Xenon in PDB 1ux9: Mapping Protein Matrix Cavities in Human Cytoglobin Through Xe Atom Binding: A Crystallographic Investigation

The structure of Mapping Protein Matrix Cavities in Human Cytoglobin Through Xe Atom Binding: A Crystallographic Investigation, PDB code: 1ux9 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)	29.8 / 2.4
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	47.840, 70.520, 98.730, 90.00, 90.00, 90.00
R / Rfree (%)	19.163 / 23.804

The structure of Mapping Protein Matrix Cavities in Human Cytoglobin Through Xe Atom Binding: A Crystallographic Investigation also contains other interesting chemical elements:

Iron

(Fe)

4 atoms

The binding sites of Xenon atom in the Mapping Protein Matrix Cavities in Human Cytoglobin Through Xe Atom Binding: A Crystallographic Investigation (pdb code 1ux9). This binding sites where shown within 5.0 Angstroms radius around Xenon atom.
In total 7 binding sites of Xenon where determined in the Mapping Protein Matrix Cavities in Human Cytoglobin Through Xe Atom Binding: A Crystallographic Investigation, PDB code: 1ux9:
Jump to Xenon binding site number: 1; 2; 3; 4; 5; 6; 7;

Xenon binding site 1 out of 7 in the Mapping Protein Matrix Cavities in Human Cytoglobin Through Xe Atom Binding: A Crystallographic Investigation


Mono view


Stereo pair view

A full contact list of Xenon with other atoms in the Xe binding site number 1 of Mapping Protein Matrix Cavities in Human Cytoglobin Through Xe Atom Binding: A Crystallographic Investigation within 5.0Å range: probe atom residue distance (Å) B Occ A:Xe802 b:26.7 occ:0.70 CG2 A:ILE131 3.9 20.4 1.0 XE A:XE1174 4.0 44.7 0.4 CB A:ARG155 4.1 25.7 1.0 CA A:ARG155 4.1 25.5 1.0 CG A:ARG155 4.1 26.4 1.0 CD2 A:LEU132 4.2 31.6 1.0 CD1 A:ILE158 4.3 28.9 1.0 CB A:ILE131 4.3 20.0 1.0 OG A:SER128 4.3 23.1 1.0 O A:SER128 4.3 17.8 1.0 CD1 A:ILE131 4.4 20.4 1.0 CB A:SER128 4.5 19.6 1.0 N A:ARG155 4.5 25.1 1.0 CA A:SER128 4.6 19.5 1.0 CE3 A:TRP151 4.6 22.5 1.0 CZ3 A:TRP151 4.6 23.5 1.0 C A:SER128 4.9 19.1 1.0

Xenon binding site 2 out of 7 in the Mapping Protein Matrix Cavities in Human Cytoglobin Through Xe Atom Binding: A Crystallographic Investigation


Mono view


Stereo pair view

A full contact list of Xenon with other atoms in the Xe binding site number 2 of Mapping Protein Matrix Cavities in Human Cytoglobin Through Xe Atom Binding: A Crystallographic Investigation within 5.0Å range: probe atom residue distance (Å) B Occ A:Xe1173 b:25.2 occ:0.70 O A:GLY42 3.6 26.1 1.0 CE A:MET86 3.6 35.9 1.0 CG2 A:ILE45 3.7 21.1 1.0 CG1 A:VAL85 3.8 24.2 1.0 CA A:GLY42 4.0 26.1 1.0 CB A:ILE45 4.0 21.4 1.0 CB A:VAL85 4.1 23.5 1.0 CG A:MET86 4.2 27.4 1.0 CG A:LEU46 4.2 22.4 1.0 C A:GLY42 4.2 25.6 1.0 CD1 A:ILE45 4.3 23.3 1.0 SD A:MET86 4.4 32.7 1.0 O A:ALA82 4.5 23.7 1.0 CD2 A:LEU46 4.5 22.9 1.0 CG2 A:VAL85 4.7 22.9 1.0 CA A:ALA82 4.7 23.8 1.0 CG1 A:ILE45 4.8 21.9 1.0 CD1 A:LEU46 4.9 22.4 1.0 N A:MET86 4.9 24.4 1.0 N A:LEU46 4.9 21.6 1.0 CB A:ALA82 5.0 23.9 1.0

Xenon binding site 3 out of 7 in the Mapping Protein Matrix Cavities in Human Cytoglobin Through Xe Atom Binding: A Crystallographic Investigation


Mono view


Stereo pair view

A full contact list of Xenon with other atoms in the Xe binding site number 3 of Mapping Protein Matrix Cavities in Human Cytoglobin Through Xe Atom Binding: A Crystallographic Investigation within 5.0Å range: probe atom residue distance (Å) B Occ A:Xe1174 b:44.7 occ:0.40 CD1 A:LEU89 3.6 28.0 1.0 CD2 A:LEU154 3.8 24.5 1.0 CZ3 A:TRP151 3.9 23.5 1.0 XE A:XE802 4.0 26.7 0.7 CB A:LEU89 4.1 25.3 1.0 CZ3 A:TRP31 4.1 27.5 1.0 CG2 A:VAL93 4.2 27.1 1.0 CG A:LEU89 4.2 27.6 1.0 CD1 A:ILE158 4.3 28.9 1.0 CE3 A:TRP31 4.5 28.6 1.0 CH2 A:TRP151 4.5 23.7 1.0 CG A:LEU154 4.5 25.2 1.0 CD2 A:LEU89 4.6 27.1 1.0 CH2 A:TRP31 4.8 27.3 1.0 CE3 A:TRP151 4.9 22.5 1.0 CG2 A:ILE131 4.9 20.4 1.0

Xenon binding site 4 out of 7 in the Mapping Protein Matrix Cavities in Human Cytoglobin Through Xe Atom Binding: A Crystallographic Investigation


Mono view


Stereo pair view

A full contact list of Xenon with other atoms in the Xe binding site number 4 of Mapping Protein Matrix Cavities in Human Cytoglobin Through Xe Atom Binding: A Crystallographic Investigation within 5.0Å range: probe atom residue distance (Å) B Occ A:Xe1175 b:42.7 occ:0.30 CD1 A:LEU34 3.3 40.3 1.0 CE A:MET86 3.4 35.9 1.0 CD1 A:ILE45 3.5 23.3 1.0 CZ3 A:TRP31 3.5 27.5 1.0 CG2 A:ILE131 3.7 20.4 1.0 SD A:MET86 4.1 32.7 1.0 CH2 A:TRP31 4.3 27.3 1.0 CG1 A:VAL41 4.3 28.2 1.0 CE3 A:TRP31 4.4 28.6 1.0 CG2 A:VAL135 4.4 24.0 1.0 CG1 A:ILE131 4.7 18.6 1.0 CG A:LEU34 4.7 38.4 1.0 CB A:ILE131 4.8 20.0 1.0 CG1 A:ILE45 5.0 21.9 1.0

Xenon binding site 5 out of 7 in the Mapping Protein Matrix Cavities in Human Cytoglobin Through Xe Atom Binding: A Crystallographic Investigation


Mono view


Stereo pair view

A full contact list of Xenon with other atoms in the Xe binding site number 5 of Mapping Protein Matrix Cavities in Human Cytoglobin Through Xe Atom Binding: A Crystallographic Investigation within 5.0Å range: probe atom residue distance (Å) B Occ B:Xe1173 b:23.6 occ:0.70 CG1 B:VAL85 3.7 28.3 1.0 O B:GLY42 3.7 23.9 1.0 CD1 B:LEU46 3.8 20.6 1.0 CB B:VAL85 3.9 27.8 1.0 CG2 B:ILE45 3.9 19.9 1.0 CA B:GLY42 4.0 25.1 1.0 SD B:MET86 4.1 27.6 1.0 CB B:ILE45 4.1 19.8 1.0 C B:GLY42 4.3 24.2 1.0 CG B:MET86 4.4 25.9 1.0 CD1 B:ILE45 4.4 20.3 1.0 O B:ALA82 4.5 24.1 1.0 CA B:ALA82 4.6 25.0 1.0 CG2 B:VAL85 4.7 26.8 1.0 CG B:LEU46 4.8 22.0 1.0 CD1 B:ILE131 4.8 21.7 1.0 CG1 B:ILE131 4.8 21.4 1.0 N B:MET86 4.9 27.2 1.0 CG1 B:ILE45 4.9 20.0 1.0 CD2 B:LEU46 4.9 21.8 1.0 N B:LEU46 4.9 19.9 1.0

Xenon binding site 6 out of 7 in the Mapping Protein Matrix Cavities in Human Cytoglobin Through Xe Atom Binding: A Crystallographic Investigation


Mono view


Stereo pair view

A full contact list of Xenon with other atoms in the Xe binding site number 6 of Mapping Protein Matrix Cavities in Human Cytoglobin Through Xe Atom Binding: A Crystallographic Investigation within 5.0Å range: probe atom residue distance (Å) B Occ B:Xe1174 b:32.6 occ:0.70 CG2 B:ILE131 3.9 23.2 1.0 CB B:ARG155 4.0 26.6 1.0 OG B:SER128 4.0 23.9 1.0 CA B:ARG155 4.1 26.5 1.0 CD1 B:ILE158 4.1 26.6 1.0 CG B:ARG155 4.1 27.3 1.0 O B:SER128 4.2 19.6 1.0 XE B:XE1175 4.2 38.9 0.4 N B:ARG155 4.4 26.9 1.0 CB B:ILE131 4.5 22.6 1.0 CB B:SER128 4.5 19.8 1.0 CZ3 B:TRP151 4.6 33.6 1.0 CE3 B:TRP151 4.6 32.7 1.0 CA B:SER128 4.6 20.4 1.0 CD1 B:ILE131 4.8 21.7 1.0 C B:SER128 4.8 19.7 1.0

Xenon binding site 7 out of 7 in the Mapping Protein Matrix Cavities in Human Cytoglobin Through Xe Atom Binding: A Crystallographic Investigation


Mono view


Stereo pair view

A full contact list of Xenon with other atoms in the Xe binding site number 7 of Mapping Protein Matrix Cavities in Human Cytoglobin Through Xe Atom Binding: A Crystallographic Investigation within 5.0Å range: probe atom residue distance (Å) B Occ B:Xe1175 b:38.9 occ:0.40 CZ3 B:TRP151 3.8 33.6 1.0 CD2 B:LEU154 3.8 25.9 1.0 CZ3 B:TRP31 4.1 28.8 1.0 CG B:LEU89 4.2 20.4 1.0 XE B:XE1174 4.2 32.6 0.7 CG2 B:VAL93 4.2 24.6 1.0 CH2 B:TRP151 4.3 32.2 1.0 CB B:LEU89 4.3 23.7 1.0 CE3 B:TRP31 4.3 27.8 1.0 CD1 B:ILE158 4.4 26.6 1.0 CH2 B:TRP31 4.7 29.5 1.0 CD2 B:LEU89 4.7 23.4 1.0 CG B:LEU154 4.8 28.0 1.0 CE3 B:TRP151 4.8 32.7 1.0 O B:LEU89 5.0 25.0 1.0

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