SMTL ID : 5bke.1

Crystal structure of AAD-2 in complex with Mn(II) and N-oxalylglycine

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.15 Å

Oligo State

homo-heptamer

Ligands

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

MN.1: 5 residues within 4Å: Chain A: H.115, D.117, H.264, R.279 Ligands: OGA.2 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.115, A:D.117, A:H.264, H2O.3 MN.4: 5 residues within 4Å: Chain B: H.115, D.117, H.264, R.279 Ligands: OGA.5 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.115, B:D.117, B:H.264, H2O.14 MN.7: 5 residues within 4Å: Chain C: H.115, D.117, H.264, R.279 Ligands: OGA.8 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:H.115, C:D.117, C:H.264 MN.9: 5 residues within 4Å: Chain D: H.115, D.117, H.264, R.279 Ligands: OGA.10 4 PLIP interactions: 3 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:H.115, D:D.117, D:H.264, H2O.32 MN.12: 5 residues within 4Å: Chain E: H.115, D.117, H.264, R.279 Ligands: OGA.13 4 PLIP interactions: 3 interactions with chain E, 1 Ligand-Water interactions Metal complexes: E:H.115, E:D.117, E:H.264, H2O.37 MN.15: 6 residues within 4Å: Chain F: N.111, H.115, D.117, H.264, R.279 Ligands: OGA.16 4 PLIP interactions: 3 interactions with chain F, 1 Ligand-Water interactions Metal complexes: F:H.115, F:D.117, F:H.264, H2O.42 MN.18: 6 residues within 4Å: Chain G: N.111, H.115, D.117, H.264, R.279 Ligands: OGA.19 4 PLIP interactions: 3 interactions with chain G, 1 Ligand-Water interactions Metal complexes: G:H.115, G:D.117, G:H.264, H2O.55

7 x OGA: N-OXALYLGLYCINE(Non-covalent)

OGA.2: 12 residues within 4Å: Chain A: V.88, N.111, H.115, D.117, L.130, T.142, W.257, H.264, V.266, R.275, R.279 Ligands: MN.1 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:N.111, A:T.142 Water bridges: A:V.88, A:R.275, A:R.279 Salt bridges: A:H.264, A:R.275, A:R.279 OGA.5: 12 residues within 4Å: Chain B: V.88, N.111, H.115, D.117, L.130, T.142, W.257, H.264, V.266, R.275, R.279 Ligands: MN.4 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:N.111 Water bridges: B:V.88, B:R.275, B:R.279 Salt bridges: B:H.264, B:R.275, B:R.279 OGA.8: 12 residues within 4Å: Chain C: V.88, N.111, H.115, D.117, L.130, T.142, W.257, H.264, V.266, R.275, R.279 Ligands: MN.7 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:V.88 Water bridges: C:R.275 Salt bridges: C:H.264, C:R.275, C:R.279 OGA.10: 12 residues within 4Å: Chain D: V.88, N.111, H.115, D.117, L.130, T.142, W.257, H.264, V.266, R.275, R.279 Ligands: MN.9 8 PLIP interactions: 8 interactions with chain D Hydrogen bonds: D:T.142 Water bridges: D:N.111, D:R.275, D:R.279, D:R.279 Salt bridges: D:H.264, D:R.275, D:R.279 OGA.13: 12 residues within 4Å: Chain E: V.88, N.111, H.115, D.117, L.130, T.142, W.257, H.264, V.266, R.275, R.279 Ligands: MN.12 7 PLIP interactions: 7 interactions with chain E Hydrogen bonds: E:V.88 Water bridges: E:N.111, E:N.111, E:N.111 Salt bridges: E:H.264, E:R.275, E:R.279 OGA.16: 11 residues within 4Å: Chain F: N.111, H.115, D.117, L.130, T.142, W.257, H.264, V.266, R.275, R.279 Ligands: MN.15 5 PLIP interactions: 5 interactions with chain F Water bridges: F:N.111, F:N.111 Salt bridges: F:H.264, F:R.275, F:R.279 OGA.19: 11 residues within 4Å: Chain G: N.111, H.115, D.117, L.130, T.142, W.257, H.264, V.266, R.275, R.279 Ligands: MN.18 7 PLIP interactions: 7 interactions with chain G Hydrogen bonds: G:T.142 Water bridges: G:N.111, G:N.111, G:N.111 Salt bridges: G:H.264, G:R.275, G:R.279

6 x K: POTASSIUM ION(Non-covalent)

K.3: 4 residues within 4Å: Chain A: D.117, S.118, F.120, H.215 No protein-ligand interaction detected (PLIP) K.6: 4 residues within 4Å: Chain B: D.117, S.118, F.120, H.215 No protein-ligand interaction detected (PLIP) K.11: 3 residues within 4Å: Chain D: D.117, S.118, H.215 No protein-ligand interaction detected (PLIP) K.14: 2 residues within 4Å: Chain E: D.117, S.118 No protein-ligand interaction detected (PLIP) K.17: 4 residues within 4Å: Chain F: D.117, S.118, F.120, H.215 No protein-ligand interaction detected (PLIP) K.20: 4 residues within 4Å: Chain G: D.117, S.118, F.120, H.215 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chekan, J.R. et al., Molecular basis for enantioselective herbicide degradation imparted by aryloxyalkanoate dioxygenases in transgenic plants. Proc.Natl.Acad.Sci.USA (2019)

Release Date

2019-06-12

Peptides

Alpha-ketoglutarate-dependent 2,4-dichlorophenoxyacetate dioxygenase: ABCDEFG

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

Alpha-ketoglutarate-dependent 2,4-dichlorophenoxyacetate dioxygenase