Chlorine in PDB 1rky: Pplo + Xe

All present enzymatic activity of Pplo + Xe:
1.4.3.13;

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

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

Magnesium	(Mg)	3 atoms
Xenon	(Xe)	8 atoms
Calcium	(Ca)	2 atoms
Copper	(Cu)	1 atom

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

Chlorine binding site 1 out of 6 in the Pplo + Xe


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Pplo + Xe within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl811 b:40.5 occ:1.00 O A:HOH2200 3.1 39.7 1.0 O A:HOH2461 3.1 43.1 1.0 O A:HOH2489 3.3 54.2 1.0 N A:ASP665 3.3 28.6 1.0 N A:TYR664 3.3 27.4 1.0 N A:LEU663 3.7 27.1 1.0 CA A:TYR664 3.9 25.9 1.0 C A:ALA662 3.9 25.8 1.0 CB A:TYR664 3.9 31.2 1.0 CG1 A:VAL171 4.0 36.5 1.0 CB A:ASP665 4.0 31.6 1.0 C A:TYR664 4.0 28.6 1.0 CA A:ASP665 4.2 30.8 1.0 CA A:ALA662 4.2 25.8 1.0 CG A:PRO222 4.2 51.4 1.0 C A:LEU663 4.4 27.2 1.0 O A:ALA662 4.4 27.2 1.0 CD1 A:TYR664 4.5 34.2 1.0 CA A:LEU663 4.5 23.8 1.0 O A:HOH2315 4.6 51.5 1.0 C A:ASP665 4.6 30.9 1.0 CB A:ALA662 4.7 26.6 1.0 CD2 A:HIS220 4.7 33.1 1.0 CG A:TYR664 4.7 28.4 1.0 O A:ASP665 4.8 29.2 1.0 CB A:VAL171 5.0 29.3 1.0 CB A:LEU663 5.0 25.5 1.0

Chlorine binding site 2 out of 6 in the Pplo + Xe


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Pplo + Xe within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl812 b:41.7 occ:1.00 O A:HOH2470 2.9 42.9 1.0 N A:SER165 3.2 33.0 1.0 N A:LYS166 3.3 31.2 1.0 CB A:LYS164 3.6 30.7 1.0 CA A:LYS164 3.6 25.8 1.0 OG A:SER165 3.6 32.5 1.0 CB A:LYS166 3.8 36.7 1.0 O A:HOH2359 3.8 50.1 1.0 CG A:LYS166 3.8 28.2 1.0 C A:LYS164 3.8 28.5 1.0 CG A:LYS164 4.0 30.8 1.0 CA A:SER165 4.1 31.5 1.0 CA A:LYS166 4.1 32.2 1.0 CD A:LYS166 4.1 31.8 1.0 C A:SER165 4.2 33.1 1.0 CB A:SER165 4.4 32.6 1.0 O A:HOH2241 4.5 39.6 1.0 O A:LYS166 4.5 32.1 1.0 NZ A:LYS166 4.6 64.8 1.0 C A:LYS166 4.8 29.3 1.0 CD A:LYS164 4.8 32.9 1.0 N A:LYS164 4.9 28.8 1.0 O A:GLY163 4.9 34.9 1.0

Chlorine binding site 3 out of 6 in the Pplo + Xe


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Pplo + Xe within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl813 b:43.0 occ:1.00 O A:HOH2107 2.9 29.2 1.0 O A:HOH2233 2.9 36.7 1.0 O A:HOH2485 3.1 52.1 1.0 N A:ASP297 3.2 31.8 1.0 CB A:ASP297 3.8 36.6 1.0 CB A:ASP521 3.9 34.9 0.7 CA A:ILE296 3.9 27.3 1.0 CB A:ASP521 3.9 33.8 0.3 CA A:ASP297 4.0 30.8 1.0 C A:ILE296 4.0 33.8 1.0 ND1 A:HIS520 4.1 30.1 1.0 CG2 A:ILE296 4.1 31.2 1.0 CG2 A:VAL522 4.1 29.1 1.0 CE1 A:HIS520 4.2 29.0 1.0 OD2 A:ASP521 4.3 34.4 0.3 CG A:ASP521 4.4 39.6 0.7 CB A:ILE296 4.5 31.7 1.0 OD2 A:ASP521 4.5 40.6 0.7 CG A:ASP521 4.6 46.0 0.3 O A:ASP297 4.6 34.0 1.0 C A:ASP297 4.7 32.7 1.0 O A:HOH2309 4.7 39.0 1.0 O A:LYS295 4.7 34.9 1.0 O A:HOH2226 4.7 28.4 1.0 N A:VAL522 4.7 27.7 1.0 CA A:ASP521 4.9 30.8 1.0 N A:ASP521 5.0 32.8 1.0

Chlorine binding site 4 out of 6 in the Pplo + Xe


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Pplo + Xe within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl814 b:48.4 occ:0.80 N A:ARG574 3.0 26.6 1.0 CA A:ALA573 3.7 28.4 1.0 C A:ALA573 3.8 25.7 1.0 CB A:ARG574 3.8 28.1 1.0 CA A:ARG574 3.9 24.6 1.0 O A:ARG574 4.3 28.3 1.0 O A:ILE572 4.5 25.8 1.0 CB A:ALA573 4.6 30.5 1.0 C A:ARG574 4.6 32.6 1.0 N A:ALA573 4.6 22.9 1.0 O A:HOH2351 4.9 50.5 1.0 C A:ILE572 4.9 26.7 1.0 O A:ALA573 5.0 27.2 1.0

Chlorine binding site 5 out of 6 in the Pplo + Xe


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Pplo + Xe within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl815 b:46.3 occ:0.80 O A:HOH2606 3.0 52.2 1.0 N A:TYR421 3.2 23.9 1.0 O A:HOH2604 3.6 54.1 1.0 CA A:GLY420 3.7 26.4 1.0 C A:GLY420 3.9 29.8 1.0 CB A:TYR421 3.9 27.9 1.0 O A:TYR421 4.0 27.0 1.0 CD1 A:TYR421 4.0 29.5 1.0 CA A:TYR421 4.0 25.0 1.0 O A:HOH2433 4.2 51.5 1.0 CG A:TYR421 4.4 29.2 1.0 O A:ALA419 4.5 29.6 1.0 C A:TYR421 4.5 27.9 1.0 ND2 A:ASN764 4.8 43.3 1.0 N A:GLY420 4.9 23.5 1.0 NH2 A:ARG331 5.0 30.0 1.0

Chlorine binding site 6 out of 6 in the Pplo + Xe


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Pplo + Xe within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl816 b:49.2 occ:0.50 O A:HOH2499 3.3 52.5 1.0 O A:HOH2008 3.3 46.0 0.5 CG A:ASP259 3.3 41.5 1.0 OD1 A:ASP259 3.5 45.2 1.0 CB A:ASP259 3.6 33.0 1.0 CZ A:PHE91 3.6 30.9 1.0 OD2 A:ASP259 3.7 38.3 1.0 CE1 A:PHE91 3.8 29.3 1.0 CA A:ASP259 3.9 32.2 1.0 O A:HOH2173 4.5 36.2 1.0 CE2 A:PHE91 4.6 32.3 1.0 N A:ASP259 4.7 35.8 1.0 O A:ARG258 4.7 37.9 1.0 O A:HOH2353 4.9 45.3 1.0 CD1 A:PHE91 4.9 34.6 1.0

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