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Xenon in PDB 2w6x: Crystal Structure of Sperm Whale Myoglobin Mutant Yqrf in Complex with Xenon

Protein crystallography data

The structure of Crystal Structure of Sperm Whale Myoglobin Mutant Yqrf in Complex with Xenon, PDB code: 2w6x 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) 29.75 / 1.73
Space group P 6
Cell size a, b, c (Å), α, β, γ (°) 90.781, 90.781, 45.279, 90.00, 90.00, 120.00
R / Rfree (%) 15.9 / 19.5

Other elements in 2w6x:

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

Iron (Fe) 1 atom

Xenon Binding Sites:

The binding sites of Xenon atom in the Crystal Structure of Sperm Whale Myoglobin Mutant Yqrf in Complex with Xenon (pdb code 2w6x). This binding sites where shown within 5.0 Angstroms radius around Xenon atom.
In total 3 binding sites of Xenon where determined in the Crystal Structure of Sperm Whale Myoglobin Mutant Yqrf in Complex with Xenon, PDB code: 2w6x:
Jump to Xenon binding site number: 1; 2; 3;

Xenon binding site 1 out of 3 in 2w6x

Go back to Xenon Binding Sites List in 2w6x
Xenon binding site 1 out of 3 in the Crystal Structure of Sperm Whale Myoglobin Mutant Yqrf 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 Yqrf in Complex with Xenon within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Xe1155

b:14.2
occ:0.20
OG A:SER108 3.1 9.2 1.0
CD2 A:PHE138 3.3 12.3 1.0
CE2 A:PHE138 3.3 13.5 1.0
CBB A:HEM1154 3.5 15.1 1.0
CAB A:HEM1154 3.8 12.8 1.0
O A:LEU104 3.8 9.1 1.0
CG A:ARG139 4.0 8.3 1.0
CD2 A:LEU135 4.4 7.9 1.0
CD1 A:PHE107 4.5 14.4 1.0
CB A:SER108 4.5 8.1 1.0
CZ A:PHE138 4.5 13.7 1.0
CG A:PHE138 4.5 10.4 1.0
CB A:LEU104 4.5 9.9 1.0
CD A:ARG139 4.5 8.5 1.0
C A:LEU104 4.6 9.1 1.0
N A:SER108 4.7 7.5 1.0
O A:LEU135 4.8 7.6 1.0
CA A:SER108 4.8 7.7 1.0
CB A:LEU135 4.8 6.7 1.0
CA A:LEU104 4.8 9.2 1.0
CD2 A:LEU104 5.0 11.4 1.0

Xenon binding site 2 out of 3 in 2w6x

Go back to Xenon Binding Sites List in 2w6x
Xenon binding site 2 out of 3 in the Crystal Structure of Sperm Whale Myoglobin Mutant Yqrf 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 Yqrf in Complex with Xenon within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Xe1156

b:9.0
occ:0.50
CZ A:PHE107 3.5 13.8 1.0
CE2 A:TYR29 3.6 15.4 1.0
CD2 A:TYR29 3.6 15.0 1.0
CE2 A:PHE107 3.7 15.4 1.0
O A:GLY25 3.8 6.5 1.0
CZ A:TYR29 3.9 16.5 1.0
CA A:GLY65 4.0 8.5 1.0
CG2 A:ILE28 4.0 6.6 1.0
CG A:TYR29 4.0 12.0 1.0
CA A:GLY25 4.1 6.1 1.0
CD2 A:LEU69 4.1 7.8 1.0
CG A:LEU69 4.1 6.8 1.0
CB A:ILE28 4.2 6.2 1.0
CE1 A:TYR29 4.2 15.5 1.0
O A:GLY65 4.2 8.0 1.0
CD1 A:TYR29 4.3 14.7 1.0
CG1 A:VAL68 4.3 9.2 1.0
C A:GLY25 4.4 6.5 1.0
CB A:VAL68 4.4 8.8 1.0
N A:TYR29 4.5 7.2 1.0
OH A:TYR29 4.5 18.0 1.0
C A:GLY65 4.6 8.6 1.0
CD1 A:LEU69 4.7 7.9 1.0
CB A:TYR29 4.8 9.5 1.0
CE1 A:PHE107 4.8 15.9 1.0
O A:HOH2056 4.9 24.4 1.0
C A:ILE28 5.0 6.6 1.0
CA A:TYR29 5.0 8.9 1.0

Xenon binding site 3 out of 3 in 2w6x

Go back to Xenon Binding Sites List in 2w6x
Xenon binding site 3 out of 3 in the Crystal Structure of Sperm Whale Myoglobin Mutant Yqrf 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 Yqrf in Complex with Xenon within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Xe1157

b:15.3
occ:1.00
CG A:HIS93 3.7 9.0 1.0
CD2 A:HIS93 3.8 8.6 1.0
C3B A:HEM1154 3.9 12.4 1.0
CZ A:PHE138 4.0 13.7 1.0
ND1 A:HIS93 4.0 9.3 1.0
C4B A:HEM1154 4.0 10.9 1.0
CD2 A:LEU104 4.1 11.4 1.0
NE2 A:HIS93 4.1 8.0 1.0
CB A:HIS93 4.1 8.4 1.0
CE1 A:HIS93 4.2 9.7 1.0
C2B A:HEM1154 4.2 11.6 1.0
CD1 A:ILE142 4.3 11.0 1.0
NB A:HEM1154 4.3 10.4 1.0
CAB A:HEM1154 4.3 12.8 1.0
CHC A:HEM1154 4.4 11.0 1.0
CD1 A:LEU104 4.5 12.6 1.0
C1B A:HEM1154 4.5 11.2 1.0
CB A:LEU89 4.5 10.3 1.0
CE2 A:PHE138 4.5 13.5 1.0
O A:LEU89 4.5 9.1 1.0
CG1 A:ILE142 4.7 10.0 1.0
CD2 A:LEU89 4.8 14.6 1.0
C A:LEU89 4.8 9.1 1.0
CG2 A:ILE142 4.8 10.0 1.0
CG A:LEU104 4.9 10.2 1.0
CMB A:HEM1154 5.0 12.2 1.0
CE1 A:PHE138 5.0 13.9 1.0
OH A:TYR146 5.0 11.6 1.0

Reference:

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.
Page generated: Wed Dec 16 02:39:40 2020

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