Atomistry » Xenon, Xe » PDB 1w53-3pk4 » 2w6y
Atomistry »
  Xenon, Xe »
    PDB 1w53-3pk4 »
      2w6y »

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

Protein crystallography data

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

Other elements in 2w6y:

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

Xenon Binding Sites:

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 2w6y

Go back to Xenon Binding Sites List in 2w6y
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 2w6y

Go back to Xenon Binding Sites List in 2w6y
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 2w6y

Go back to Xenon Binding Sites List in 2w6y
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 2w6y

Go back to Xenon Binding Sites List in 2w6y
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

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

Last articles

Zn in 7M6U
Zn in 7NNG
Zn in 7NEE
Zn in 7NEU
Zn in 7M3K
Zn in 7KWD
Zn in 7KYH
Zn in 7KNG
Zn in 7KY2
Zn in 7KYF
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy