Manganese 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 Binding Sites:
The binding sites of Manganese atom in the Psao and Xenon
(pdb code 1w2z). This binding sites where shown within
5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the
Psao and Xenon, PDB code: 1w2z:
Jump to Manganese binding site number:
1;
2;
3;
4;
Manganese binding site 1 out
of 4 in 1w2z
Go back to
Manganese Binding Sites List in 1w2z
Manganese binding site 1 out
of 4 in the Psao and Xenon
 Mono view
 Stereo pair view
|
|
A full contact list of Manganese with other atoms in the Mn binding
site number 1 of Psao and Xenon within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mn702
b:36.6
occ:1.00
|
O
|
A:HOH2174
|
2.3
|
23.0
|
1.0
|
|
O
|
A:ILE593
|
2.3
|
11.7
|
1.0
|
|
OD1
|
A:ASP451
|
2.3
|
8.4
|
1.0
|
|
O
|
A:PHE452
|
2.4
|
13.5
|
1.0
|
|
OD1
|
A:ASP592
|
2.4
|
13.8
|
1.0
|
|
OD1
|
A:ASP453
|
2.5
|
12.8
|
1.0
|
|
H
|
A:ILE593
|
2.9
|
12.3
|
1.0
|
|
C
|
A:ILE593
|
3.4
|
11.8
|
1.0
|
|
C
|
A:PHE452
|
3.4
|
13.7
|
1.0
|
|
N
|
A:ILE593
|
3.4
|
12.6
|
1.0
|
|
CG
|
A:ASP451
|
3.6
|
12.0
|
1.0
|
|
CG
|
A:ASP592
|
3.6
|
15.4
|
1.0
|
|
CG
|
A:ASP453
|
3.6
|
13.4
|
1.0
|
|
HA
|
A:ASP592
|
3.7
|
14.6
|
1.0
|
|
HA
|
A:ASP453
|
3.7
|
11.5
|
1.0
|
|
NZ
|
A:LYS48
|
3.9
|
12.9
|
1.0
|
|
CA
|
A:ILE593
|
4.0
|
10.5
|
1.0
|
|
HA
|
A:ASP451
|
4.1
|
10.9
|
1.0
|
|
HG21
|
A:VAL594
|
4.1
|
13.7
|
1.0
|
|
C
|
A:ASP592
|
4.1
|
14.8
|
1.0
|
|
N
|
A:ASP453
|
4.1
|
12.6
|
1.0
|
|
OD2
|
A:ASP451
|
4.2
|
14.3
|
1.0
|
|
C
|
A:ASP451
|
4.2
|
11.2
|
1.0
|
|
N
|
A:PHE452
|
4.2
|
12.3
|
1.0
|
|
HB2
|
A:TYR557
|
4.2
|
16.5
|
1.0
|
|
CA
|
A:ASP453
|
4.2
|
11.2
|
1.0
|
|
OD2
|
A:ASP592
|
4.2
|
21.1
|
1.0
|
|
CA
|
A:ASP592
|
4.2
|
14.9
|
1.0
|
|
HA
|
A:VAL594
|
4.3
|
11.8
|
1.0
|
|
OD2
|
A:ASP453
|
4.3
|
11.6
|
1.0
|
|
HA
|
A:THR457
|
4.4
|
13.2
|
1.0
|
|
HG22
|
A:VAL594
|
4.4
|
13.7
|
1.0
|
|
H
|
A:PHE452
|
4.4
|
12.1
|
1.0
|
|
HG13
|
A:ILE593
|
4.4
|
11.3
|
1.0
|
|
O
|
A:THR457
|
4.4
|
17.6
|
1.0
|
|
CA
|
A:PHE452
|
4.4
|
12.6
|
1.0
|
|
OD1
|
A:ASN459
|
4.5
|
10.7
|
1.0
|
|
O
|
A:ASP451
|
4.5
|
11.8
|
1.0
|
|
N
|
A:VAL594
|
4.5
|
10.9
|
1.0
|
|
CA
|
A:ASP451
|
4.5
|
11.0
|
1.0
|
|
CB
|
A:ASP592
|
4.5
|
14.6
|
1.0
|
|
CB
|
A:ASP453
|
4.5
|
9.1
|
1.0
|
|
CB
|
A:ASP451
|
4.6
|
12.7
|
1.0
|
|
HA
|
A:ILE593
|
4.7
|
11.1
|
1.0
|
|
CG2
|
A:VAL594
|
4.7
|
15.6
|
1.0
|
|
HG12
|
A:ILE593
|
4.8
|
11.3
|
1.0
|
|
CA
|
A:VAL594
|
4.8
|
12.0
|
1.0
|
|
HB2
|
A:PHE452
|
4.9
|
12.7
|
1.0
|
|
H
|
A:ASP453
|
4.9
|
12.5
|
1.0
|
|
CG1
|
A:ILE593
|
5.0
|
13.8
|
1.0
|
|
Manganese binding site 2 out
of 4 in 1w2z
Go back to
Manganese Binding Sites List in 1w2z
Manganese binding site 2 out
of 4 in the Psao and Xenon
 Mono view
 Stereo pair view
|
|
A full contact list of Manganese with other atoms in the Mn binding
site number 2 of Psao and Xenon within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mn702
b:33.8
occ:1.00
|
OD1
|
B:ASP453
|
2.3
|
9.9
|
1.0
|
|
O
|
B:PHE452
|
2.3
|
13.8
|
1.0
|
|
OD1
|
B:ASP451
|
2.3
|
11.0
|
1.0
|
|
OD1
|
B:ASP592
|
2.4
|
12.3
|
1.0
|
|
O
|
B:ILE593
|
2.4
|
11.7
|
1.0
|
|
O
|
B:HOH2141
|
2.5
|
25.9
|
1.0
|
|
H
|
B:ILE593
|
3.0
|
12.3
|
1.0
|
|
C
|
B:PHE452
|
3.4
|
13.6
|
1.0
|
|
CG
|
B:ASP453
|
3.4
|
10.2
|
1.0
|
|
C
|
B:ILE593
|
3.5
|
11.7
|
1.0
|
|
N
|
B:ILE593
|
3.5
|
12.0
|
1.0
|
|
CG
|
B:ASP451
|
3.6
|
11.4
|
1.0
|
|
HA
|
B:ASP453
|
3.6
|
11.5
|
1.0
|
|
CG
|
B:ASP592
|
3.6
|
16.2
|
1.0
|
|
HA
|
B:ASP592
|
3.7
|
14.6
|
1.0
|
|
NZ
|
B:LYS48
|
3.9
|
15.4
|
1.0
|
|
N
|
B:ASP453
|
4.0
|
12.9
|
1.0
|
|
OD2
|
B:ASP453
|
4.1
|
14.1
|
1.0
|
|
HA
|
B:ASP451
|
4.1
|
10.9
|
1.0
|
|
CA
|
B:ASP453
|
4.1
|
11.3
|
1.0
|
|
CA
|
B:ILE593
|
4.1
|
10.8
|
1.0
|
|
C
|
B:ASP451
|
4.2
|
11.5
|
1.0
|
|
OD2
|
B:ASP451
|
4.2
|
14.8
|
1.0
|
|
C
|
B:ASP592
|
4.2
|
14.7
|
1.0
|
|
N
|
B:PHE452
|
4.2
|
12.2
|
1.0
|
|
OD2
|
B:ASP592
|
4.3
|
17.1
|
1.0
|
|
HG21
|
B:VAL594
|
4.3
|
13.4
|
1.0
|
|
CA
|
B:ASP592
|
4.3
|
14.9
|
1.0
|
|
HA
|
B:THR457
|
4.3
|
13.2
|
1.0
|
|
HA
|
B:VAL594
|
4.4
|
11.8
|
1.0
|
|
CB
|
B:ASP453
|
4.4
|
10.7
|
1.0
|
|
HG13
|
B:ILE593
|
4.4
|
11.1
|
1.0
|
|
HB2
|
B:TYR557
|
4.4
|
16.5
|
1.0
|
|
O
|
B:ASP451
|
4.4
|
11.8
|
1.0
|
|
CA
|
B:PHE452
|
4.4
|
12.9
|
1.0
|
|
O
|
B:THR457
|
4.4
|
18.0
|
1.0
|
|
H
|
B:PHE452
|
4.4
|
12.1
|
1.0
|
|
OD1
|
B:ASN459
|
4.5
|
11.0
|
1.0
|
|
CA
|
B:ASP451
|
4.5
|
10.8
|
1.0
|
|
CB
|
B:ASP592
|
4.6
|
14.2
|
1.0
|
|
N
|
B:VAL594
|
4.6
|
11.0
|
1.0
|
|
CB
|
B:ASP451
|
4.6
|
10.5
|
1.0
|
|
HG22
|
B:VAL594
|
4.7
|
13.4
|
1.0
|
|
H
|
B:ASP453
|
4.8
|
12.5
|
1.0
|
|
HA
|
B:ILE593
|
4.8
|
11.1
|
1.0
|
|
HG12
|
B:ILE593
|
4.8
|
11.1
|
1.0
|
|
HB2
|
B:PHE452
|
4.9
|
12.8
|
1.0
|
|
CA
|
B:VAL594
|
4.9
|
12.0
|
1.0
|
|
CG2
|
B:VAL594
|
4.9
|
13.4
|
1.0
|
|
HB2
|
B:ASP453
|
5.0
|
10.8
|
1.0
|
|
HB3
|
B:ASP453
|
5.0
|
10.8
|
1.0
|
|
CG1
|
B:ILE593
|
5.0
|
9.2
|
1.0
|
|
Manganese binding site 3 out
of 4 in 1w2z
Go back to
Manganese Binding Sites List in 1w2z
Manganese binding site 3 out
of 4 in the Psao and Xenon
 Mono view
 Stereo pair view
|
|
A full contact list of Manganese with other atoms in the Mn binding
site number 3 of Psao and Xenon within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mn702
b:35.5
occ:1.00
|
O
|
C:PHE452
|
2.3
|
13.6
|
1.0
|
|
OD1
|
C:ASP451
|
2.3
|
11.0
|
1.0
|
|
OD1
|
C:ASP453
|
2.3
|
13.7
|
1.0
|
|
OD1
|
C:ASP592
|
2.4
|
14.3
|
1.0
|
|
O
|
C:ILE593
|
2.4
|
11.3
|
1.0
|
|
O
|
C:HOH2124
|
2.5
|
21.6
|
1.0
|
|
H
|
C:ILE593
|
3.1
|
12.3
|
1.0
|
|
C
|
C:PHE452
|
3.3
|
13.9
|
1.0
|
|
CG
|
C:ASP453
|
3.5
|
12.9
|
1.0
|
|
CG
|
C:ASP451
|
3.5
|
11.6
|
1.0
|
|
CG
|
C:ASP592
|
3.5
|
16.8
|
1.0
|
|
C
|
C:ILE593
|
3.6
|
11.6
|
1.0
|
|
N
|
C:ILE593
|
3.6
|
12.2
|
1.0
|
|
HA
|
C:ASP453
|
3.6
|
11.5
|
1.0
|
|
NZ
|
C:LYS48
|
3.7
|
15.1
|
1.0
|
|
HA
|
C:ASP592
|
3.8
|
14.6
|
1.0
|
|
N
|
C:ASP453
|
4.0
|
12.8
|
1.0
|
|
C
|
C:ASP451
|
4.1
|
11.4
|
1.0
|
|
HA
|
C:ASP451
|
4.1
|
10.9
|
1.0
|
|
OD2
|
C:ASP592
|
4.1
|
17.0
|
1.0
|
|
N
|
C:PHE452
|
4.1
|
12.2
|
1.0
|
|
OD2
|
C:ASP451
|
4.1
|
13.9
|
1.0
|
|
CA
|
C:ASP453
|
4.1
|
11.3
|
1.0
|
|
OD2
|
C:ASP453
|
4.2
|
12.7
|
1.0
|
|
CA
|
C:ILE593
|
4.2
|
10.8
|
1.0
|
|
HG21
|
C:VAL594
|
4.2
|
13.6
|
1.0
|
|
C
|
C:ASP592
|
4.3
|
14.9
|
1.0
|
|
O
|
C:ASP451
|
4.3
|
11.3
|
1.0
|
|
HA
|
C:THR457
|
4.3
|
13.2
|
1.0
|
|
CA
|
C:ASP592
|
4.4
|
14.7
|
1.0
|
|
CA
|
C:PHE452
|
4.4
|
12.6
|
1.0
|
|
H
|
C:PHE452
|
4.4
|
12.1
|
1.0
|
|
HA
|
C:VAL594
|
4.4
|
11.8
|
1.0
|
|
HB2
|
C:TYR557
|
4.4
|
16.4
|
1.0
|
|
CB
|
C:ASP453
|
4.4
|
10.0
|
1.0
|
|
HG13
|
C:ILE593
|
4.4
|
11.1
|
1.0
|
|
O
|
C:THR457
|
4.4
|
17.7
|
1.0
|
|
CA
|
C:ASP451
|
4.5
|
11.0
|
1.0
|
|
OD1
|
C:ASN459
|
4.5
|
9.2
|
1.0
|
|
CB
|
C:ASP592
|
4.6
|
17.0
|
1.0
|
|
CB
|
C:ASP451
|
4.6
|
12.2
|
1.0
|
|
N
|
C:VAL594
|
4.7
|
11.2
|
1.0
|
|
H
|
C:ASP453
|
4.7
|
12.5
|
1.0
|
|
HB2
|
C:PHE452
|
4.8
|
12.7
|
1.0
|
|
HA
|
C:ILE593
|
4.8
|
11.1
|
1.0
|
|
HG12
|
C:ILE593
|
4.8
|
11.1
|
1.0
|
|
HG22
|
C:VAL594
|
4.9
|
13.6
|
1.0
|
|
CG2
|
C:VAL594
|
5.0
|
15.8
|
1.0
|
|
CA
|
C:VAL594
|
5.0
|
11.5
|
1.0
|
|
Manganese binding site 4 out
of 4 in 1w2z
Go back to
Manganese Binding Sites List in 1w2z
Manganese binding site 4 out
of 4 in the Psao and Xenon
 Mono view
 Stereo pair view
|
|
A full contact list of Manganese with other atoms in the Mn binding
site number 4 of Psao and Xenon within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Mn702
b:36.8
occ:1.00
|
O
|
D:PHE452
|
2.2
|
13.6
|
1.0
|
|
OD1
|
D:ASP453
|
2.3
|
13.4
|
1.0
|
|
OD1
|
D:ASP451
|
2.3
|
9.2
|
1.0
|
|
OD1
|
D:ASP592
|
2.4
|
12.6
|
1.0
|
|
O
|
D:ILE593
|
2.5
|
11.3
|
1.0
|
|
O
|
D:HOH2145
|
2.6
|
24.9
|
1.0
|
|
H
|
D:ILE593
|
3.1
|
12.3
|
1.0
|
|
C
|
D:PHE452
|
3.3
|
13.5
|
1.0
|
|
CG
|
D:ASP453
|
3.5
|
8.3
|
1.0
|
|
CG
|
D:ASP451
|
3.5
|
11.2
|
1.0
|
|
HA
|
D:ASP453
|
3.5
|
11.5
|
1.0
|
|
C
|
D:ILE593
|
3.6
|
11.4
|
1.0
|
|
N
|
D:ILE593
|
3.6
|
11.9
|
1.0
|
|
CG
|
D:ASP592
|
3.6
|
16.3
|
1.0
|
|
HA
|
D:ASP592
|
3.7
|
14.6
|
1.0
|
|
NZ
|
D:LYS48
|
3.9
|
15.9
|
1.0
|
|
N
|
D:ASP453
|
4.0
|
12.6
|
1.0
|
|
CA
|
D:ASP453
|
4.1
|
11.2
|
1.0
|
|
HA
|
D:ASP451
|
4.1
|
10.9
|
1.0
|
|
C
|
D:ASP451
|
4.1
|
11.6
|
1.0
|
|
OD2
|
D:ASP451
|
4.1
|
12.5
|
1.0
|
|
N
|
D:PHE452
|
4.2
|
12.2
|
1.0
|
|
CA
|
D:ILE593
|
4.2
|
10.7
|
1.0
|
|
OD2
|
D:ASP453
|
4.2
|
10.2
|
1.0
|
|
HG21
|
D:VAL594
|
4.2
|
13.4
|
1.0
|
|
OD2
|
D:ASP592
|
4.3
|
18.5
|
1.0
|
|
C
|
D:ASP592
|
4.3
|
14.7
|
1.0
|
|
HA
|
D:THR457
|
4.3
|
13.2
|
1.0
|
|
O
|
D:ASP451
|
4.3
|
11.8
|
1.0
|
|
CA
|
D:ASP592
|
4.3
|
14.8
|
1.0
|
|
HG13
|
D:ILE593
|
4.4
|
11.0
|
1.0
|
|
CB
|
D:ASP453
|
4.4
|
10.2
|
1.0
|
|
CA
|
D:PHE452
|
4.4
|
12.9
|
1.0
|
|
HB2
|
D:TYR557
|
4.4
|
16.6
|
1.0
|
|
HA
|
D:VAL594
|
4.4
|
11.8
|
1.0
|
|
H
|
D:PHE452
|
4.4
|
12.1
|
1.0
|
|
O
|
D:THR457
|
4.5
|
18.3
|
1.0
|
|
CA
|
D:ASP451
|
4.5
|
10.7
|
1.0
|
|
CB
|
D:ASP592
|
4.6
|
14.1
|
1.0
|
|
CB
|
D:ASP451
|
4.6
|
10.8
|
1.0
|
|
HG22
|
D:VAL594
|
4.6
|
13.4
|
1.0
|
|
N
|
D:VAL594
|
4.7
|
10.8
|
1.0
|
|
OD1
|
D:ASN459
|
4.7
|
13.7
|
1.0
|
|
H
|
D:ASP453
|
4.7
|
12.5
|
1.0
|
|
HG12
|
D:ILE593
|
4.8
|
11.0
|
1.0
|
|
HA
|
D:ILE593
|
4.9
|
11.1
|
1.0
|
|
CG2
|
D:VAL594
|
4.9
|
12.3
|
1.0
|
|
HB2
|
D:PHE452
|
4.9
|
12.7
|
1.0
|
|
HB3
|
D:ASP453
|
5.0
|
10.7
|
1.0
|
|
CG1
|
D:ILE593
|
5.0
|
10.6
|
1.0
|
|
HB2
|
D:ASP453
|
5.0
|
10.7
|
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: Sat Oct 5 12:53:16 2024
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