SMTL ID : 1asq.2 (1 other biounit)

X-RAY STRUCTURES AND MECHANISTIC IMPLICATIONS OF THREE FUNCTIONAL DERIVATIVES OF ASCORBATE OXIDASE FROM ZUCCHINI: REDUCED-, PEROXIDE-, AND AZIDE-FORMS

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.32 Å

Oligo State

homo-tetramer

Ligands

4 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.1: 4 residues within 4Å: Chain A: W.71, F.90, N.92, P.532 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:W.71, A:P.532 Hydrogen bonds: A:N.92 NAG.10: 5 residues within 4Å: Chain B: V.45, W.71, F.90, N.92, P.532 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:W.71, B:P.532 Hydrogen bonds: B:N.92 NAG.18: 4 residues within 4Å: Chain C: W.71, F.90, N.92, P.532 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:W.71, C:P.532 Hydrogen bonds: C:N.92 NAG.27: 5 residues within 4Å: Chain D: V.45, W.71, F.90, N.92, P.532 3 PLIP interactions: 3 interactions with chain D Hydrophobic interactions: D:W.71, D:P.532 Hydrogen bonds: D:N.92

18 x CU: COPPER (II) ION(Non-covalent)

CU.2: 4 residues within 4Å: Chain A: H.445, C.507, H.512, M.517 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.445, A:C.507, A:H.512 CU.3: 5 residues within 4Å: Chain A: H.106, H.450, H.506 Ligands: AZI.7, AZI.8 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.106, A:H.450, A:H.506 CU.4: 6 residues within 4Å: Chain A: H.60, H.62, H.104, H.508 Ligands: CU.5, AZI.8 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.62, A:H.104, A:H.508 CU.5: 6 residues within 4Å: Chain A: H.60, H.62, H.448, H.450 Ligands: CU.4, OH.6 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Ligand interactions Metal complexes: A:H.60, A:H.448, OH.6 CU.9: 2 residues within 4Å: Chain A: H.286 Chain B: H.286 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Metal complexes: A:H.286, B:H.286 CU.11: 4 residues within 4Å: Chain B: H.445, C.507, H.512, M.517 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:H.445, B:C.507, B:H.512 CU.12: 5 residues within 4Å: Chain B: H.106, H.450, H.506 Ligands: AZI.16, AZI.17 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:H.106, B:H.450, B:H.506 CU.13: 6 residues within 4Å: Chain B: H.62, H.104, H.448, H.508 Ligands: CU.14, AZI.17 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:H.62, B:H.104, B:H.508 CU.14: 7 residues within 4Å: Chain B: H.60, H.62, H.448, H.450 Ligands: CU.13, OH.15, AZI.17 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Ligand interactions Metal complexes: B:H.60, B:H.448, OH.15 CU.19: 4 residues within 4Å: Chain C: H.445, C.507, H.512, M.517 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:H.445, C:C.507, C:H.512 CU.20: 5 residues within 4Å: Chain C: H.106, H.450, H.506 Ligands: AZI.24, AZI.25 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:H.106, C:H.450, C:H.506 CU.21: 6 residues within 4Å: Chain C: H.60, H.62, H.104, H.508 Ligands: CU.22, AZI.25 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:H.62, C:H.104, C:H.508 CU.22: 6 residues within 4Å: Chain C: H.60, H.62, H.448, H.450 Ligands: CU.21, OH.23 3 PLIP interactions: 2 interactions with chain C, 1 Ligand-Ligand interactions Metal complexes: C:H.60, C:H.448, OH.23 CU.26: 2 residues within 4Å: Chain C: H.286 Chain D: H.286 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain C Metal complexes: D:H.286, C:H.286 CU.28: 4 residues within 4Å: Chain D: H.445, C.507, H.512, M.517 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:H.445, D:C.507, D:H.512 CU.29: 5 residues within 4Å: Chain D: H.106, H.450, H.506 Ligands: AZI.33, AZI.34 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:H.106, D:H.450, D:H.506 CU.30: 6 residues within 4Å: Chain D: H.62, H.104, H.448, H.508 Ligands: CU.31, AZI.34 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:H.62, D:H.104, D:H.508 CU.31: 7 residues within 4Å: Chain D: H.60, H.62, H.448, H.450 Ligands: CU.30, OH.32, AZI.34 3 PLIP interactions: 2 interactions with chain D, 1 Ligand-Ligand interactions Metal complexes: D:H.60, D:H.448, OH.32

4 x OH: HYDROXIDE ION(Non-covalent)

OH.6: 6 residues within 4Å: Chain A: H.60, W.61, H.62, G.63, H.448 Ligands: CU.5 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.63 Water bridges: A:D.73, A:G.451, A:G.451 OH.15: 5 residues within 4Å: Chain B: H.60, H.62, G.63, H.448 Ligands: CU.14 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:G.63, B:L.449 Water bridges: B:G.451, B:G.451 OH.23: 6 residues within 4Å: Chain C: H.60, W.61, H.62, G.63, H.448 Ligands: CU.22 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:G.63 Water bridges: C:D.73, C:G.451, C:G.451 OH.32: 5 residues within 4Å: Chain D: H.60, H.62, G.63, H.448 Ligands: CU.31 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:G.63, D:L.449 Water bridges: D:G.451, D:G.451

8 x AZI: AZIDE ION(Non-covalent)

AZI.7: 8 residues within 4Å: Chain A: T.75, I.78, H.106, H.450, A.504, H.506, L.513 Ligands: CU.3 No protein-ligand interaction detected (PLIP) AZI.8: 9 residues within 4Å: Chain A: H.104, H.106, R.111, H.448, H.450, H.506, H.508 Ligands: CU.3, CU.4 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.510 Water bridges: A:R.111, A:R.111 AZI.16: 7 residues within 4Å: Chain B: T.75, I.78, H.106, H.450, A.504, H.506 Ligands: CU.12 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:H.506, B:H.506 Water bridges: B:A.504, B:A.504, B:V.519 AZI.17: 11 residues within 4Å: Chain B: H.104, H.106, R.111, H.448, H.450, H.506, H.508, L.513 Ligands: CU.12, CU.13, CU.14 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:H.104, B:H.506, B:H.506 Water bridges: B:R.111, B:R.111 AZI.24: 8 residues within 4Å: Chain C: T.75, I.78, H.106, H.450, A.504, H.506, L.513 Ligands: CU.20 No protein-ligand interaction detected (PLIP) AZI.25: 9 residues within 4Å: Chain C: H.104, H.106, R.111, H.448, H.450, H.506, H.508 Ligands: CU.20, CU.21 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:E.510 Water bridges: C:R.111, C:R.111 AZI.33: 7 residues within 4Å: Chain D: T.75, I.78, H.106, H.450, A.504, H.506 Ligands: CU.29 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:H.506, D:H.506 Water bridges: D:A.504, D:A.504, D:V.519 AZI.34: 11 residues within 4Å: Chain D: H.104, H.106, R.111, H.448, H.450, H.506, H.508, L.513 Ligands: CU.29, CU.30, CU.31 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:H.104, D:H.506, D:H.506 Water bridges: D:R.111, D:R.111

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Messerschmidt, A. et al., X-ray structures and mechanistic implications of three functional derivatives of ascorbate oxidase from zucchini. Reduced, peroxide and azide forms. J.Mol.Biol. (1993)

Release Date

1994-01-31

Peptides

ASCORBATE OXIDASE: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

ASCORBATE OXIDASE

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