SMTL ID : 5lww.1

Crystal structure of a laccase-like multicopper oxidase McoG from Aspergillus niger bound to zinc

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.65 Å

Oligo State

monomer

Ligands

1 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.1: 8 residues within 4Å: Chain A: N.33, L.46, M.73, E.74, N.75, N.76, Y.535 Ligands: NAG.5 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.75

1 x NAG- BMA: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Non-covalent)

NAG-BMA.2: 7 residues within 4Å: Chain A: E.134, T.166, D.168, E.169, P.545 Ligands: NAG.5, MAN.6 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.169

1 x NAG- NAG- BMA- MAN: alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN.3: 10 residues within 4Å: Chain A: T.56, E.58, L.141, D.153, L.154, G.155, M.156, V.157, N.189, F.206 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.56 Water bridges: A:E.58, A:D.153

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

NAG.4: 4 residues within 4Å: Chain A: N.373, R.540, L.542, Y.546 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.373 NAG.5: 9 residues within 4Å: Chain A: N.75, N.76, S.129, D.168, W.376, Y.535, E.547 Ligands: NAG-NAG.1, NAG-BMA.2 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:W.376 Hydrogen bonds: A:N.76, A:D.168 Water bridges: A:N.33

1 x MAN: alpha-D-mannopyranose(Non-covalent)

MAN.6: 3 residues within 4Å: Chain A: Q.172, A.543 Ligands: NAG-BMA.2 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:A.543

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

CU.7: 3 residues within 4Å: Chain A: H.83, H.125, H.490 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.83, A:H.125, A:H.490, H2O.7 CU.8: 5 residues within 4Å: Chain A: H.127, H.424, H.426, H.488 Ligands: CU.9 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.127, A:H.426, A:H.488, H2O.7 CU.9: 5 residues within 4Å: Chain A: H.81, H.83, H.424, H.426 Ligands: CU.8 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.81, A:H.424, H2O.6 CU.10: 5 residues within 4Å: Chain A: H.421, C.489, I.491, H.494, F.499 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.421, A:C.489, A:H.494

8 x ZN: ZINC ION(Non-covalent)

ZN.11: 3 residues within 4Å: Chain A: H.226, H.494 Ligands: CL.20 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.226, A:H.494, H2O.8 ZN.12: 2 residues within 4Å: Chain A: D.339, H.450 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.339, A:H.450, H2O.1, H2O.8 ZN.13: 1 residues within 4Å: Chain A: D.341 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.341, A:D.341 ZN.14: 2 residues within 4Å: Chain A: H.143, D.153 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.143, H2O.8, H2O.9 ZN.15: 5 residues within 4Å: Chain A: E.209, H.301, E.303, A.305, D.307 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.301, A:D.307, H2O.4 ZN.16: 2 residues within 4Å: Chain A: D.387, D.389 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.387, A:D.389 ZN.17: 2 residues within 4Å: Chain A: E.528 Ligands: ACT.21 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:E.528 ZN.18: 1 residues within 4Å: Chain A: E.303 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:E.303

1 x K: POTASSIUM ION(Non-covalent)

K.19: 1 residues within 4Å: Chain A: D.527 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.527, A:D.527, H2O.4

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.20: 2 residues within 4Å: Chain A: P.180 Ligands: ZN.11 Ligand excluded by PLIP

1 x ACT: ACETATE ION(Non-functional Binders)

ACT.21: 4 residues within 4Å: Chain A: D.524, D.527, E.528 Ligands: ZN.17 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:K.531

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.22: 2 residues within 4Å: Chain A: H.537, Y.539 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:P.534

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ferraroni, M. et al., Structure and function of Aspergillus niger laccase McoG. Biocatalysis (2017)

Release Date

2017-05-03

Peptides

Multicopper oxidase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Multicopper oxidase