Xenon in PDB 1ury: Cytoglobin Cavities

The structure of Cytoglobin Cavities, PDB code: 1ury was solved by D.De Sanctis, S.Dewilde, A.Pesce, L.Moens, P.Ascenzi, T.Hankeln, T.Burmester, M.Bolognesi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.88 / 2.4
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	47.848, 70.524, 98.728, 90.00, 90.00, 90.00
R / Rfree (%)	19.702 / 25.442

The structure of Cytoglobin Cavities also contains other interesting chemical elements:

Iron

(Fe)

4 atoms

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

Xenon binding site 1 out of 7 in the Cytoglobin Cavities


Mono view


Stereo pair view

A full contact list of Xenon with other atoms in the Xe binding site number 1 of Cytoglobin Cavities within 5.0Å range: probe atom residue distance (Å) B Occ A:Xe1172 b:34.1 occ:1.00 O A:GLY42 3.6 23.9 1.0 CG2 A:ILE45 3.6 18.0 1.0 CE A:MET86 3.6 33.4 1.0 CG1 A:VAL85 3.8 21.7 1.0 CA A:GLY42 4.0 24.0 1.0 CB A:ILE45 4.0 18.6 1.0 CB A:VAL85 4.1 21.7 1.0 C A:GLY42 4.2 23.4 1.0 CG A:MET86 4.2 25.2 1.0 CD1 A:ILE45 4.3 19.1 1.0 CG A:LEU46 4.3 20.5 1.0 SD A:MET86 4.4 31.1 1.0 O A:ALA82 4.5 22.2 1.0 CD2 A:LEU46 4.6 20.9 1.0 CG2 A:VAL85 4.7 21.0 1.0 CA A:ALA82 4.8 22.0 1.0 CG1 A:ILE45 4.8 18.4 1.0 N A:MET86 4.9 22.4 1.0 CD1 A:LEU46 5.0 20.3 1.0 CB A:ALA82 5.0 22.1 1.0 N A:LEU46 5.0 19.1 1.0

Xenon binding site 2 out of 7 in the Cytoglobin Cavities


Mono view


Stereo pair view

A full contact list of Xenon with other atoms in the Xe binding site number 2 of Cytoglobin Cavities within 5.0Å range: probe atom residue distance (Å) B Occ A:Xe1173 b:60.3 occ:0.50 CE A:MET86 3.4 33.4 1.0 CD1 A:LEU34 3.5 39.8 1.0 CD1 A:ILE45 3.5 19.1 1.0 CZ3 A:TRP31 3.5 25.3 1.0 CG2 A:ILE131 3.7 16.9 1.0 SD A:MET86 4.1 31.1 1.0 CH2 A:TRP31 4.3 25.4 1.0 CG1 A:VAL41 4.3 26.3 1.0 CE3 A:TRP31 4.4 27.0 1.0 CG2 A:VAL135 4.4 22.2 1.0 CG1 A:ILE131 4.7 15.6 1.0 CB A:ILE131 4.8 16.9 1.0 CG A:LEU34 4.8 37.5 1.0 CG1 A:ILE45 5.0 18.4 1.0 CD2 A:LEU34 5.0 39.8 1.0

Xenon binding site 3 out of 7 in the Cytoglobin Cavities


Mono view


Stereo pair view

A full contact list of Xenon with other atoms in the Xe binding site number 3 of Cytoglobin Cavities within 5.0Å range: probe atom residue distance (Å) B Occ A:Xe1174 b:56.7 occ:0.60 CD1 A:LEU89 3.6 26.9 1.0 CD2 A:LEU154 3.9 22.6 1.0 CZ3 A:TRP151 3.9 22.0 1.0 XE A:XE1176 4.0 35.9 1.0 CZ3 A:TRP31 4.1 25.3 1.0 CB A:LEU89 4.1 24.1 1.0 CG2 A:VAL93 4.2 27.1 1.0 CG A:LEU89 4.2 26.3 1.0 CD1 A:ILE158 4.3 27.6 1.0 CH2 A:TRP151 4.5 22.3 1.0 CE3 A:TRP31 4.5 27.0 1.0 CG A:LEU154 4.6 23.8 1.0 CD2 A:LEU89 4.6 26.0 1.0 CH2 A:TRP31 4.8 25.4 1.0 CG2 A:ILE131 4.8 16.9 1.0 CE3 A:TRP151 4.8 21.1 1.0

Xenon binding site 4 out of 7 in the Cytoglobin Cavities


Mono view


Stereo pair view

A full contact list of Xenon with other atoms in the Xe binding site number 4 of Cytoglobin Cavities within 5.0Å range: probe atom residue distance (Å) B Occ A:Xe1176 b:35.9 occ:1.00 CG2 A:ILE131 3.9 16.9 1.0 XE A:XE1174 4.0 56.7 0.6 CB A:ARG155 4.0 24.2 1.0 CA A:ARG155 4.1 24.0 1.0 CG A:ARG155 4.1 24.6 1.0 CD1 A:ILE158 4.3 27.6 1.0 CD2 A:LEU132 4.3 27.9 1.0 CB A:ILE131 4.3 16.9 1.0 O A:SER128 4.3 14.8 1.0 OG A:SER128 4.3 19.9 1.0 CD1 A:ILE131 4.4 17.5 1.0 CB A:SER128 4.5 16.6 1.0 N A:ARG155 4.5 23.9 1.0 CA A:SER128 4.6 16.4 1.0 CE3 A:TRP151 4.6 21.1 1.0 CZ3 A:TRP151 4.6 22.0 1.0 C A:SER128 4.9 15.9 1.0 CG1 A:ILE131 5.0 15.6 1.0

Xenon binding site 5 out of 7 in the Cytoglobin Cavities


Mono view


Stereo pair view

A full contact list of Xenon with other atoms in the Xe binding site number 5 of Cytoglobin Cavities within 5.0Å range: probe atom residue distance (Å) B Occ B:Xe1172 b:31.5 occ:1.00 CD1 B:LEU46 3.7 18.2 1.0 O B:GLY42 3.7 20.6 1.0 CG1 B:VAL85 3.7 25.4 1.0 CB B:VAL85 3.9 25.3 1.0 CG2 B:ILE45 3.9 16.7 1.0 CA B:GLY42 4.0 22.3 1.0 SD B:MET86 4.1 24.3 1.0 CB B:ILE45 4.1 17.2 1.0 C B:GLY42 4.3 21.3 1.0 CG B:MET86 4.4 23.3 1.0 CD1 B:ILE45 4.4 17.9 1.0 O B:ALA82 4.5 21.9 1.0 CA B:ALA82 4.6 22.7 1.0 CG2 B:VAL85 4.7 24.5 1.0 CD1 B:ILE131 4.8 18.9 1.0 CG B:LEU46 4.8 19.5 1.0 CG1 B:ILE131 4.8 18.3 1.0 CG1 B:ILE45 4.9 17.7 1.0 N B:MET86 4.9 24.9 1.0 CD2 B:LEU46 4.9 18.8 1.0 N B:LEU46 5.0 17.1 1.0

Xenon binding site 6 out of 7 in the Cytoglobin Cavities


Mono view


Stereo pair view

A full contact list of Xenon with other atoms in the Xe binding site number 6 of Cytoglobin Cavities within 5.0Å range: probe atom residue distance (Å) B Occ B:Xe1173 b:43.0 occ:1.00 CG2 B:ILE131 3.9 20.6 1.0 CB B:ARG155 3.9 25.6 1.0 OG B:SER128 4.0 20.9 1.0 CA B:ARG155 4.0 25.5 1.0 CD1 B:ILE158 4.1 24.5 1.0 CG B:ARG155 4.1 26.2 1.0 O B:SER128 4.2 17.2 1.0 XE B:XE1174 4.2 58.0 0.7 N B:ARG155 4.4 25.8 1.0 CB B:ILE131 4.5 19.9 1.0 CB B:SER128 4.5 16.9 1.0 CE3 B:TRP151 4.6 31.1 1.0 CZ3 B:TRP151 4.6 31.6 1.0 CA B:SER128 4.6 17.6 1.0 C B:SER128 4.8 17.1 1.0 CD1 B:ILE131 4.9 18.9 1.0

Xenon binding site 7 out of 7 in the Cytoglobin Cavities


Mono view


Stereo pair view

A full contact list of Xenon with other atoms in the Xe binding site number 7 of Cytoglobin Cavities within 5.0Å range: probe atom residue distance (Å) B Occ B:Xe1174 b:58.0 occ:0.70 CZ3 B:TRP151 3.7 31.6 1.0 CD2 B:LEU154 3.8 23.6 1.0 CZ3 B:TRP31 4.1 27.6 1.0 CG B:LEU89 4.2 19.1 1.0 CG2 B:VAL93 4.2 24.4 1.0 XE B:XE1173 4.2 43.0 1.0 CH2 B:TRP151 4.3 30.2 1.0 CB B:LEU89 4.3 22.0 1.0 CE3 B:TRP31 4.3 26.8 1.0 CD1 B:ILE158 4.5 24.5 1.0 CD2 B:LEU89 4.6 21.2 1.0 CH2 B:TRP31 4.7 28.5 1.0 CG B:LEU154 4.7 26.6 1.0 CE3 B:TRP151 4.8 31.1 1.0 O B:LEU89 4.9 23.1 1.0

D.De Sanctis, S.Dewilde, A.Pesce, L.Moens, P.Ascenzi, T.Hankeln, T.Burmester, M.Bolognesi. Cytoglobin Cavities Biochem.Biophys.Res.Commun. V. 316 1217 2004.
ISSN: ISSN 0006-291X
PubMed: 15044115
DOI: 10.1016/J.BBRC.2004.03.007