Xenon in PDB 2w6y: Crystal Structure of Sperm Whale Myoglobin Mutant Yqr in Complex with Xenon

The structure of Crystal Structure of Sperm Whale Myoglobin Mutant Yqr in Complex with Xenon, PDB code: 2w6y was solved by A.E.Miele, F.Draghi, F.Renzi, G.Sciara, K.A.Johnson, 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)	26.00 / 1.60
Space group	P 6
Cell size a, b, c (Å), α, β, γ (°)	90.626, 90.626, 45.505, 90.00, 90.00, 120.00
R / Rfree (%)	16.5 / 19.6

The structure of Crystal Structure of Sperm Whale Myoglobin Mutant Yqr in Complex with Xenon also contains other interesting chemical elements:

Iron

(Fe)

1 atom

The binding sites of Xenon atom in the Crystal Structure of Sperm Whale Myoglobin Mutant Yqr in Complex with Xenon (pdb code 2w6y). This binding sites where shown within 5.0 Angstroms radius around Xenon atom.
In total 4 binding sites of Xenon where determined in the Crystal Structure of Sperm Whale Myoglobin Mutant Yqr in Complex with Xenon, PDB code: 2w6y:
Jump to Xenon binding site number: 1; 2; 3; 4;

Xenon binding site 1 out of 4 in the Crystal Structure of Sperm Whale Myoglobin Mutant Yqr 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 Crystal Structure of Sperm Whale Myoglobin Mutant Yqr in Complex with Xenon within 5.0Å range: probe atom residue distance (Å) B Occ A:Xe1158 b:43.0 occ:0.20 CE2 A:PHE138 2.8 8.9 1.0 CD2 A:PHE138 2.9 7.6 1.0 OG A:SER108 3.1 6.2 1.0 CBB A:HEM1154 3.6 8.7 1.0 CAB A:HEM1154 3.8 6.2 1.0 O A:LEU104 3.9 6.0 1.0 CG A:ARG139 4.0 5.3 1.0 CZ A:PHE138 4.0 9.4 1.0 CG2 A:ILE107 4.1 5.7 1.0 CG A:PHE138 4.2 7.1 1.0 CB A:SER108 4.5 6.3 1.0 CB A:LEU104 4.5 6.6 1.0 CD2 A:LEU135 4.5 6.8 1.0 CD A:ARG139 4.5 7.0 1.0 C A:LEU104 4.7 6.3 1.0 O A:LEU135 4.8 6.7 1.0 N A:SER108 4.8 4.8 1.0 CA A:SER108 4.8 5.4 1.0 CA A:LEU104 4.8 6.1 1.0 CB A:LEU135 4.9 6.2 1.0 CB A:PHE138 5.0 7.0 1.0

Xenon binding site 2 out of 4 in the Crystal Structure of Sperm Whale Myoglobin Mutant Yqr 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 Crystal Structure of Sperm Whale Myoglobin Mutant Yqr in Complex with Xenon within 5.0Å range: probe atom residue distance (Å) B Occ A:Xe1159 b:2.0 occ:0.40 CG2 A:ILE28 3.8 5.0 1.0 O A:GLY25 3.9 5.1 1.0 CD2 A:TYR29 4.0 7.6 1.0 CE2 A:TYR29 4.0 9.0 1.0 CG1 A:VAL68 4.0 6.2 1.0 CB A:VAL68 4.1 7.0 1.0 CA A:GLY65 4.1 6.2 1.0 CB A:ILE28 4.1 4.4 1.0 CD2 A:LEU69 4.1 5.7 1.0 CG A:TYR29 4.1 6.9 1.0 CZ A:TYR29 4.2 8.9 1.0 CA A:GLY25 4.2 4.7 1.0 CG A:LEU69 4.2 5.4 1.0 O A:GLY65 4.3 6.2 1.0 CE1 A:TYR29 4.3 8.9 1.0 CD1 A:TYR29 4.3 8.0 1.0 CD1 A:ILE107 4.4 5.1 1.0 N A:TYR29 4.4 5.7 1.0 C A:GLY25 4.5 5.1 1.0 CG2 A:VAL68 4.6 7.7 1.0 C A:GLY65 4.7 6.4 1.0 OH A:TYR29 4.8 13.4 1.0 CD1 A:LEU69 4.8 7.7 1.0 CB A:TYR29 4.9 7.3 1.0 C A:ILE28 4.9 5.4 1.0 CA A:TYR29 5.0 6.4 1.0

Xenon binding site 3 out of 4 in the Crystal Structure of Sperm Whale Myoglobin Mutant Yqr 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 Crystal Structure of Sperm Whale Myoglobin Mutant Yqr in Complex with Xenon within 5.0Å range: probe atom residue distance (Å) B Occ A:Xe1160 b:8.2 occ:0.72 CG A:LEU89 3.5 8.5 0.5 CG A:HIS93 3.7 6.8 1.0 CD2 A:HIS93 3.8 6.2 1.0 CD2 A:LEU89 3.8 8.9 0.5 CZ A:PHE138 3.9 9.4 1.0 C3B A:HEM1154 4.0 4.8 1.0 CD2 A:LEU104 4.0 7.5 1.0 CD1 A:LEU89 4.0 10.3 0.5 C4B A:HEM1154 4.1 5.4 1.0 ND1 A:HIS93 4.1 6.5 1.0 CB A:HIS93 4.1 5.4 1.0 NE2 A:HIS93 4.1 5.4 1.0 C2B A:HEM1154 4.3 5.6 1.0 CE1 A:HIS93 4.3 7.1 1.0 CD1 A:LEU104 4.3 8.1 1.0 CD1 A:ILE142 4.4 9.7 1.0 NB A:HEM1154 4.4 4.5 1.0 CAB A:HEM1154 4.4 6.2 1.0 C1B A:HEM1154 4.5 4.7 1.0 CHC A:HEM1154 4.5 6.3 1.0 O A:LEU89 4.5 6.1 1.0 CB A:LEU89 4.5 7.0 0.5 CE2 A:PHE138 4.6 8.9 1.0 CG1 A:ILE142 4.6 8.0 1.0 CB A:LEU89 4.6 7.9 0.5 CE1 A:PHE138 4.8 9.2 1.0 CG2 A:ILE142 4.8 7.6 1.0 C A:LEU89 4.8 6.7 1.0 CG A:LEU104 4.8 6.5 1.0 OH A:TYR146 4.9 8.6 1.0 CMB A:HEM1154 4.9 5.6 1.0 CD2 A:LEU89 4.9 6.0 0.5

Xenon binding site 4 out of 4 in the Crystal Structure of Sperm Whale Myoglobin Mutant Yqr 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 Crystal Structure of Sperm Whale Myoglobin Mutant Yqr in Complex with Xenon within 5.0Å range: probe atom residue distance (Å) B Occ A:Xe1161 b:8.9 occ:0.20 O A:HOH2119 3.0 8.1 1.0 O A:ALA134 3.2 5.9 1.0 CE1 A:HIS82 3.3 7.9 1.0 ND1 A:HIS82 3.5 8.3 1.0 CB A:PHE138 3.6 7.0 1.0 N A:PHE138 3.7 6.1 1.0 CA A:PHE138 3.8 6.1 1.0 CG2 A:ILE75 3.9 6.6 1.0 CH2 A:TRP7 4.1 7.0 1.0 C A:ALA134 4.1 5.5 1.0 CD2 A:LEU137 4.2 8.4 1.0 CG A:LEU137 4.3 6.9 1.0 CB A:LEU137 4.3 6.7 1.0 CD2 A:LEU76 4.4 6.5 1.0 C A:LEU137 4.5 6.1 1.0 NE2 A:HIS82 4.6 7.1 1.0 CA A:ALA134 4.6 5.4 1.0 CG A:PHE138 4.7 7.1 1.0 CB A:ALA134 4.8 5.9 1.0 CZ3 A:TRP7 4.8 6.4 1.0 CG A:HIS82 4.8 7.4 1.0 CD1 A:PHE138 4.9 8.1 1.0 CA A:LEU137 5.0 6.4 1.0

A.E.Miele, F.Draghi, K.A.Johnson, F.Renzi, G.Sciara, M.Brunori, B.Vallone, C.Savino. When the Same Fold Does Not Mean the Same Function: the Case of Xenon Cavities in Hemoglobin and Myoglobin To Be Published.