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Xenon in PDB 1rky: Pplo + Xe

Enzymatic activity of Pplo + Xe

All present enzymatic activity of Pplo + Xe:
1.4.3.13;

Protein crystallography data

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

Resolution Low / High (Å) 31.47 / 1.68
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 140.144, 66.702, 108.620, 90.00, 119.24, 90.00
R / Rfree (%) 15.1 / 18.2

Other elements in 1rky:

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

Magnesium (Mg) 3 atoms
Calcium (Ca) 2 atoms
Chlorine (Cl) 6 atoms
Copper (Cu) 1 atom

Xenon Binding Sites:

The binding sites of Xenon atom in the Pplo + Xe (pdb code 1rky). This binding sites where shown within 5.0 Angstroms radius around Xenon atom.
In total 8 binding sites of Xenon where determined in the Pplo + Xe, PDB code: 1rky:
Jump to Xenon binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Xenon binding site 1 out of 8 in 1rky

Go back to Xenon Binding Sites List in 1rky
Xenon binding site 1 out of 8 in the Pplo + Xe


Mono view


Stereo pair view

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

b:27.8
occ:0.63
 CD1 A:ILE371 2.3 27.6 0.4
CG1 A:ILE371 3.5 19.4 0.4
CG2 A:ILE371 3.9 23.7 0.6
CE2 A:TYR612 3.9 21.2 1.0
CG2 A:VAL372 3.9 25.8 1.0
CH2 A:TRP347 4.0 24.6 1.0
CB A:LEU492 4.0 22.9 1.0
CZ3 A:TRP347 4.0 23.1 1.0
CB A:LEU715 4.2 19.3 1.0
CD1 A:LEU715 4.2 22.2 1.0
CD2 A:LEU492 4.3 37.2 1.0
CB A:ILE371 4.3 25.9 0.6
O A:GLY490 4.3 20.6 1.0
CB A:ILE371 4.4 24.7 0.4
CD2 A:TYR612 4.4 19.7 1.0
CZ A:TYR612 4.5 23.7 1.0
OH A:TYR612 4.6 24.0 1.0
CD1 A:ILE371 4.7 47.9 0.6
O A:LEU715 4.8 22.3 1.0
CG2 A:ILE364 4.8 23.7 1.0
CG A:LEU492 4.8 30.7 1.0
N A:LEU492 4.8 20.7 1.0
CG A:LEU715 4.9 24.9 1.0

Xenon binding site 2 out of 8 in 1rky

Go back to Xenon Binding Sites List in 1rky
Xenon binding site 2 out of 8 in the Pplo + Xe


Mono view


Stereo pair view

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

b:41.1
occ:0.72
 O A:THR276 3.5 40.3 1.0
CE1 A:TYR268 3.6 42.7 1.0
C A:THR276 3.6 35.7 1.0
O A:MET265 3.6 39.2 1.0
C A:LEU266 3.7 42.6 1.0
CD1 A:TYR268 3.7 40.2 1.0
N A:GLU267 3.7 36.1 1.0
O A:LEU266 3.7 33.1 1.0
N A:SER277 3.8 39.6 1.0
CA A:SER277 3.8 42.0 1.0
CG A:MET265 3.8 42.0 1.0
C A:MET265 3.9 41.0 1.0
CA A:GLU267 3.9 31.1 1.0
C A:GLU267 4.0 30.7 1.0
CB A:MET265 4.1 30.4 1.0
N A:LEU266 4.2 30.3 1.0
O A:TYR275 4.2 35.8 1.0
CA A:THR276 4.3 33.8 1.0
N A:TYR268 4.3 30.3 1.0
CZ A:TYR268 4.3 40.4 1.0
CA A:LEU266 4.4 27.8 1.0
C A:SER277 4.4 30.0 1.0
O A:GLU267 4.5 32.1 1.0
CG A:TYR268 4.5 42.1 1.0
N A:ALA278 4.6 35.0 1.0
CA A:MET265 4.7 30.9 1.0
OH A:TYR268 4.9 36.6 1.0

Xenon binding site 3 out of 8 in 1rky

Go back to Xenon Binding Sites List in 1rky
Xenon binding site 3 out of 8 in the Pplo + Xe


Mono view


Stereo pair view

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

b:34.7
occ:0.52
 XE A:XE908 2.1 39.2 0.2
XE A:XE907 3.1 39.7 0.1
O A:ALA709 3.8 28.1 1.0
C A:ALA709 4.0 30.6 1.0
O A:VAL496 4.1 21.1 1.0
CG1 A:VAL496 4.1 24.2 1.0
N A:HIS710 4.2 25.4 1.0
CB A:LEU692 4.2 28.7 1.0
CB A:ALA498 4.3 28.4 1.0
N A:ALA498 4.4 22.5 1.0
C A:HIS710 4.4 26.6 1.0
CA A:HIS710 4.4 26.3 1.0
CD2 A:LEU692 4.5 32.9 1.0
N A:ALA711 4.5 23.4 1.0
CB A:ALA711 4.5 21.0 1.0
CA A:ARG497 4.5 21.8 1.0
C A:VAL496 4.5 24.6 1.0
C A:ARG497 4.6 23.7 1.0
CG2 A:VAL496 4.8 26.0 1.0
N A:ARG497 4.8 20.7 1.0
CA A:ALA709 4.9 28.2 1.0
O A:HIS710 4.9 24.0 1.0
CG A:LEU692 4.9 35.6 1.0
CB A:ALA709 4.9 28.8 1.0
CD1 A:LEU532 5.0 34.4 0.8
CB A:VAL496 5.0 24.2 1.0
CA A:ALA498 5.0 29.2 1.0

Xenon binding site 4 out of 8 in 1rky

Go back to Xenon Binding Sites List in 1rky
Xenon binding site 4 out of 8 in the Pplo + Xe


Mono view


Stereo pair view

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

b:38.3
occ:0.38
 O A:HOH2634 1.7 38.0 0.6
O A:TYR413 3.6 28.8 1.0
O A:HOH2177 3.8 32.3 1.0
O A:ASP414 3.9 27.7 1.0
C A:CYS415 4.0 31.3 1.0
N A:PRO416 4.0 28.1 1.0
CA A:CYS415 4.0 31.8 1.0
NH1 A:ARG470 4.0 26.1 1.0
CD A:PRO416 4.0 28.6 1.0
C A:ASP414 4.1 28.3 1.0
N A:CYS415 4.2 26.9 1.0
O A:HOH2425 4.3 43.7 1.0
O A:HOH2016 4.4 23.2 1.0
C A:TYR413 4.4 27.3 1.0
CG A:PRO416 4.5 35.7 1.0
O A:CYS415 4.6 27.7 1.0
O A:HOH2454 4.8 44.6 1.0
CA A:PRO416 4.8 28.1 1.0
CA A:ASP414 5.0 22.1 1.0

Xenon binding site 5 out of 8 in 1rky

Go back to Xenon Binding Sites List in 1rky
Xenon binding site 5 out of 8 in the Pplo + Xe


Mono view


Stereo pair view

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

b:38.9
occ:0.40
 OE1 A:GLN549 3.8 49.9 1.0
CD A:PRO588 3.9 28.1 1.0
O A:HOH2345 4.0 38.2 1.0
CB A:LEU595 4.0 19.4 1.0
N A:LEU595 4.0 21.7 1.0
O A:HOH2325 4.1 40.5 1.0
C A:ILE594 4.1 28.7 1.0
CG A:PRO588 4.2 29.7 1.0
C A:GLY593 4.2 29.1 1.0
N A:ILE594 4.3 21.4 1.0
CA A:LEU595 4.3 17.1 1.0
CB A:GLN549 4.3 27.5 1.0
O A:ILE594 4.4 26.8 1.0
CA A:GLY593 4.5 25.7 1.0
O A:GLY593 4.5 24.8 1.0
CE3 A:TRP587 4.6 24.5 1.0
CA A:ILE594 4.7 22.9 1.0
O A:HOH2415 4.7 45.7 1.0
CZ3 A:TRP587 4.8 26.4 1.0
CD1 A:LEU595 4.8 25.4 1.0
CD A:GLN549 4.9 54.7 1.0
CB A:PRO588 4.9 30.3 1.0
CG2 A:ILE585 4.9 31.7 1.0
CG A:LEU595 4.9 26.2 1.0
O A:HOH2020 5.0 22.9 1.0

Xenon binding site 6 out of 8 in 1rky

Go back to Xenon Binding Sites List in 1rky
Xenon binding site 6 out of 8 in the Pplo + Xe


Mono view


Stereo pair view

A full contact list of Xenon with other atoms in the Xe binding site number 6 of Pplo + Xe within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Xe906

b:43.9
occ:0.34
 NZ A:LYS66 3.6 69.4 1.0
CG1 A:VAL69 3.7 34.8 1.0
OE1 A:GLN70 3.7 48.4 1.0
N A:GLN70 3.9 33.8 1.0
O A:LYS66 4.0 31.8 1.0
CA A:GLN70 4.1 30.7 1.0
CB A:VAL69 4.1 30.1 1.0
CB A:PHE432 4.2 33.8 1.0
CB A:GLN70 4.2 37.7 1.0
CD A:GLN70 4.3 37.9 1.0
CG A:LYS66 4.3 40.6 1.0
C A:VAL69 4.4 30.7 1.0
CE2 A:PHE427 4.4 32.3 1.0
O A:HOH2562 4.4 62.4 1.0
CD2 A:PHE427 4.6 34.3 1.0
CE A:LYS66 4.8 63.3 1.0
CD2 A:PHE432 4.8 40.4 1.0
O A:VAL69 4.9 31.9 1.0
CG A:PHE432 4.9 30.6 1.0
CG A:GLN70 4.9 36.5 1.0
CA A:VAL69 4.9 29.4 1.0
NE2 A:GLN70 4.9 42.5 1.0
CD2 A:LEU73 4.9 48.2 1.0
N A:PHE432 4.9 29.5 1.0
C A:LYS66 5.0 27.2 1.0

Xenon binding site 7 out of 8 in 1rky

Go back to Xenon Binding Sites List in 1rky
Xenon binding site 7 out of 8 in the Pplo + Xe


Mono view


Stereo pair view

A full contact list of Xenon with other atoms in the Xe binding site number 7 of Pplo + Xe within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Xe907

b:39.7
occ:0.15
 CD1 A:LEU532 2.3 34.4 0.8
XE A:XE908 2.5 39.2 0.2
XE A:XE903 3.1 34.7 0.5
CA A:GLY691 3.5 27.5 1.0
C A:GLY691 3.8 23.7 1.0
O A:LEU690 3.8 23.7 1.0
CG A:LEU532 3.8 36.0 0.8
N A:GLY691 3.9 22.6 1.0
CB A:HIS530 3.9 25.9 1.0
CG1 A:VAL496 3.9 24.2 1.0
C A:LEU690 4.0 23.0 1.0
O A:HIS530 4.1 23.5 1.0
N A:LEU692 4.1 19.2 1.0
C A:HIS530 4.3 20.0 1.0
O A:GLY691 4.3 24.6 1.0
CD2 A:LEU532 4.5 34.6 0.8
CB A:ALA711 4.5 21.0 1.0
N A:LEU532 4.6 18.9 1.0
CB A:LEU692 4.6 28.7 1.0
CB A:LEU532 4.7 26.2 1.0
CB A:LEU690 4.7 18.9 1.0
N A:VAL531 4.7 20.7 1.0
CA A:VAL531 4.8 19.8 1.0
CA A:HIS530 4.8 20.2 1.0
CG A:HIS530 4.9 27.9 1.0
C A:VAL531 4.9 21.1 1.0

Xenon binding site 8 out of 8 in 1rky

Go back to Xenon Binding Sites List in 1rky
Xenon binding site 8 out of 8 in the Pplo + Xe


Mono view


Stereo pair view

A full contact list of Xenon with other atoms in the Xe binding site number 8 of Pplo + Xe within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Xe908

b:39.2
occ:0.21
 XE A:XE903 2.1 34.7 0.5
XE A:XE907 2.5 39.7 0.1
CD1 A:LEU532 3.8 34.4 0.8
CB A:ALA498 3.9 28.4 1.0
CB A:HIS530 3.9 25.9 1.0
CG A:HIS530 4.2 27.9 1.0
CE1 A:TYR480 4.2 38.2 1.0
CG1 A:VAL496 4.3 24.2 1.0
CG2 A:VAL496 4.3 26.0 1.0
CD1 A:TYR480 4.4 40.3 1.0
ND1 A:HIS530 4.5 29.6 1.0
CD2 A:HIS530 4.7 31.8 1.0
N A:ALA498 4.8 22.5 1.0
CB A:LEU692 4.9 28.7 1.0
CA A:ALA498 4.9 29.2 1.0
CG A:LEU532 4.9 36.0 0.8
C A:ARG497 4.9 23.7 1.0
CB A:VAL496 5.0 24.2 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 12 17:59:04 2024

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