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Copper in PDB 1w2z: Psao and Xenon

Enzymatic activity of Psao and Xenon

All present enzymatic activity of Psao and Xenon:
1.4.3.6;

Protein crystallography data

The structure of Psao and Xenon, PDB code: 1w2z was solved by A.P.Duff, D.M.Trambaiolo, A.E.Cohen, P.J.Ellis, G.A.Juda, E.M.Shepard, D.B.Langley, D.M.Dooley, H.C.Freeman, J.M.Guss, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.88 / 2.24
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 89.507, 196.268, 89.665, 90.00, 107.46, 90.00
R / Rfree (%) 17.9 / 22.4

Other elements in 1w2z:

The structure of Psao and Xenon also contains other interesting chemical elements:

Manganese (Mn) 4 atoms
Xenon (Xe) 8 atoms
Iodine (I) 176 atoms

Copper Binding Sites:

The binding sites of Copper atom in the Psao and Xenon (pdb code 1w2z). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 4 binding sites of Copper where determined in the Psao and Xenon, PDB code: 1w2z:
Jump to Copper binding site number: 1; 2; 3; 4;

Copper binding site 1 out of 4 in 1w2z

Go back to Copper Binding Sites List in 1w2z
Copper binding site 1 out of 4 in the Psao and Xenon


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of Psao and Xenon within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu701

b:34.1
occ:1.00
NE2 A:HIS442 2.1 8.4 1.0
NE2 A:HIS444 2.2 12.7 1.0
ND1 A:HIS603 2.2 10.8 1.0
O A:HOH2106 2.9 33.0 1.0
CD2 A:HIS442 2.9 10.7 1.0
CD2 A:HIS444 3.0 13.7 1.0
HD2 A:HIS444 3.0 13.3 1.0
HB2 A:HIS603 3.0 14.6 1.0
HD2 A:HIS442 3.1 10.0 1.0
CE1 A:HIS442 3.1 11.6 1.0
CG A:HIS603 3.1 14.1 1.0
CE1 A:HIS603 3.2 12.1 1.0
HB3 A:HIS603 3.3 14.6 1.0
CE1 A:HIS444 3.3 17.9 1.0
CB A:HIS603 3.3 14.8 1.0
HE1 A:HIS442 3.3 10.6 1.0
HE1 A:HIS603 3.4 13.7 1.0
HE1 A:HIS444 3.6 13.1 1.0
HD12 A:LEU407 3.6 33.7 1.0
CG A:HIS442 4.1 10.8 1.0
ND1 A:HIS442 4.1 10.3 1.0
HD13 A:ILE601 4.2 24.2 1.0
CG A:HIS444 4.2 13.7 1.0
CD2 A:HIS603 4.3 18.1 1.0
NE2 A:HIS603 4.3 16.3 1.0
ND1 A:HIS444 4.3 9.4 1.0
HE3 A:MET613 4.4 21.9 0.6
O2 A:TPQ387 4.5 26.6 0.4
CD1 A:LEU407 4.5 35.2 1.0
HD12 A:ILE601 4.6 24.2 1.0
HD11 A:LEU407 4.7 33.7 1.0
HD13 A:LEU407 4.8 33.7 1.0
HD22 A:LEU411 4.8 13.4 1.0
CA A:HIS603 4.8 14.6 1.0
CD1 A:ILE601 4.8 25.5 1.0
HE2 A:MET613 4.9 29.0 0.4
H3 A:TPQ387 4.9 27.6 0.4

Copper binding site 2 out of 4 in 1w2z

Go back to Copper Binding Sites List in 1w2z
Copper binding site 2 out of 4 in the Psao and Xenon


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of Psao and Xenon within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu701

b:31.4
occ:1.00
ND1 B:HIS603 2.0 12.6 1.0
NE2 B:HIS442 2.1 10.8 1.0
NE2 B:HIS444 2.1 11.1 1.0
O B:HOH2086 2.8 32.2 1.0
CD2 B:HIS442 2.9 10.5 1.0
CG B:HIS603 3.0 16.0 1.0
CE1 B:HIS603 3.0 13.1 1.0
HB2 B:HIS603 3.0 14.7 1.0
CD2 B:HIS444 3.1 15.7 1.0
CE1 B:HIS442 3.1 12.6 1.0
HD2 B:HIS442 3.1 10.1 1.0
CE1 B:HIS444 3.1 14.8 1.0
HE1 B:HIS603 3.2 13.7 1.0
HD2 B:HIS444 3.2 13.3 1.0
HB3 B:HIS603 3.2 14.7 1.0
CB B:HIS603 3.3 15.4 1.0
HE1 B:HIS444 3.3 12.9 1.0
HE1 B:HIS442 3.3 10.8 1.0
HD12 B:LEU407 3.5 33.9 1.0
CG B:HIS442 4.1 12.5 1.0
ND1 B:HIS442 4.1 10.5 1.0
NE2 B:HIS603 4.1 13.0 1.0
CD2 B:HIS603 4.1 16.3 1.0
ND1 B:HIS444 4.2 11.2 1.0
CG B:HIS444 4.2 12.3 1.0
HD13 B:ILE601 4.3 24.2 1.0
HE2 B:MET613 4.3 21.9 0.6
CD1 B:LEU407 4.4 36.2 1.0
HD23 B:LEU407 4.5 33.0 1.0
HD21 B:LEU407 4.6 33.0 1.0
H3 B:TPQ387 4.6 27.6 0.4
O2 B:TPQ387 4.6 26.3 0.4
HD12 B:ILE601 4.6 24.2 1.0
HD11 B:LEU407 4.7 33.9 1.0
HD13 B:LEU407 4.7 33.9 1.0
CA B:HIS603 4.8 14.6 1.0
HE2 B:MET613 4.9 29.0 0.4
CD1 B:ILE601 4.9 23.9 1.0
HD22 B:LEU411 4.9 13.3 1.0
CD2 B:LEU407 4.9 34.2 1.0
HD2 B:HIS603 5.0 15.5 1.0

Copper binding site 3 out of 4 in 1w2z

Go back to Copper Binding Sites List in 1w2z
Copper binding site 3 out of 4 in the Psao and Xenon


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 3 of Psao and Xenon within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cu701

b:33.7
occ:1.00
NE2 C:HIS444 2.1 12.6 1.0
NE2 C:HIS442 2.1 8.7 1.0
ND1 C:HIS603 2.1 12.0 1.0
O C:HOH2059 2.9 39.3 1.0
CD2 C:HIS442 2.9 10.3 1.0
HB2 C:HIS603 3.0 14.6 1.0
CE1 C:HIS444 3.0 11.3 1.0
CG C:HIS603 3.0 16.1 1.0
HD2 C:HIS442 3.1 9.9 1.0
CE1 C:HIS442 3.1 8.4 1.0
CE1 C:HIS603 3.1 16.4 1.0
CD2 C:HIS444 3.1 13.0 1.0
HE1 C:HIS444 3.2 12.6 1.0
HB3 C:HIS603 3.3 14.6 1.0
HE1 C:HIS603 3.3 13.9 1.0
HD2 C:HIS444 3.3 13.2 1.0
CB C:HIS603 3.3 14.0 1.0
HE1 C:HIS442 3.4 10.4 1.0
HD12 C:LEU407 3.7 33.7 1.0
CG C:HIS442 4.1 10.4 1.0
ND1 C:HIS442 4.1 11.1 1.0
ND1 C:HIS444 4.2 7.5 1.0
CD2 C:HIS603 4.2 15.5 1.0
NE2 C:HIS603 4.2 13.0 1.0
CG C:HIS444 4.2 14.3 1.0
HD13 C:ILE601 4.3 24.3 1.0
O2 C:TPQ387 4.3 27.0 0.4
HD12 C:ILE601 4.4 24.3 1.0
HE3 C:MET613 4.4 21.8 0.6
CD1 C:LEU407 4.5 35.0 1.0
HD11 C:LEU407 4.7 33.7 1.0
HE2 C:MET613 4.8 29.1 0.4
CD1 C:ILE601 4.8 25.6 1.0
HD13 C:LEU407 4.8 33.7 1.0
CA C:HIS603 4.8 14.4 1.0
HD22 C:LEU411 4.8 13.3 1.0
H3 C:TPQ387 5.0 27.7 0.4

Copper binding site 4 out of 4 in 1w2z

Go back to Copper Binding Sites List in 1w2z
Copper binding site 4 out of 4 in the Psao and Xenon


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 4 of Psao and Xenon within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cu701

b:29.5
occ:1.00
NE2 D:HIS444 2.0 10.2 1.0
ND1 D:HIS603 2.0 11.6 1.0
NE2 D:HIS442 2.1 8.4 1.0
O D:HOH2083 2.8 36.9 1.0
CD2 D:HIS442 3.0 9.1 1.0
CG D:HIS603 3.0 14.6 1.0
HB2 D:HIS603 3.0 14.6 1.0
CE1 D:HIS444 3.0 15.0 1.0
CD2 D:HIS444 3.0 13.7 1.0
CE1 D:HIS603 3.1 16.7 1.0
CE1 D:HIS442 3.1 13.6 1.0
HD2 D:HIS442 3.1 9.8 1.0
HB3 D:HIS603 3.2 14.6 1.0
HE1 D:HIS444 3.2 12.9 1.0
HD2 D:HIS444 3.2 13.2 1.0
CB D:HIS603 3.3 14.5 1.0
HE1 D:HIS603 3.3 14.0 1.0
HE1 D:HIS442 3.3 10.7 1.0
HD12 D:LEU407 3.7 33.8 1.0
CG D:HIS442 4.1 8.5 1.0
ND1 D:HIS442 4.1 9.6 1.0
ND1 D:HIS444 4.1 11.8 1.0
CD2 D:HIS603 4.1 14.8 1.0
NE2 D:HIS603 4.1 14.4 1.0
CG D:HIS444 4.2 11.8 1.0
HE3 D:MET613 4.3 21.9 0.6
HD13 D:ILE601 4.4 24.2 1.0
CD1 D:LEU407 4.5 36.0 1.0
HD12 D:ILE601 4.6 24.2 1.0
HD11 D:LEU407 4.6 33.8 1.0
O2 D:TPQ387 4.7 27.9 0.4
HD13 D:LEU407 4.8 33.8 1.0
CA D:HIS603 4.8 14.4 1.0
HD22 D:LEU411 4.8 13.3 1.0
CD1 D:ILE601 4.9 25.5 1.0
HD2 D:HIS603 5.0 15.4 1.0

Reference:

A.P.Duff, D.M.Trambaiolo, A.E.Cohen, P.J.Ellis, G.A.Juda, E.M.Shepard, D.B.Langley, D.M.Dooley, H.C.Freeman, J.M.Guss. Using Xenon As A Probe For Dioxygen-Binding Sites in Copper Amine Oxidases. J.Mol.Biol. V. 344 599 2004.
ISSN: ISSN 0022-2836
PubMed: 15533431
DOI: 10.1016/J.JMB.2004.09.075
Page generated: Sun Dec 13 11:02:38 2020

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