SMTL ID : 1w2z.1 (1 other biounit)

PSAO and Xenon

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.24 Å

Oligo State

homo-dimer

Ligands

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

CU.1: 4 residues within 4Å: Chain A: L.407, H.442, H.444, H.603 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.442, A:H.444, A:H.603, H2O.5 CU.53: 4 residues within 4Å: Chain B: L.407, H.442, H.444, H.603 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.442, B:H.444, B:H.603, H2O.10

2 x MN: MANGANESE (II) ION(Non-covalent)

MN.2: 6 residues within 4Å: Chain A: K.48, D.451, F.452, D.453, D.592, I.593 6 PLIP interactions: 5 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.451, A:F.452, A:D.453, A:D.592, A:I.593, H2O.7 MN.54: 6 residues within 4Å: Chain B: K.48, D.451, F.452, D.453, D.592, I.593 6 PLIP interactions: 5 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.451, B:F.452, B:D.453, B:D.592, B:I.593, H2O.13

4 x XE: XENON(Non-covalent)

XE.3: 7 residues within 4Å: Chain A: F.452, V.508, Y.523, R.524, L.525, M.595, L.622 No protein-ligand interaction detected (PLIP) XE.4: 5 residues within 4Å: Chain A: I.405, L.407, Y.446, I.601, T.618 No protein-ligand interaction detected (PLIP) XE.55: 6 residues within 4Å: Chain B: F.452, V.508, Y.523, R.524, L.525, L.622 No protein-ligand interaction detected (PLIP) XE.56: 5 residues within 4Å: Chain B: I.405, L.407, Y.446, I.601, T.618 No protein-ligand interaction detected (PLIP)

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

NAG.5: 3 residues within 4Å: Chain A: N.131, S.133, E.134 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.131, A:S.133 NAG.6: 7 residues within 4Å: Chain A: N.558, T.560, E.561, W.581, Q.584, R.586 Ligands: IOD.48 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.558, A:E.561 NAG.57: 3 residues within 4Å: Chain B: N.131, S.133, E.134 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:N.131, B:S.133, B:S.133, B:E.134 NAG.58: 6 residues within 4Å: Chain B: N.558, T.560, E.561, W.581, Q.584, R.586 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:N.558, B:E.561, B:Q.584, B:Q.584, B:R.586

94 x IOD: IODIDE ION(Non-functional Binders)

IOD.7: 6 residues within 4Å: Chain A: G.500, I.529, P.530 Chain B: G.500, I.529, P.530 Ligand excluded by PLIP IOD.8: 1 residues within 4Å: Chain A: R.470 Ligand excluded by PLIP IOD.9: 4 residues within 4Å: Chain A: L.114, Y.118, K.185, I.186 Ligand excluded by PLIP IOD.10: 4 residues within 4Å: Chain A: P.64, N.83, R.85, I.86 Ligand excluded by PLIP IOD.11: 5 residues within 4Å: Chain A: G.215, P.216 Chain B: N.242, Y.263, L.265 Ligand excluded by PLIP IOD.12: 3 residues within 4Å: Chain A: K.66, N.83, V.90 Ligand excluded by PLIP IOD.13: 3 residues within 4Å: Chain A: K.217, H.219 Chain B: Q.227 Ligand excluded by PLIP IOD.14: 4 residues within 4Å: Chain A: P.46, E.47, H.50, I.63 Ligand excluded by PLIP IOD.15: 5 residues within 4Å: Chain A: P.226, Q.227, R.640, V.642 Chain B: S.220 Ligand excluded by PLIP IOD.16: 4 residues within 4Å: Chain A: N.549, Y.550, W.553, A.579 Ligand excluded by PLIP IOD.17: 6 residues within 4Å: Chain A: D.250, A.253, V.256, K.276, K.562, W.563 Ligand excluded by PLIP IOD.18: 3 residues within 4Å: Chain A: T.14, H.236, Y.329 Ligand excluded by PLIP IOD.19: 3 residues within 4Å: Chain A: I.89, S.91, D.92 Ligand excluded by PLIP IOD.20: 5 residues within 4Å: Chain A: P.289, E.291, Y.294 Chain B: S.476, K.477 Ligand excluded by PLIP IOD.21: 4 residues within 4Å: Chain A: G.456, T.457, H.458, N.510 Ligand excluded by PLIP IOD.22: 5 residues within 4Å: Chain A: G.500, L.501, A.502, P.503 Chain B: H.532 Ligand excluded by PLIP IOD.23: 4 residues within 4Å: Chain A: K.396, S.400, K.402, E.621 Ligand excluded by PLIP IOD.24: 4 residues within 4Å: Chain A: E.16, E.17, A.20, L.84 Ligand excluded by PLIP IOD.25: 3 residues within 4Å: Chain A: L.52, R.272, G.456 Ligand excluded by PLIP IOD.26: 5 residues within 4Å: Chain A: I.418, I.424, K.425, E.426, L.428 Ligand excluded by PLIP IOD.27: 3 residues within 4Å: Chain A: R.586, E.587, K.591 Ligand excluded by PLIP IOD.28: 3 residues within 4Å: Chain A: P.212, P.213, F.214 Ligand excluded by PLIP IOD.29: 5 residues within 4Å: Chain A: Y.40, V.70, P.101, I.102, R.252 Ligand excluded by PLIP IOD.30: 4 residues within 4Å: Chain A: P.289, T.290 Chain B: S.475, S.476 Ligand excluded by PLIP IOD.31: 2 residues within 4Å: Chain A: P.30, N.33 Ligand excluded by PLIP IOD.32: 3 residues within 4Å: Chain A: R.35, N.74, S.75 Ligand excluded by PLIP IOD.33: 4 residues within 4Å: Chain A: R.371, L.637, S.638 Chain B: R.317 Ligand excluded by PLIP IOD.34: 2 residues within 4Å: Chain A: P.119, P.120 Ligand excluded by PLIP IOD.35: 2 residues within 4Å: Chain A: K.421, D.422 Ligand excluded by PLIP IOD.36: 4 residues within 4Å: Chain A: F.214, G.215, K.217 Chain B: L.637 Ligand excluded by PLIP IOD.37: 4 residues within 4Å: Chain A: S.237, F.245, H.246, L.259 Ligand excluded by PLIP IOD.38: 3 residues within 4Å: Chain A: P.64, R.65, R.85 Ligand excluded by PLIP IOD.39: 4 residues within 4Å: Chain A: K.48, D.49, L.52, T.457 Ligand excluded by PLIP IOD.40: 4 residues within 4Å: Chain A: N.352, I.353 Chain B: R.379, L.615 Ligand excluded by PLIP IOD.41: 4 residues within 4Å: Chain A: K.463, I.497, A.504, L.506 Ligand excluded by PLIP IOD.42: 4 residues within 4Å: Chain A: H.57, P.58, T.59, L.60 Ligand excluded by PLIP IOD.43: 4 residues within 4Å: Chain A: E.369, S.370 Chain B: I.314, R.317 Ligand excluded by PLIP IOD.44: 3 residues within 4Å: Chain A: R.53, T.56, H.57 Ligand excluded by PLIP IOD.45: 5 residues within 4Å: Chain A: L.10, D.45, P.46, Y.275, K.276 Ligand excluded by PLIP IOD.46: 4 residues within 4Å: Chain A: I.112, K.113, L.116 Chain B: P.363 Ligand excluded by PLIP IOD.47: 5 residues within 4Å: Chain A: I.497, I.499, G.500, A.504, L.506 Ligand excluded by PLIP IOD.48: 4 residues within 4Å: Chain A: Y.557, N.558, R.559 Ligands: NAG.6 Ligand excluded by PLIP IOD.49: 4 residues within 4Å: Chain A: D.106, S.332, A.333, N.334 Ligand excluded by PLIP IOD.50: 6 residues within 4Å: Chain A: T.164, V.165, E.204, Y.205, Q.206, K.209 Ligand excluded by PLIP IOD.51: 4 residues within 4Å: Chain A: L.466, E.505 Chain B: H.602 Ligands: IOD.106 Ligand excluded by PLIP IOD.52: 3 residues within 4Å: Chain A: P.320, P.321 Chain B: Y.350 Ligand excluded by PLIP IOD.59: 5 residues within 4Å: Chain A: N.242, Y.263, L.265 Chain B: G.215, P.216 Ligand excluded by PLIP IOD.60: 4 residues within 4Å: Chain B: P.64, N.83, R.85, I.86 Ligand excluded by PLIP IOD.61: 2 residues within 4Å: Chain B: N.83, V.90 Ligand excluded by PLIP IOD.62: 4 residues within 4Å: Chain B: G.456, T.457, H.458, N.510 Ligand excluded by PLIP IOD.63: 6 residues within 4Å: Chain A: T.222, W.644 Chain B: H.224, P.226, V.642, P.645 Ligand excluded by PLIP IOD.64: 6 residues within 4Å: Chain B: D.250, A.253, V.256, K.276, K.562, W.563 Ligand excluded by PLIP IOD.65: 4 residues within 4Å: Chain B: P.46, E.47, H.50, I.63 Ligand excluded by PLIP IOD.66: 3 residues within 4Å: Chain B: R.586, E.587, K.591 Ligand excluded by PLIP IOD.67: 4 residues within 4Å: Chain B: S.237, F.245, H.246, L.259 Ligand excluded by PLIP IOD.68: 2 residues within 4Å: Chain B: P.212, P.213 Ligand excluded by PLIP IOD.69: 4 residues within 4Å: Chain B: K.463, I.497, A.504, L.506 Ligand excluded by PLIP IOD.70: 3 residues within 4Å: Chain B: T.14, H.236, Y.329 Ligand excluded by PLIP IOD.71: 3 residues within 4Å: Chain B: L.52, R.272, G.456 Ligand excluded by PLIP IOD.72: 3 residues within 4Å: Chain B: K.396, K.402, E.621 Ligand excluded by PLIP IOD.73: 5 residues within 4Å: Chain B: I.418, I.424, K.425, E.426, L.428 Ligand excluded by PLIP IOD.74: 3 residues within 4Å: Chain B: P.212, P.213, F.214 Ligand excluded by PLIP IOD.75: 4 residues within 4Å: Chain B: L.19, A.20, T.23, R.87 Ligand excluded by PLIP IOD.76: 2 residues within 4Å: Chain B: K.421, D.422 Ligand excluded by PLIP IOD.77: 4 residues within 4Å: Chain B: H.57, P.58, T.59, L.60 Ligand excluded by PLIP IOD.78: 3 residues within 4Å: Chain B: R.35, N.74, S.75 Ligand excluded by PLIP IOD.79: 5 residues within 4Å: Chain B: L.221, T.222, S.223, P.321 Ligands: IOD.103 Ligand excluded by PLIP IOD.80: 4 residues within 4Å: Chain B: K.48, D.49, L.52, T.457 Ligand excluded by PLIP IOD.81: 5 residues within 4Å: Chain B: Y.40, V.70, P.101, I.102, R.252 Ligand excluded by PLIP IOD.82: 4 residues within 4Å: Chain B: E.16, E.17, A.20, L.84 Ligand excluded by PLIP IOD.83: 4 residues within 4Å: Chain A: S.476, K.477 Chain B: E.291, Y.294 Ligand excluded by PLIP IOD.84: 3 residues within 4Å: Chain A: Q.227 Chain B: K.217, H.219 Ligand excluded by PLIP IOD.85: 4 residues within 4Å: Chain B: N.549, Y.550, W.553, A.579 Ligand excluded by PLIP IOD.86: 5 residues within 4Å: Chain B: I.72, S.75, F.100, R.152, D.182 Ligand excluded by PLIP IOD.87: 4 residues within 4Å: Chain A: H.532 Chain B: G.500, A.502, P.503 Ligand excluded by PLIP IOD.88: 3 residues within 4Å: Chain B: I.424, K.425, E.426 Ligand excluded by PLIP IOD.89: 3 residues within 4Å: Chain B: W.144, F.145, E.147 Ligand excluded by PLIP IOD.90: 4 residues within 4Å: Chain B: L.114, Y.118, K.185, I.186 Ligand excluded by PLIP IOD.91: 4 residues within 4Å: Chain A: R.317 Chain B: R.371, L.637, S.638 Ligand excluded by PLIP IOD.92: 4 residues within 4Å: Chain A: L.637 Chain B: F.214, G.215, K.217 Ligand excluded by PLIP IOD.93: 3 residues within 4Å: Chain A: H.602 Chain B: L.466, E.505 Ligand excluded by PLIP IOD.94: 4 residues within 4Å: Chain B: K.15, L.19, T.336, P.337 Ligand excluded by PLIP IOD.95: 3 residues within 4Å: Chain A: K.635 Chain B: Q.210, S.211 Ligand excluded by PLIP IOD.96: 7 residues within 4Å: Chain B: T.173, G.174, R.192, D.193, E.195, E.292, K.414 Ligand excluded by PLIP IOD.97: 4 residues within 4Å: Chain A: P.363 Chain B: I.112, K.113, L.116 Ligand excluded by PLIP IOD.98: 3 residues within 4Å: Chain B: P.64, R.65, R.85 Ligand excluded by PLIP IOD.99: 5 residues within 4Å: Chain B: L.10, D.45, P.46, Y.275, K.276 Ligand excluded by PLIP IOD.100: 4 residues within 4Å: Chain A: R.379, L.615 Chain B: N.352, I.353 Ligand excluded by PLIP IOD.101: 3 residues within 4Å: Chain B: Q.7, P.9, R.65 Ligand excluded by PLIP IOD.102: 4 residues within 4Å: Chain A: N.519 Chain B: K.421, K.431, L.432 Ligand excluded by PLIP IOD.103: 6 residues within 4Å: Chain A: V.642 Chain B: T.222, S.223, P.321, H.322 Ligands: IOD.79 Ligand excluded by PLIP IOD.104: 5 residues within 4Å: Chain B: I.497, I.499, G.500, A.504, L.506 Ligand excluded by PLIP IOD.105: 5 residues within 4Å: Chain B: V.165, E.204, Y.205, Q.206, K.209 Ligand excluded by PLIP IOD.106: 6 residues within 4Å: Chain A: L.466, P.503, A.504, E.505 Chain B: H.602 Ligands: IOD.51 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Duff, A.P. et al., Using Xenon as a Probe for Dioxygen-Binding Sites in Copper Amine Oxidases. J.Mol.Biol. (2004)

Release Date

2004-11-17

Peptides

AMINE OXIDASE, COPPER CONTAINING: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

AMINE OXIDASE, COPPER CONTAINING

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