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Xenon in PDB 1rjo: Agao + Xe

Enzymatic activity of Agao + Xe

All present enzymatic activity of Agao + Xe:
1.4.3.6;

Protein crystallography data

The structure of Agao + Xe, PDB code: 1rjo was solved by J.M.Guss, D.M.Trambaiolo, A.P.Duff, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 26.30 / 1.67
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 158.009, 63.189, 92.149, 90.00, 112.09, 90.00
R / Rfree (%) 15.7 / 17.8

Other elements in 1rjo:

The structure of Agao + Xe also contains other interesting chemical elements:

Copper (Cu) 1 atom
Sodium (Na) 1 atom

Xenon Binding Sites:

The binding sites of Xenon atom in the Agao + Xe (pdb code 1rjo). This binding sites where shown within 5.0 Angstroms radius around Xenon atom.
In total 7 binding sites of Xenon where determined in the Agao + Xe, PDB code: 1rjo:
Jump to Xenon binding site number: 1; 2; 3; 4; 5; 6; 7;

Xenon binding site 1 out of 7 in 1rjo

Go back to Xenon Binding Sites List in 1rjo
Xenon binding site 1 out of 7 in the Agao + Xe


Mono view


Stereo pair view

A full contact list of Xenon with other atoms in the Xe binding site number 1 of Agao + Xe within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Xe901

b:28.3
occ:0.30
CD2 A:LEU245 3.0 22.0 1.0
CD1 A:LEU390 3.6 19.1 1.0
CG2 A:ILE238 3.6 22.5 1.0
CB A:TRP243 3.8 14.5 1.0
CB A:ILE238 3.8 19.1 1.0
CB A:TRP240 4.0 11.4 1.0
O A:ILE238 4.0 15.8 1.0
O A:TRP243 4.1 13.3 1.0
C A:ILE238 4.2 15.1 1.0
N A:TRP240 4.2 14.5 1.0
C A:TRP243 4.2 14.8 1.0
CG A:LEU245 4.3 19.7 1.0
CG A:MET371 4.4 15.7 1.0
CA A:SER244 4.5 17.0 1.0
N A:SER244 4.5 14.8 1.0
N A:GLU239 4.5 14.8 1.0
C A:GLU239 4.6 16.3 1.0
N A:LEU245 4.6 14.0 1.0
CA A:GLU239 4.6 16.4 1.0
CD1 A:LEU245 4.6 21.2 1.0
CA A:TRP240 4.7 13.1 1.0
C A:SER244 4.7 16.5 1.0
CA A:ILE238 4.7 14.1 1.0
O A:TRP240 4.7 12.9 1.0
CA A:TRP243 4.7 13.2 1.0
CG A:TRP243 4.8 13.5 1.0
CG1 A:ILE238 4.9 21.8 1.0
CB A:MET371 5.0 14.6 1.0

Xenon binding site 2 out of 7 in 1rjo

Go back to Xenon Binding Sites List in 1rjo
Xenon binding site 2 out of 7 in the Agao + Xe


Mono view


Stereo pair view

A full contact list of Xenon with other atoms in the Xe binding site number 2 of Agao + Xe within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Xe902

b:22.2
occ:0.20
CD1 A:LEU590 2.5 20.6 0.5
CB A:ALA402 3.4 18.2 1.0
CG A:LEU590 3.6 17.5 0.5
CD2 A:LEU590 3.7 24.4 0.5
CG1 A:VAL607 3.8 17.4 1.0
N A:ALA402 3.8 14.1 1.0
O A:ALA400 3.9 14.1 1.0
O A:ASP605 3.9 15.6 1.0
CE1 A:PHE435 4.0 14.9 1.0
CA A:ALA402 4.2 15.1 1.0
CB A:ALA400 4.2 16.8 1.0
C A:ALA400 4.2 15.3 1.0
CZ A:PHE435 4.2 17.2 1.0
N A:VAL607 4.2 15.3 1.0
C A:THR606 4.4 16.3 1.0
C A:LYS401 4.5 15.9 1.0
CA A:THR606 4.5 15.1 1.0
CB A:LEU590 4.5 20.7 0.5
CB A:LEU590 4.5 18.0 0.5
C A:ASP605 4.6 16.0 1.0
CB A:VAL607 4.6 17.3 1.0
CG A:LEU590 4.7 23.9 0.5
N A:LYS401 4.7 15.2 1.0
CD2 A:LEU590 4.7 20.9 0.5
CA A:LYS401 4.8 15.1 1.0
N A:THR606 4.8 14.7 1.0
CA A:ALA400 4.9 14.4 1.0
CB A:HIS433 4.9 13.5 1.0

Xenon binding site 3 out of 7 in 1rjo

Go back to Xenon Binding Sites List in 1rjo
Xenon binding site 3 out of 7 in the Agao + Xe


Mono view


Stereo pair view

A full contact list of Xenon with other atoms in the Xe binding site number 3 of Agao + Xe within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Xe903

b:39.0
occ:0.40
CD A:ARG71 3.4 27.4 1.0
O A:LEU90 3.9 12.1 1.0
CB A:ASP91 4.0 12.3 1.0
N A:ASP91 4.0 9.3 1.0
C A:LEU90 4.0 12.5 1.0
NE A:ARG71 4.0 30.3 1.0
CA A:ASP91 4.2 10.3 1.0
O A:GLU89 4.2 12.4 1.0
O A:HOH1509 4.2 43.0 1.0
CB A:GLU89 4.3 19.8 1.0
OE1 A:GLU89 4.3 25.6 1.0
C A:GLU89 4.4 15.4 1.0
N A:LEU90 4.7 13.3 1.0
CG A:ARG71 4.7 24.1 1.0
CG A:ASP91 4.8 14.0 1.0
CA A:LEU90 4.8 12.0 1.0
CZ A:ARG71 4.8 32.7 1.0
CB A:ARG71 4.9 21.6 1.0
OD2 A:ASP91 5.0 16.3 1.0
O A:HOH1496 5.0 42.9 1.0

Xenon binding site 4 out of 7 in 1rjo

Go back to Xenon Binding Sites List in 1rjo
Xenon binding site 4 out of 7 in the Agao + Xe


Mono view


Stereo pair view

A full contact list of Xenon with other atoms in the Xe binding site number 4 of Agao + Xe within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Xe904

b:20.0
occ:0.15
CD1 A:ILE373 3.4 24.4 1.0
O A:TRP388 3.4 14.4 1.0
CG A:LEU390 3.5 16.9 1.0
CG1 A:ILE373 3.6 20.0 1.0
O A:MET371 3.7 15.4 1.0
CD1 A:LEU390 3.7 19.1 1.0
C A:TRP388 3.8 12.6 1.0
CB A:ILE373 3.9 15.6 1.0
N A:LEU390 4.0 12.9 1.0
N A:ILE373 4.0 13.2 1.0
CB A:TRP388 4.1 14.1 1.0
N A:TYR389 4.1 13.2 1.0
C A:TYR389 4.2 14.9 1.0
CG A:MET371 4.2 15.7 1.0
CA A:TYR389 4.2 13.3 1.0
C A:MET371 4.2 15.2 1.0
CB A:LEU390 4.4 15.5 1.0
CD2 A:LEU390 4.5 19.0 1.0
CB A:MET371 4.5 14.6 1.0
C A:VAL372 4.5 15.0 1.0
CD1 A:LEU257 4.6 14.8 1.0
CA A:TRP388 4.6 11.7 1.0
CD1 A:LEU245 4.6 21.2 1.0
CA A:ILE373 4.6 13.4 1.0
N A:VAL372 4.7 13.7 1.0
CA A:VAL372 4.7 13.7 1.0
CA A:LEU390 4.8 14.0 1.0
O A:TYR389 4.8 12.8 1.0

Xenon binding site 5 out of 7 in 1rjo

Go back to Xenon Binding Sites List in 1rjo
Xenon binding site 5 out of 7 in the Agao + Xe


Mono view


Stereo pair view

A full contact list of Xenon with other atoms in the Xe binding site number 5 of Agao + Xe within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Xe905

b:30.1
occ:0.15
CD1 A:LEU42 3.2 17.9 1.0
CA A:GLY333 3.5 13.8 1.0
CD1 A:ILE39 3.6 26.9 1.0
N A:GLN24 3.6 14.7 1.0
CG1 A:VAL23 3.7 14.3 1.0
CA A:GLN24 3.8 13.4 1.0
O A:ILE20 3.9 13.5 1.0
O A:GLY333 3.9 12.8 1.0
CB A:VAL23 4.0 15.3 1.0
CB A:GLN24 4.0 13.9 1.0
OG A:SER329 4.0 13.0 1.0
C A:VAL23 4.1 13.3 1.0
CD1 A:LEU27 4.2 14.8 1.0
C A:GLY333 4.2 14.2 1.0
CG1 A:ILE39 4.3 22.7 1.0
CG2 A:ILE20 4.6 15.3 1.0
O A:VAL23 4.7 12.9 1.0
CG A:LEU42 4.7 16.0 1.0
CB A:SER329 4.7 13.4 1.0
CA A:VAL23 4.7 13.9 1.0
N A:GLY333 4.7 12.6 1.0
CG A:GLN24 4.8 13.9 1.0
C A:ILE20 4.9 12.7 1.0

Xenon binding site 6 out of 7 in 1rjo

Go back to Xenon Binding Sites List in 1rjo
Xenon binding site 6 out of 7 in the Agao + Xe


Mono view


Stereo pair view

A full contact list of Xenon with other atoms in the Xe binding site number 6 of Agao + Xe within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Xe909

b:48.6
occ:0.20
O A:HOH1261 3.2 28.3 1.0
O A:VAL327 3.5 15.0 1.0
CD2 A:LEU42 3.5 17.9 1.0
CB A:ALA15 3.8 17.3 1.0
O A:LEU42 3.9 15.9 1.0
CD1 A:ILE20 3.9 22.4 1.0
O A:HOH1232 4.1 27.0 1.0
CA A:ILE328 4.2 15.5 1.0
CG1 A:ILE20 4.2 19.0 1.0
CE2 A:PHE60 4.4 16.8 1.0
CA A:GLY43 4.4 15.4 1.0
C A:VAL327 4.4 16.1 1.0
C A:LEU42 4.5 15.5 1.0
O A:HOH1330 4.6 33.7 1.0
O A:HOH1403 4.7 39.4 1.0
N A:SER329 4.8 14.0 1.0
N A:ILE328 4.8 16.1 1.0
N A:GLY43 4.8 15.3 1.0
C A:ILE328 4.8 16.6 1.0
CG A:LEU42 4.9 16.0 1.0
N A:VAL44 4.9 18.5 1.0
CD2 A:PHE60 4.9 16.0 1.0
CB A:ILE328 5.0 15.9 1.0
CG2 A:ILE328 5.0 16.7 1.0

Xenon binding site 7 out of 7 in 1rjo

Go back to Xenon Binding Sites List in 1rjo
Xenon binding site 7 out of 7 in the Agao + Xe


Mono view


Stereo pair view

A full contact list of Xenon with other atoms in the Xe binding site number 7 of Agao + Xe within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Xe910

b:61.8
occ:0.30
O A:HOH1746 2.0 39.6 0.7
O A:HOH1583 3.2 45.5 1.0
CA A:GLY380 3.9 16.4 1.0
CD A:PRO136 4.1 21.9 1.0
CH2 A:TRP168 4.4 15.0 1.0
CZ2 A:TRP168 4.5 13.7 1.0
O A:HOH1603 4.6 41.4 1.0
C A:GLY380 4.7 15.2 1.0
CA A:ALA135 4.8 16.9 1.0
N A:GLY380 5.0 17.6 1.0
CG A:PRO136 5.0 23.3 1.0
CB A:ALA135 5.0 18.8 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: Wed Dec 16 02:39:23 2020

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