Atomistry » Xenon, Xe » PDB 1c10-1w2z » 1rky
Atomistry »
  Xenon, Xe »
    PDB 1c10-1w2z »
      1rky »

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

Last articles

Zn in 9MJ5
Zn in 9HNW
Zn in 9G0L
Zn in 9FNE
Zn in 9DZN
Zn in 9E0I
Zn in 9D32
Zn in 9DAK
Zn in 8ZXC
Zn in 8ZUF
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy