2 interactions with chain B, 4 interactions with chain A, 1 Ligand-Ligand interactions Hydrogen bonds: B:Y.766, A:H.583, A:H.583, A:Y.772, G.4 Salt bridges: B:H.767, A:H.583 GLY.6: 11 residues within 4Å: Chain C: F.316, H.583, P.584, N.678, S.681, C.682, W.696, W.697, Y.772 Chain D: Y.766, H.767 7 PLIP interactions: 2 Ligand-Ligand interactions, 4 interactions with chain C, 1 interactions with chain D Hydrogen bonds: G.6, G.6, C:H.583, C:H.583, C:S.681 Salt bridges: C:H.583, D:H.767 GLY.8: 9 residues within 4Å: Chain C: Y.766, H.767 Chain D: F.316, H.583, N.678, S.681, C.682, W.696, W.697 4 PLIP interactions: 3 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:H.583, D:W.696 Salt bridges: D:H.583, C:H.767

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mamounis, K.J. et al., Kinetic and structural evidence that Asp-678 plays multiple roles in catalysis by the quinoprotein glycine oxidase. J.Biol.Chem. (2019)

Release Date

2019-10-23

Peptides

Glycine Oxidase GoxA: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Glycine Oxidase GoxA