SMTL ID : 6xlr.1

The 1.23 Angstrom crystal structure of galactose oxidase variant with genetically incorporated Cl2-Tyr272

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.23 Å

Oligo State

monomer

Ligands

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

CU.1: 6 residues within 4Å: Chain A: F.228, C.229, X.273, Y.496, H.497, H.582 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:Y.496, A:H.497, A:H.582, H2O.4

1 x CA: CALCIUM ION(Non-covalent)

CA.2: 6 residues within 4Å: Chain A: K.30, D.33, N.35, T.38, A.142, E.143 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:K.30, A:N.35, A:T.38, A:T.38, A:E.143

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

ACT.3: 10 residues within 4Å: Chain A: W.337, R.372, A.379, A.382, T.399, F.400, G.401, N.414, A.415, H.416 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:W.337, A:A.382 Hydrogen bonds: A:T.399, A:H.416 Water bridges: A:P.380 Salt bridges: A:R.372, A:H.416 ACT.4: 7 residues within 4Å: Chain A: L.185, T.205, R.218, V.220, Y.254, D.259, W.261 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:L.185, A:Y.254 Hydrogen bonds: A:W.261 Water bridges: A:T.205, A:R.218, A:Y.254 Salt bridges: A:R.218 ACT.5: 7 residues within 4Å: Chain A: W.341, A.392, V.393, K.394, G.395, L.420, G.421 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:W.341 Hydrogen bonds: A:G.421 Water bridges: A:K.342, A:K.342 Salt bridges: A:K.342 ACT.6: 4 residues within 4Å: Chain A: R.85, T.131, E.132, A.133 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.131 Water bridges: A:R.85 Salt bridges: A:R.85

12 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 6 residues within 4Å: Chain A: V.393, P.592, L.593, T.594, Q.606, P.608 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.594, A:T.594 Water bridges: A:Q.606, A:Q.606 GOL.8: 9 residues within 4Å: Chain A: Q.156, P.157, G.158, L.159, G.160, R.161, N.532, Y.535, G.539 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.158, A:G.160, A:G.160 GOL.9: 4 residues within 4Å: Chain A: V.478, Y.485, Q.487, N.532 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.487, A:N.532 Water bridges: A:D.450, A:N.532 GOL.10: 6 residues within 4Å: Chain A: V.269, F.296, E.297, K.298, N.299, P.314 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.299, A:N.299 Water bridges: A:N.299, A:P.314 GOL.11: 3 residues within 4Å: Chain A: Y.89, R.126, V.128 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.126 GOL.12: 6 residues within 4Å: Chain A: G.163, P.164, R.507, I.528, T.530, Y.535 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:G.163, A:R.507, A:T.530, A:Y.535 Water bridges: A:G.163, A:R.507 GOL.13: 8 residues within 4Å: Chain A: A.2, D.109, T.111, T.112, K.113, N.192, D.193, F.524 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:T.111, A:T.112, A:N.192 Water bridges: A:A.2, A:D.109, A:D.109 GOL.14: 4 residues within 4Å: Chain A: L.159, Y.437, Y.485, K.486 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.486, A:K.486 GOL.15: 2 residues within 4Å: Chain A: Y.359, D.365 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.365 Water bridges: A:Y.359, A:V.366 GOL.16: 5 residues within 4Å: Chain A: F.438, P.470, V.471, F.472, T.473 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:P.470, A:F.472, A:T.473 GOL.17: 4 residues within 4Å: Chain A: E.196, C.516, G.517, D.518 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.518 GOL.18: 1 residues within 4Å: Chain A: T.180 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.180 Water bridges: A:Y.618, A:Y.618

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Li, J. et al., Formation of Monofluorinated Radical Cofactor in Galactose Oxidase through Copper-Mediated C-F Bond Scission. J.Am.Chem.Soc. (2020)

Release Date

2021-02-03

Peptides

Galactose oxidase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Galactose oxidase

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