SMTL ID : 3x42.1

Crystal structure of copper amine oxidase from Arthrobacter globiformis in the presence of sodium bromide

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.88 Å

Oligo State

homo-dimer

Ligands

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

CU.1: 3 residues within 4Å: Chain A: H.423, H.425, H.584 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.423, A:H.425, A:H.584, H2O.6, H2O.10 CU.15: 3 residues within 4Å: Chain B: H.423, H.425, H.584 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:H.423, B:H.425, B:H.584, H2O.28, H2O.35

8 x BR: BROMIDE ION(Non-covalent)

BR.2: 5 residues within 4Å: Chain A: S.521, R.524, R.525, S.554, G.555 Ligand excluded by PLIP BR.3: 3 residues within 4Å: Chain A: H.337, S.366, Y.379 Ligand excluded by PLIP BR.4: 2 residues within 4Å: Chain A: L.119, D.120 Ligand excluded by PLIP BR.5: 3 residues within 4Å: Chain A: G.26, P.27, E.28 Ligand excluded by PLIP BR.16: 4 residues within 4Å: Chain B: S.521, R.524, S.554, G.555 Ligand excluded by PLIP BR.17: 3 residues within 4Å: Chain B: H.337, S.366, Y.379 Ligand excluded by PLIP BR.18: 3 residues within 4Å: Chain B: G.26, P.27, E.28 Ligand excluded by PLIP BR.19: 2 residues within 4Å: Chain B: L.119, D.120 Ligand excluded by PLIP

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

NA.6: 6 residues within 4Å: Chain A: R.41, D.432, M.433, F.438, D.573, I.574 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.41, A:D.573, A:D.573, A:I.574 NA.20: 6 residues within 4Å: Chain B: R.41, D.432, M.433, F.438, D.573, I.574 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.41, B:D.573, B:I.574

2 x K: POTASSIUM ION(Non-covalent)

K.7: 2 residues within 4Å: Chain A: V.71, T.72 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:V.71, A:T.72, H2O.9 K.21: 2 residues within 4Å: Chain B: V.71, T.72 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:V.71, H2O.37

13 x GOL: GLYCEROL(Non-functional Binders)

GOL.8: 10 residues within 4Å: Chain A: R.524, R.525, T.546, F.549, V.550, H.553, S.554, G.555, G.556, A.557 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:P.545, A:F.549, A:H.553, A:S.554, A:A.557 Water bridges: A:A.527 GOL.9: 4 residues within 4Å: Chain A: E.339, R.362, K.393 Ligands: GOL.12 12 PLIP interactions: 4 interactions with chain B, 8 interactions with chain A Water bridges: B:D.340, B:D.340, B:I.343, B:R.359, A:E.339, A:E.339, A:E.339, A:Y.381, A:E.391, A:K.393 Hydrogen bonds: A:R.362, A:K.393 GOL.10: 7 residues within 4Å: Chain A: N.360, Y.383, D.385, T.387, E.389, K.602 Ligands: GOL.12 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:N.360, A:T.387, A:E.389, A:K.602 Water bridges: A:N.360, A:D.385, A:D.385 GOL.11: 6 residues within 4Å: Chain A: V.151, D.153, H.162, V.189, P.190, A.191 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.153 GOL.12: 8 residues within 4Å: Chain A: W.341, R.362, Y.381, E.389, E.391 Ligands: GOL.9, GOL.10, GOL.25 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.362, A:R.362, A:Y.381 Water bridges: A:E.389, A:E.391 GOL.13: 5 residues within 4Å: Chain A: L.582, D.597 Chain B: H.507, K.602, R.604 8 PLIP interactions: 1 interactions with chain B, 7 interactions with chain A Hydrogen bonds: B:K.602, A:D.597 Water bridges: A:Q.511, A:Q.511, A:T.583, A:D.597, A:D.597, A:T.598 GOL.14: 5 residues within 4Å: Chain A: H.507, K.602, R.604 Chain B: L.582, D.597 9 PLIP interactions: 6 interactions with chain B, 3 interactions with chain A Water bridges: B:Q.511, B:D.597, B:D.597, B:D.597, B:T.598, B:T.598, A:R.604 Hydrogen bonds: A:K.602, A:K.602 GOL.22: 7 residues within 4Å: Chain A: V.596 Chain B: N.360, Y.383, D.385, T.387, E.389, K.602 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:N.360, B:D.385, B:K.602, B:K.602 Water bridges: B:W.341 GOL.23: 7 residues within 4Å: Chain B: Y.33, V.36, L.37, D.38, R.266, R.543, Y.544 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:V.36, B:D.38, B:Y.544, B:Y.544 Water bridges: B:E.245, B:R.266 GOL.24: 6 residues within 4Å: Chain A: D.340, W.341 Chain B: E.339, R.362, K.393 Ligands: GOL.25 8 PLIP interactions: 6 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:R.362, B:K.393 Water bridges: B:E.339, B:E.339, B:E.391, B:K.393, A:D.340, A:W.341 GOL.25: 7 residues within 4Å: Chain B: W.341, R.362, Y.381, E.389, E.391 Ligands: GOL.12, GOL.24 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:R.362, B:R.362, B:Y.381, B:Y.381 Water bridges: B:E.389, B:E.389, B:E.389, B:H.509, B:K.602 GOL.26: 3 residues within 4Å: Chain A: D.409 Chain B: S.463, R.464 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Water bridges: A:D.409, B:Q.450 Hydrogen bonds: B:R.464 GOL.27: 2 residues within 4Å: Chain A: H.509 Chain B: H.509 9 PLIP interactions: 2 interactions with chain B, 7 interactions with chain A Water bridges: B:N.510, B:N.510, A:H.509, A:N.510, A:N.510, A:Q.511, A:Q.511, A:Q.511 Hydrogen bonds: A:H.509

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Murakawa, T. et al., Probing the Catalytic Mechanism of Copper Amine Oxidase from Arthrobacter globiformis with Halide Ions. J.Biol.Chem. (2015)

Release Date

2015-08-19

Peptides

Phenylethylamine oxidase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Phenylethylamine oxidase

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