Xenon in PDB 2w6v: Structure of Human Deoxy Hemoglobin A in Complex with Xenon

The structure of Structure of Human Deoxy Hemoglobin A in Complex with Xenon, PDB code: 2w6v 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)	22.90 / 1.80
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	62.645, 82.328, 53.552, 90.00, 99.79, 90.00
R / Rfree (%)	16.2 / 21.6

The structure of Structure of Human Deoxy Hemoglobin A in Complex with Xenon also contains other interesting chemical elements:

Iron

(Fe)

4 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 15;

Binding sites:

The binding sites of Xenon atom in the Structure of Human Deoxy Hemoglobin A in Complex with Xenon (pdb code 2w6v). This binding sites where shown within 5.0 Angstroms radius around Xenon atom.
In total 15 binding sites of Xenon where determined in the Structure of Human Deoxy Hemoglobin A in Complex with Xenon, PDB code: 2w6v:
Jump to Xenon binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Xenon binding site 1 out of 15 in the Structure of Human Deoxy Hemoglobin A in Complex with Xenon


Mono view


Stereo pair view

A full contact list of Xenon with other atoms in the Xe binding site number 1 of Structure of Human Deoxy Hemoglobin A in Complex with Xenon within 5.0Å range: probe atom residue distance (Å) B Occ A:Xe1145 b:25.8 occ:0.30 CD1 A:TRP14 2.7 30.4 0.3 NE1 A:TRP14 2.9 30.0 0.3 CE3 A:TRP14 3.1 29.4 0.5 CE2 A:PHE128 3.3 20.6 1.0 CZ3 A:TRP14 3.3 28.8 0.5 CD2 A:PHE128 3.5 20.7 1.0 CE3 A:TRP14 3.7 28.3 0.2 CD2 A:TRP14 3.7 28.8 0.5 CH2 A:TRP14 4.1 28.4 0.5 CG A:TRP14 4.1 29.8 0.3 CZ3 A:TRP14 4.1 28.2 0.2 CD2 A:TRP14 4.1 28.3 0.2 CD2 A:LEU125 4.2 16.3 1.0 CE2 A:TRP14 4.2 29.9 0.3 CD2 A:LEU129 4.3 16.6 1.0 CG2 A:VAL70 4.3 19.0 1.0 CE2 A:TRP14 4.4 27.8 0.5 CG1 A:VAL10 4.4 21.2 1.0 CZ A:PHE128 4.4 17.4 1.0 CG A:TRP14 4.5 28.3 0.5 CD1 A:LEU109 4.5 21.3 1.0 CZ2 A:TRP14 4.6 29.5 0.5 CG A:TRP14 4.6 28.4 0.2 CB A:LEU66 4.7 18.1 1.0 CG A:PHE128 4.8 17.0 1.0 CB A:TRP14 4.8 28.9 0.2 CD2 A:TRP14 4.8 30.4 0.3 CB A:TRP14 4.8 29.1 0.5 CD1 A:LEU66 4.9 18.9 1.0 CH2 A:TRP14 4.9 28.3 0.2 CE2 A:TRP14 4.9 27.8 0.2 CD2 A:LEU66 4.9 19.1 1.0 CB A:TRP14 4.9 29.8 0.3 CG A:LEU129 4.9 13.4 1.0

Xenon binding site 2 out of 15 in the Structure of Human Deoxy Hemoglobin A in Complex with Xenon


Mono view


Stereo pair view

A full contact list of Xenon with other atoms in the Xe binding site number 2 of Structure of Human Deoxy Hemoglobin A in Complex with Xenon within 5.0Å range: probe atom residue distance (Å) B Occ A:Xe1146 b:22.8 occ:0.20 XE A:XE1146 0.0 22.8 0.2 XE A:XE1146 1.8 29.9 0.4 CB A:TYR24 3.4 20.9 1.0 CD2 A:LEU105 3.5 13.7 1.0 C A:TYR24 3.8 20.5 1.0 O A:TYR24 3.9 20.3 1.0 CH2 A:TRP14 3.9 28.4 0.5 CZ3 A:TRP14 4.0 28.2 0.2 CZ3 A:TRP14 4.0 28.8 0.5 CD2 A:LEU109 4.1 21.6 1.0 N A:GLY25 4.1 20.3 1.0 CH2 A:TRP14 4.2 28.3 0.2 CA A:TYR24 4.3 21.0 1.0 CG A:LEU109 4.3 18.7 1.0 CG2 A:THR108 4.4 13.5 1.0 O A:LEU105 4.5 13.7 1.0 CG A:TYR24 4.5 19.9 1.0 CB A:THR108 4.6 14.8 1.0 CA A:GLY25 4.6 18.8 1.0 CG A:LEU105 4.7 14.7 1.0 CB A:LEU105 4.7 15.2 1.0 CD2 A:TYR24 4.7 20.4 1.0 CA A:LEU105 4.8 14.7 1.0 CB A:ALA28 4.9 15.3 1.0 CD1 A:LEU109 5.0 21.3 1.0

Xenon binding site 3 out of 15 in the Structure of Human Deoxy Hemoglobin A in Complex with Xenon


Mono view


Stereo pair view

A full contact list of Xenon with other atoms in the Xe binding site number 3 of Structure of Human Deoxy Hemoglobin A in Complex with Xenon within 5.0Å range: probe atom residue distance (Å) B Occ A:Xe1146 b:29.9 occ:0.40 XE A:XE1146 0.0 29.9 0.4 XE A:XE1146 1.8 22.8 0.2 CH2 A:TRP14 2.6 28.4 0.5 CH2 A:TRP14 2.8 28.3 0.2 CZ3 A:TRP14 3.1 28.2 0.2 CZ3 A:TRP14 3.3 28.8 0.5 CZ2 A:TRP14 3.7 29.5 0.5 CD2 A:LEU105 3.7 13.7 1.0 N A:GLY25 4.0 20.3 1.0 CB A:TYR24 4.0 20.9 1.0 CD1 A:LEU66 4.0 18.9 1.0 CZ2 A:TRP14 4.1 28.4 0.2 O A:ALA21 4.1 29.3 1.0 C A:TYR24 4.3 20.5 1.0 CA A:GLY25 4.3 18.8 1.0 CZ2 A:TRP14 4.4 30.3 0.3 CE3 A:TRP14 4.5 28.3 0.2 CB A:ALA63 4.7 23.3 1.0 CA A:ALA63 4.7 23.1 1.0 CE3 A:TRP14 4.7 29.4 0.5 O A:TYR24 4.7 20.3 1.0 CA A:TYR24 4.8 21.0 1.0 CE2 A:TRP14 4.9 27.8 0.5 NE1 A:TRP14 4.9 30.0 0.3 CE2 A:TRP14 4.9 29.9 0.3

Xenon binding site 4 out of 15 in the Structure of Human Deoxy Hemoglobin A in Complex with Xenon


Mono view


Stereo pair view

A full contact list of Xenon with other atoms in the Xe binding site number 4 of Structure of Human Deoxy Hemoglobin A in Complex with Xenon within 5.0Å range: probe atom residue distance (Å) B Occ A:Xe1147 b:28.9 occ:0.30 XE A:XE1147 0.0 28.9 0.3 XE A:XE1147 0.9 32.7 0.2 CD1 A:PHE46 2.4 32.1 1.0 CE1 A:PHE46 2.5 36.0 1.0 CG A:PHE46 3.6 29.2 1.0 CZ A:PHE46 3.7 35.8 1.0 CD1 A:PHE43 3.8 20.2 1.0 O A:GLN54 3.8 18.6 1.0 CB A:HIS58 3.9 19.8 1.0 CA A:VAL55 3.9 18.6 1.0 CG2 A:VAL55 3.9 19.3 1.0 CE1 A:PHE43 3.9 19.4 1.0 N A:VAL55 4.0 18.5 1.0 C A:GLN54 4.0 18.4 1.0 CD2 A:LEU48 4.0 25.3 1.0 CG A:HIS58 4.3 22.0 1.0 CB A:PHE46 4.3 24.6 1.0 CD2 A:HIS58 4.4 21.8 1.0 CB A:VAL55 4.5 18.4 1.0 CD2 A:PHE46 4.5 32.5 1.0 CG A:PHE43 4.5 19.2 1.0 CE2 A:PHE46 4.6 35.2 1.0 CZ A:PHE33 4.6 20.0 1.0 CE2 A:PHE33 4.6 15.8 1.0 CB A:GLN54 4.7 19.3 1.0 CZ A:PHE43 4.8 21.2 1.0 CA A:GLN54 5.0 19.1 1.0

Xenon binding site 5 out of 15 in the Structure of Human Deoxy Hemoglobin A in Complex with Xenon


Mono view


Stereo pair view

A full contact list of Xenon with other atoms in the Xe binding site number 5 of Structure of Human Deoxy Hemoglobin A in Complex with Xenon within 5.0Å range: probe atom residue distance (Å) B Occ A:Xe1147 b:32.7 occ:0.20 XE A:XE1147 0.0 32.7 0.2 XE A:XE1147 0.9 28.9 0.3 CD1 A:PHE46 3.2 32.1 1.0 CE1 A:PHE46 3.2 36.0 1.0 CE1 A:PHE43 3.7 19.4 1.0 CB A:HIS58 3.7 19.8 1.0 CD1 A:PHE43 3.7 20.2 1.0 CD2 A:HIS58 3.9 21.8 1.0 CA A:VAL55 3.9 18.6 1.0 CG2 A:VAL55 3.9 19.3 1.0 CG A:HIS58 4.0 22.0 1.0 CZ A:PHE33 4.0 20.0 1.0 CE2 A:PHE33 4.1 15.8 1.0 CD2 A:LEU48 4.2 25.3 1.0 O A:GLN54 4.2 18.6 1.0 CZ A:PHE43 4.3 21.2 1.0 CG A:PHE46 4.3 29.2 1.0 CD1 A:LEU29 4.3 15.8 1.0 N A:VAL55 4.4 18.5 1.0 CZ A:PHE46 4.4 35.8 1.0 CB A:VAL55 4.4 18.4 1.0 CG A:PHE43 4.4 19.2 1.0 C A:GLN54 4.5 18.4 1.0 CG1 A:VAL55 4.8 20.2 1.0 CE2 A:PHE43 4.9 22.0 1.0 CD2 A:PHE43 4.9 21.4 1.0 NE2 A:HIS58 4.9 21.1 1.0 CB A:PHE46 5.0 24.6 1.0 O A:VAL55 5.0 17.1 1.0 C A:VAL55 5.0 18.7 1.0

Xenon binding site 6 out of 15 in the Structure of Human Deoxy Hemoglobin A in Complex with Xenon


Mono view


Stereo pair view

A full contact list of Xenon with other atoms in the Xe binding site number 6 of Structure of Human Deoxy Hemoglobin A in Complex with Xenon within 5.0Å range: probe atom residue distance (Å) B Occ B:Xe1150 b:20.2 occ:0.40 XE B:XE1150 0.0 20.2 0.4 XE B:XE1150 0.7 16.2 0.5 O B:HOH2109 3.5 38.3 1.0 O B:PHE103 3.6 13.9 1.0 CA B:GLY107 3.8 14.8 1.0 CBB B:HEM1147 3.8 20.5 1.0 N B:GLY107 4.0 14.5 1.0 O B:VAL134 4.1 14.9 1.0 CE1 B:PHE71 4.2 17.8 1.0 CG1 B:VAL137 4.2 18.0 1.0 CB B:VAL134 4.2 14.9 1.0 CAB B:HEM1147 4.3 18.2 1.0 CA B:VAL134 4.4 14.9 1.0 CD1 B:PHE71 4.4 17.2 1.0 CB B:VAL137 4.4 14.6 1.0 CG1 B:VAL134 4.5 13.1 1.0 C B:LEU106 4.7 14.4 1.0 C B:PHE103 4.7 14.7 1.0 C B:VAL134 4.7 15.0 1.0 N B:ALA138 4.8 15.9 1.0 CD2 B:LEU106 4.8 11.6 1.0 CG B:LEU106 4.9 11.8 1.0 CB B:LEU106 4.9 13.3 1.0

Xenon binding site 7 out of 15 in the Structure of Human Deoxy Hemoglobin A in Complex with Xenon


Mono view


Stereo pair view

A full contact list of Xenon with other atoms in the Xe binding site number 7 of Structure of Human Deoxy Hemoglobin A in Complex with Xenon within 5.0Å range: probe atom residue distance (Å) B Occ B:Xe1150 b:16.2 occ:0.50 XE B:XE1150 0.0 16.2 0.5 XE B:XE1150 0.7 20.2 0.4 O B:PHE103 3.4 13.9 1.0 O B:VAL134 3.7 14.9 1.0 CG1 B:VAL137 4.0 18.0 1.0 CBB B:HEM1147 4.0 20.5 1.0 CB B:VAL137 4.1 14.6 1.0 N B:ALA138 4.1 15.9 1.0 CA B:GLY107 4.1 14.8 1.0 O B:HOH2109 4.2 38.3 1.0 N B:GLY107 4.2 14.5 1.0 C B:PHE103 4.3 14.7 1.0 CAB B:HEM1147 4.4 18.2 1.0 CB B:VAL134 4.4 14.9 1.0 CA B:VAL134 4.4 14.9 1.0 CB B:ALA138 4.4 17.3 1.0 C B:VAL134 4.5 15.0 1.0 CA B:ALA138 4.5 16.3 1.0 CE1 B:PHE71 4.6 17.8 1.0 CB B:PHE103 4.6 13.9 1.0 C B:VAL137 4.7 15.8 1.0 CA B:PHE103 4.8 14.4 1.0 CD1 B:PHE71 4.8 17.2 1.0 CG1 B:VAL134 4.8 13.1 1.0 CA B:VAL137 5.0 14.6 1.0

Xenon binding site 8 out of 15 in the Structure of Human Deoxy Hemoglobin A in Complex with Xenon


Mono view


Stereo pair view

A full contact list of Xenon with other atoms in the Xe binding site number 8 of Structure of Human Deoxy Hemoglobin A in Complex with Xenon within 5.0Å range: probe atom residue distance (Å) B Occ B:Xe1151 b:42.1 occ:0.50 O B:HOH2002 3.4 34.0 1.0 CB B:ALA10 3.5 17.5 1.0 O B:HOH2121 4.0 18.7 1.0 CB B:PRO125 4.1 17.7 1.0 O B:PRO125 4.1 17.0 1.0 O B:GLU6 4.1 22.8 1.0 C B:PRO125 4.2 16.9 1.0 CA B:GLU7 4.4 21.4 1.0 N B:VAL126 4.4 16.4 1.0 CG B:GLU7 4.5 21.0 1.0 C B:GLU6 4.5 22.6 1.0 CG2 B:VAL126 4.6 15.8 1.0 N B:GLU7 4.6 21.7 1.0 O B:HOH2005 4.7 30.1 1.0 CA B:VAL126 4.7 16.4 1.0 CA B:PRO125 4.8 17.3 1.0 O B:HOH2120 5.0 27.1 1.0 CA B:ALA10 5.0 19.4 1.0

Xenon binding site 9 out of 15 in the Structure of Human Deoxy Hemoglobin A in Complex with Xenon


Mono view


Stereo pair view

A full contact list of Xenon with other atoms in the Xe binding site number 9 of Structure of Human Deoxy Hemoglobin A in Complex with Xenon within 5.0Å range: probe atom residue distance (Å) B Occ C:Xe1146 b:25.9 occ:0.50 CE2 C:PHE128 3.4 16.5 1.0 CE3 C:TRP14 3.6 25.3 1.0 CD2 C:PHE128 3.6 15.2 1.0 CZ3 C:TRP14 3.9 24.9 1.0 CD2 C:TRP14 4.0 23.6 1.0 CD2 C:LEU125 4.1 16.3 1.0 CD2 C:LEU129 4.4 20.0 1.0 CG2 C:VAL70 4.5 14.7 1.0 CZ C:PHE128 4.5 14.7 1.0 CD1 C:LEU109 4.6 14.2 0.5 CG C:TRP14 4.6 22.4 1.0 CH2 C:TRP14 4.6 25.9 1.0 CD2 C:LEU109 4.6 15.2 0.5 CE2 C:TRP14 4.7 24.4 1.0 CG1 C:VAL10 4.7 15.8 1.0 CB C:LEU66 4.8 14.9 1.0 CD1 C:LEU66 4.8 17.3 1.0 CG C:PHE128 4.9 16.1 1.0 CG C:LEU129 4.9 14.1 1.0 CB C:TRP14 4.9 22.9 1.0 CD2 C:LEU66 5.0 14.6 1.0 CZ2 C:TRP14 5.0 23.8 1.0

Xenon binding site 10 out of 15 in the Structure of Human Deoxy Hemoglobin A in Complex with Xenon


Mono view


Stereo pair view

A full contact list of Xenon with other atoms in the Xe binding site number 10 of Structure of Human Deoxy Hemoglobin A in Complex with Xenon within 5.0Å range: probe atom residue distance (Å) B Occ C:Xe1147 b:21.8 occ:0.20 XE C:XE1147 0.0 21.8 0.2 XE C:XE1147 2.1 18.6 0.2 CD1 C:LEU109 2.9 12.9 0.5 CD2 C:LEU105 3.5 16.9 1.0 CB C:TYR24 3.5 16.6 1.0 CG C:LEU109 3.9 11.1 0.5 C C:TYR24 3.9 14.3 1.0 O C:TYR24 4.0 12.9 1.0 CZ3 C:TRP14 4.0 24.9 1.0 CD2 C:LEU109 4.0 10.5 0.5 N C:GLY25 4.1 14.1 1.0 O C:LEU105 4.2 14.4 1.0 CH2 C:TRP14 4.3 25.9 1.0 CA C:TYR24 4.3 15.7 1.0 CD1 C:LEU109 4.4 14.2 0.5 CB C:THR108 4.4 13.3 1.0 CG C:LEU109 4.4 14.4 0.5 CG2 C:THR108 4.5 12.8 1.0 CA C:LEU105 4.5 13.1 1.0 CB C:LEU105 4.5 13.0 1.0 CG C:LEU105 4.6 14.3 1.0 CA C:GLY25 4.7 14.4 1.0 CG C:TYR24 4.7 18.9 1.0 CB C:ALA28 4.8 13.7 1.0 C C:LEU105 4.8 13.5 1.0 CD2 C:TYR24 4.9 20.1 1.0 N C:LEU109 4.9 12.9 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