Xenon in PDB 2w72: Deoxygenated Structure of A Distal Site Hemoglobin Mutant Plus Xe

The structure of Deoxygenated Structure of A Distal Site Hemoglobin Mutant Plus Xe, PDB code: 2w72 was solved by A.E.Miele, F.Draghi, G.Sciara, K.A.Johnson, F.Renzi, B.Vallone, M.Brunori, C.Savino, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	17.32 / 1.07
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	61.957, 82.447, 53.531, 90.00, 99.60, 90.00
R / Rfree (%)	12.9 / 15.3

The structure of Deoxygenated Structure of A Distal Site Hemoglobin Mutant Plus Xe also contains other interesting chemical elements:

Potassium	(K)	3 atoms
Iron	(Fe)	4 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 23;

Binding sites:

The binding sites of Xenon atom in the Deoxygenated Structure of A Distal Site Hemoglobin Mutant Plus Xe (pdb code 2w72). This binding sites where shown within 5.0 Angstroms radius around Xenon atom.
In total 23 binding sites of Xenon where determined in the Deoxygenated Structure of A Distal Site Hemoglobin Mutant Plus Xe, PDB code: 2w72:
Jump to Xenon binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Xenon binding site 1 out of 23 in the Deoxygenated Structure of A Distal Site Hemoglobin Mutant Plus Xe


Mono view


Stereo pair view

A full contact list of Xenon with other atoms in the Xe binding site number 1 of Deoxygenated Structure of A Distal Site Hemoglobin Mutant Plus Xe within 5.0Å range: probe atom residue distance (Å) B Occ A:Xe1146 b:16.3 occ:0.30 XE A:XE1146 0.0 16.3 0.3 XE A:XE1146 1.4 22.8 0.1 CZ3 A:TRP14 1.9 21.7 0.5 CH2 A:TRP14 2.5 22.1 0.5 CE3 A:TRP14 2.5 19.3 0.5 CE2 A:PHE128 2.9 15.6 1.0 CZ2 A:TRP14 3.4 20.9 0.5 CD2 A:TRP14 3.4 17.1 0.5 CD2 A:PHE128 3.4 13.1 1.0 CE3 A:TRP14 3.5 13.2 0.5 CE2 A:TRP14 3.7 18.1 0.5 CD2 A:TRP14 3.8 10.8 0.5 CZ3 A:TRP14 3.8 13.2 0.5 CZ A:PHE128 4.0 16.4 1.0 CD2 A:LEU125 4.1 11.0 1.0 CG A:TRP14 4.3 11.3 0.5 CD2 A:LEU129 4.3 12.2 1.0 CG2 A:VAL70 4.3 11.8 1.0 CE2 A:TRP14 4.4 9.7 0.5 CH2 A:TRP14 4.4 14.3 0.5 CG A:TRP14 4.6 16.6 0.5 CG1 A:VAL10 4.6 9.0 0.6 CB A:TRP14 4.6 13.2 0.5 CB A:LEU66 4.6 9.7 1.0 CZ2 A:TRP14 4.7 10.8 0.5 CG A:PHE128 4.7 10.9 1.0 CD1 A:LEU66 4.7 13.2 1.0 CD2 A:LEU66 4.9 11.3 1.0 CD2 A:LEU105 4.9 12.0 0.5 NE1 A:TRP14 4.9 16.4 0.5 CG A:LEU129 5.0 8.4 1.0

Xenon binding site 2 out of 23 in the Deoxygenated Structure of A Distal Site Hemoglobin Mutant Plus Xe


Mono view


Stereo pair view

A full contact list of Xenon with other atoms in the Xe binding site number 2 of Deoxygenated Structure of A Distal Site Hemoglobin Mutant Plus Xe within 5.0Å range: probe atom residue distance (Å) B Occ A:Xe1146 b:22.8 occ:0.10 XE A:XE1146 0.0 22.8 0.1 XE A:XE1146 1.4 16.3 0.3 CZ3 A:TRP14 2.0 21.7 0.5 CH2 A:TRP14 2.6 22.1 0.5 CE3 A:TRP14 3.1 19.3 0.5 CZ3 A:TRP14 3.6 13.2 0.5 CE3 A:TRP14 3.6 13.2 0.5 CD2 A:LEU129 3.7 12.2 1.0 CE2 A:PHE128 3.8 15.6 1.0 CZ2 A:TRP14 3.8 20.9 0.5 CD2 A:LEU125 3.8 11.0 1.0 CD2 A:LEU105 3.9 12.0 0.5 CD2 A:PHE128 3.9 13.1 1.0 CD1 A:LEU109 4.1 10.1 0.5 CG A:LEU129 4.2 8.4 1.0 CD2 A:TRP14 4.2 17.1 0.5 CH2 A:TRP14 4.4 14.3 0.5 CD2 A:TRP14 4.4 10.8 0.5 CD1 A:LEU129 4.4 9.9 1.0 CD2 A:LEU109 4.4 15.2 0.5 CE2 A:TRP14 4.5 18.1 0.5 CD1 A:LEU66 4.6 13.2 1.0 CG A:LEU105 4.7 10.0 0.5 CZ2 A:TRP14 5.0 10.8 0.5 CE2 A:TRP14 5.0 9.7 0.5

Xenon binding site 3 out of 23 in the Deoxygenated Structure of A Distal Site Hemoglobin Mutant Plus Xe


Mono view


Stereo pair view

A full contact list of Xenon with other atoms in the Xe binding site number 3 of Deoxygenated Structure of A Distal Site Hemoglobin Mutant Plus Xe within 5.0Å range: probe atom residue distance (Å) B Occ A:Xe1147 b:17.1 occ:0.25 XE A:XE1147 0.0 17.1 0.2 CH2 A:TRP14 2.2 14.3 0.5 XE A:XE1147 2.5 19.5 0.1 CZ3 A:TRP14 3.0 13.2 0.5 CZ2 A:TRP14 3.2 10.8 0.5 CD1 A:LEU105 3.3 9.5 0.5 O A:ALA21 3.5 11.4 1.0 CH2 A:TRP14 3.7 22.1 0.5 CZ2 A:TRP14 3.8 20.9 0.5 N A:GLY25 3.8 9.8 1.0 CD2 A:LEU105 3.9 9.3 0.5 CD2 A:LEU105 4.0 12.0 0.5 CA A:GLY25 4.1 9.4 1.0 CB A:TYR24 4.1 10.8 1.0 CB A:ALA63 4.2 13.8 1.0 C A:TYR24 4.3 9.5 1.0 CG A:LEU105 4.3 10.0 0.5 C A:ALA21 4.3 11.4 1.0 CE3 A:TRP14 4.3 13.2 0.5 CD1 A:LEU66 4.4 13.2 1.0 CA A:ALA21 4.4 11.9 1.0 CE2 A:TRP14 4.4 9.7 0.5 CA A:ALA63 4.5 11.5 1.0 CD1 A:LEU109 4.6 15.8 0.5 CB A:ALA21 4.7 13.3 1.0 CA A:TYR24 4.8 9.7 1.0 O A:TYR24 4.8 9.8 1.0 CZ3 A:TRP14 4.8 21.7 0.5 CE2 A:TRP14 4.9 18.1 0.5 XE A:XE1149 4.9 10.9 0.1 CD2 A:TRP14 4.9 10.8 0.5

Xenon binding site 4 out of 23 in the Deoxygenated Structure of A Distal Site Hemoglobin Mutant Plus Xe


Mono view


Stereo pair view

A full contact list of Xenon with other atoms in the Xe binding site number 4 of Deoxygenated Structure of A Distal Site Hemoglobin Mutant Plus Xe within 5.0Å range: probe atom residue distance (Å) B Occ A:Xe1147 b:19.5 occ:0.10 XE A:XE1147 0.0 19.5 0.1 CD1 A:LEU105 1.5 9.5 0.5 XE A:XE1147 2.5 17.1 0.2 CD1 A:LEU109 2.7 15.8 0.5 CG A:LEU105 2.9 10.0 0.5 CD2 A:LEU105 3.3 9.3 0.5 CB A:TYR24 3.5 10.8 1.0 CD2 A:LEU105 3.6 12.0 0.5 CD2 A:LEU109 3.7 11.4 0.5 CZ3 A:TRP14 3.8 13.2 0.5 CG A:LEU109 3.9 7.7 0.5 C A:TYR24 3.9 9.5 1.0 O A:TYR24 3.9 9.8 1.0 CH2 A:TRP14 3.9 14.3 0.5 CB A:LEU105 4.1 9.7 0.5 O A:LEU105 4.1 8.9 1.0 CG A:LEU109 4.1 12.9 0.5 N A:GLY25 4.2 9.8 1.0 CA A:TYR24 4.3 9.7 1.0 CG2 A:THR108 4.3 9.4 1.0 CD1 A:LEU109 4.4 10.1 0.5 CA A:LEU105 4.4 8.5 0.5 CA A:LEU105 4.4 8.1 0.5 CB A:LEU105 4.4 7.8 0.5 CG A:LEU105 4.4 7.6 0.5 CB A:THR108 4.5 8.1 1.0 CG A:TYR24 4.5 10.9 1.0 CA A:GLY25 4.6 9.4 1.0 CD2 A:LEU109 4.6 15.2 0.5 CD2 A:TYR24 4.7 12.6 1.0 C A:LEU105 4.7 7.9 1.0 CH2 A:TRP14 4.8 22.1 0.5 N A:LEU109 4.9 8.7 1.0 CB A:ALA28 4.9 8.6 1.0

Xenon binding site 5 out of 23 in the Deoxygenated Structure of A Distal Site Hemoglobin Mutant Plus Xe


Mono view


Stereo pair view

A full contact list of Xenon with other atoms in the Xe binding site number 5 of Deoxygenated Structure of A Distal Site Hemoglobin Mutant Plus Xe within 5.0Å range: probe atom residue distance (Å) B Occ A:Xe1148 b:19.4 occ:0.15 CE1 A:PHE46 1.4 11.0 0.5 CD1 A:PHE46 1.7 13.1 0.5 CD1 A:PHE46 2.4 14.6 0.5 CE1 A:PHE46 2.6 14.6 0.5 CZ A:PHE46 2.7 13.8 0.5 CG A:PHE46 3.0 14.3 0.5 CD2 A:PHE43 3.4 9.9 1.0 CG A:PHE46 3.6 16.6 0.5 CE2 A:PHE43 3.7 10.3 1.0 CG2 A:VAL55 3.7 11.7 1.0 CE2 A:PHE46 3.7 15.7 0.5 CA A:VAL55 3.8 10.0 1.0 O A:GLN54 3.8 10.8 1.0 CD2 A:PHE46 3.8 14.7 0.5 CZ A:PHE46 3.8 16.1 0.5 CB A:GLN58 3.9 10.5 1.0 CD2 A:LEU48 3.9 14.4 1.0 N A:VAL55 4.0 9.8 1.0 C A:GLN54 4.0 10.2 1.0 CB A:PHE46 4.1 16.5 0.5 CG A:PHE43 4.2 8.6 1.0 CB A:PHE46 4.2 16.3 0.5 CG A:GLN58 4.3 10.9 1.0 CB A:VAL55 4.3 10.6 1.0 CE2 A:PHE33 4.3 9.6 1.0 CZ A:PHE33 4.4 9.0 1.0 CD2 A:PHE46 4.6 15.6 0.5 CZ A:PHE43 4.6 9.7 1.0 CB A:PHE43 4.6 9.3 1.0 CE2 A:PHE46 4.7 18.2 0.5 CB A:GLN54 4.7 12.4 1.0 CG1 A:VAL55 4.9 12.4 1.0 C A:VAL55 4.9 9.8 1.0 CD1 A:PHE43 4.9 8.6 1.0

Xenon binding site 6 out of 23 in the Deoxygenated Structure of A Distal Site Hemoglobin Mutant Plus Xe


Mono view


Stereo pair view

A full contact list of Xenon with other atoms in the Xe binding site number 6 of Deoxygenated Structure of A Distal Site Hemoglobin Mutant Plus Xe within 5.0Å range: probe atom residue distance (Å) B Occ A:Xe1149 b:10.9 occ:0.15 CD2 A:LEU105 2.4 9.3 0.5 CG A:LEU105 3.1 7.6 0.5 CD1 A:LEU105 3.2 8.6 0.5 CG1 A:VAL62 3.4 12.1 1.0 CB A:ALA28 4.0 8.6 1.0 CA A:GLY25 4.0 9.4 1.0 CD1 A:LEU101 4.0 10.0 1.0 CD2 A:LEU105 4.1 12.0 0.5 CD2 A:LEU101 4.1 9.5 1.0 O A:GLY25 4.1 9.9 1.0 CG A:LEU101 4.1 8.7 1.0 XE A:XE1150 4.2 12.4 0.1 CE1 A:TYR29 4.2 9.5 1.0 CB A:VAL62 4.3 10.2 1.0 CD1 A:LEU66 4.3 13.2 1.0 CD1 A:LEU105 4.4 9.5 0.5 CB A:LEU105 4.4 9.7 0.5 CD1 A:TYR29 4.5 8.4 1.0 CG A:LEU105 4.5 10.0 0.5 C A:GLY25 4.6 9.6 1.0 CB A:LEU105 4.6 7.8 0.5 XE A:XE1147 4.9 17.1 0.2

Xenon binding site 7 out of 23 in the Deoxygenated Structure of A Distal Site Hemoglobin Mutant Plus Xe


Mono view


Stereo pair view

A full contact list of Xenon with other atoms in the Xe binding site number 7 of Deoxygenated Structure of A Distal Site Hemoglobin Mutant Plus Xe within 5.0Å range: probe atom residue distance (Å) B Occ A:Xe1150 b:12.4 occ:0.15 CD1 A:LEU105 2.0 8.6 0.5 CBB A:HEM1142 2.7 13.4 1.0 CG A:LEU105 3.5 7.6 0.5 CAB A:HEM1142 3.6 9.6 1.0 CD2 A:LEU101 3.8 9.5 1.0 CG A:LEU101 3.8 8.7 1.0 CD2 A:LEU129 3.9 12.2 1.0 OG A:SER102 4.0 8.8 1.0 CA A:SER102 4.1 7.6 1.0 N A:SER102 4.1 7.2 1.0 CD2 A:LEU105 4.2 12.0 0.5 XE A:XE1149 4.2 10.9 0.1 C A:LEU101 4.3 7.2 1.0 O A:LEU101 4.3 7.7 1.0 CB A:LEU105 4.3 7.8 0.5 CD1 A:LEU66 4.4 13.2 1.0 CD2 A:LEU105 4.4 9.3 0.5 CB A:LEU101 4.5 7.5 1.0 CB A:LEU105 4.5 9.7 0.5 CB A:SER102 4.6 7.9 1.0 CG A:LEU129 4.8 8.4 1.0 CD1 A:LEU129 4.8 9.9 1.0 CD2 A:LEU66 4.8 11.3 1.0 C3B A:HEM1142 4.8 8.0 1.0 CB A:LEU129 5.0 8.2 1.0

Xenon binding site 8 out of 23 in the Deoxygenated Structure of A Distal Site Hemoglobin Mutant Plus Xe


Mono view


Stereo pair view

A full contact list of Xenon with other atoms in the Xe binding site number 8 of Deoxygenated Structure of A Distal Site Hemoglobin Mutant Plus Xe within 5.0Å range: probe atom residue distance (Å) B Occ A:Xe1151 b:16.0 occ:0.15 CD1 A:LEU113 2.1 17.7 1.0 CG A:LEU113 3.4 16.9 1.0 CB A:ALA13 3.5 13.7 1.0 CG A:GLU116 3.6 15.4 0.5 CB A:LEU113 3.7 14.6 1.0 CB A:GLU116 3.9 13.8 0.5 CB A:GLU116 4.1 14.1 0.5 CD1 A:PHE117 4.2 12.9 1.0 CA A:ALA13 4.2 12.1 1.0 CD1 A:LEU125 4.2 11.1 1.0 N A:PHE117 4.3 12.7 1.0 CD2 A:LEU113 4.3 18.9 1.0 C A:GLU116 4.3 13.1 1.0 CB A:LEU109 4.4 10.1 0.5 CA A:PHE117 4.4 11.2 1.0 CD2 A:LEU109 4.4 15.2 0.5 CG1 A:VAL121 4.4 12.3 1.0 CB A:PHE117 4.4 11.5 1.0 CB A:LEU109 4.5 9.4 0.5 O A:ALA13 4.5 12.7 1.0 O A:GLU116 4.5 13.2 1.0 CG A:LEU109 4.5 12.9 0.5 C A:ALA13 4.7 12.3 1.0 CA A:GLU116 4.8 13.8 0.5 CG A:PHE117 4.8 11.0 1.0 CA A:GLU116 4.8 13.7 0.5 O A:LEU109 4.8 10.6 1.0 CD2 A:LEU109 4.9 11.4 0.5 CD A:GLU116 4.9 19.8 0.5

Xenon binding site 9 out of 23 in the Deoxygenated Structure of A Distal Site Hemoglobin Mutant Plus Xe


Mono view


Stereo pair view

A full contact list of Xenon with other atoms in the Xe binding site number 9 of Deoxygenated Structure of A Distal Site Hemoglobin Mutant Plus Xe within 5.0Å range: probe atom residue distance (Å) B Occ B:Xe1151 b:12.6 occ:0.65 XE B:XE1151 0.0 12.6 0.7 XE B:XE1151 1.3 18.0 0.2 O B:PHE103 3.5 8.6 1.0 O B:HOH2173 3.5 19.5 1.0 CBB B:HEM1147 3.6 20.1 1.0 O B:VAL134 3.7 9.6 1.0 XE B:XE1151 3.9 20.5 0.1 CA B:GLY107 4.0 9.0 1.0 CG1 B:VAL137 4.0 11.7 1.0 N B:GLY107 4.1 7.4 1.0 CB B:VAL134 4.2 9.3 1.0 N B:ALA138 4.2 9.1 1.0 CAB B:HEM1147 4.3 10.3 1.0 CB B:VAL137 4.3 10.1 1.0 CA B:VAL134 4.3 9.0 1.0 C B:PHE103 4.4 7.6 1.0 C B:VAL134 4.4 9.4 1.0 CE2 B:PHE71 4.5 12.3 1.0 CB B:ALA138 4.6 10.3 1.0 CA B:ALA138 4.6 9.3 1.0 CG1 B:VAL134 4.7 10.6 1.0 CD2 B:PHE71 4.7 10.9 1.0 CB B:PHE103 4.8 8.9 1.0 C B:VAL137 4.8 8.8 1.0 CA B:PHE103 4.8 8.3 1.0 C B:LEU106 4.9 7.1 1.0

Xenon binding site 10 out of 23 in the Deoxygenated Structure of A Distal Site Hemoglobin Mutant Plus Xe


Mono view


Stereo pair view

A full contact list of Xenon with other atoms in the Xe binding site number 10 of Deoxygenated Structure of A Distal Site Hemoglobin Mutant Plus Xe within 5.0Å range: probe atom residue distance (Å) B Occ B:Xe1151 b:20.5 occ:0.10 XE B:XE1151 0.0 20.5 0.1 XE B:XE1151 2.6 18.0 0.2 CD2 B:LEU106 3.6 10.5 1.0 CD2 B:LEU110 3.6 11.4 1.0 CD2 B:PHE71 3.6 10.9 1.0 CD1 B:LEU68 3.7 11.4 0.8 CG B:LEU106 3.7 8.5 1.0 XE B:XE1151 3.9 12.6 0.7 CG B:PHE71 4.0 9.9 1.0 CE2 B:PHE71 4.0 12.3 1.0 CD1 B:LEU68 4.2 8.2 0.2 XE B:XE1152 4.3 17.5 0.1 CB B:PHE71 4.4 9.6 1.0 CAB B:HEM1147 4.4 10.3 1.0 CB B:LEU110 4.5 8.2 1.0 CG B:LEU68 4.6 9.8 0.2 CG B:LEU110 4.6 9.2 1.0 CD1 B:LEU106 4.6 10.0 1.0 CD1 B:PHE71 4.7 10.9 1.0 CZ B:PHE71 4.7 12.6 1.0 CBB B:HEM1147 4.8 20.1 1.0 O B:LEU106 4.9 7.6 1.0 CB B:LEU106 4.9 8.0 1.0 CG1 B:VAL67 4.9 9.7 1.0 CE1 B:PHE71 5.0 11.6 1.0

C.Savino, A.E.Miele, F.Draghi, K.A.Johnson, G.Sciara, M.Brunori, B.Vallone. Pattern of Cavities in Globins: the Case of Human Hemoglobin. Biopolymers V. 91 1097 2009.
ISSN: ISSN 0006-3525
PubMed: 19365817
DOI: 10.1002/BIP.21201