SMTL ID : 5mej.1

Structural study of the X-ray induced enzymatic reduction of molecular oxygen to water for laccase from Steccherinum murashkinskyi. First structure of the series with 3 min total X-ray exposition time.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.50 Å

Oligo State

monomer

Ligands

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

NAG-NAG-BMA.1: 7 residues within 4Å: Chain A: R.323, G.324, V.331, E.385, A.387, P.389, N.436 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.2: 6 residues within 4Å: Chain A: V.305, T.307, N.414, T.416, P.417, N.418 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:T.416 Water bridges: A:N.421

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

CU.3: 9 residues within 4Å: Chain A: H.65, H.110, H.112, H.400, H.402, H.452 Ligands: CU.4, CU.5, OXY.7 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.112, A:H.402, A:H.452, H2O.1, H2O.1 CU.4: 8 residues within 4Å: Chain A: H.65, H.67, H.110, H.400, H.454 Ligands: CU.3, CU.5, OXY.7 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.67, A:H.110, A:H.454, H2O.1, H2O.1 CU.5: 8 residues within 4Å: Chain A: H.65, H.67, G.68, H.400, H.402 Ligands: CU.3, CU.4, OXY.7 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.65, A:H.400, H2O.1, H2O.17 CU.6: 6 residues within 4Å: Chain A: H.397, P.398, C.453, I.455, H.458, F.463 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.397, A:C.453, A:H.458

2 x OXY: OXYGEN MOLECULE(Non-covalent)

OXY.7: 11 residues within 4Å: Chain A: H.65, H.110, H.112, H.400, H.402, H.452, H.454 Ligands: CU.3, CU.4, CU.5, OXY.8 1 PLIP interactions: 1 interactions with chain A Water bridges: A:H.452 OXY.8: 8 residues within 4Å: Chain A: H.110, S.111, H.112, Y.117, H.452, D.456, L.459 Ligands: OXY.7 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:H.110 Water bridges: A:H.112, A:H.452

1 x CIT: CITRIC ACID(Non-functional Binders)

CIT.9: 3 residues within 4Å: Chain A: T.293, T.294, T.295 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.293, A:T.293, A:T.293, A:T.295

1 x NA: SODIUM ION(Non-functional Binders)

NA.10: 2 residues within 4Å: Chain A: V.317, P.318 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:V.317 Water bridges: A:V.317, A:V.317, A:P.318, A:G.319, A:G.319

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Polyakov, K.M. et al., Structural study of the X-ray-induced enzymatic reduction of molecular oxygen to water by Steccherinum murashkinskyi laccase: insights into the reaction mechanism. Acta Crystallogr D Struct Biol (2017)

Release Date

2017-05-10

Peptides

Laccase 2: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Laccase 2

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