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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:

Xenon (Xe) 8 atoms
Iodine (I) 176 atoms
Copper (Cu) 4 atoms

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: Tue Dec 15 03:57:17 2020

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