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Xenon in PDB 4nxa: Sperm Whale Myoglobin Under Xenon Pressure 30 Bar

Protein crystallography data

The structure of Sperm Whale Myoglobin Under Xenon Pressure 30 Bar, PDB code: 4nxa was solved by N.Colloc'h, T.Prange, B.Vallone, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 1.60
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 35.370, 30.717, 63.583, 90.00, 104.48, 90.00
R / Rfree (%) 18.5 / 20.2

Other elements in 4nxa:

The structure of Sperm Whale Myoglobin Under Xenon Pressure 30 Bar also contains other interesting chemical elements:

Iron (Fe) 1 atom
Zinc (Zn) 2 atoms

Xenon Binding Sites:

The binding sites of Xenon atom in the Sperm Whale Myoglobin Under Xenon Pressure 30 Bar (pdb code 4nxa). This binding sites where shown within 5.0 Angstroms radius around Xenon atom.
In total 5 binding sites of Xenon where determined in the Sperm Whale Myoglobin Under Xenon Pressure 30 Bar, PDB code: 4nxa:
Jump to Xenon binding site number: 1; 2; 3; 4; 5;

Xenon binding site 1 out of 5 in 4nxa

Go back to Xenon Binding Sites List in 4nxa
Xenon binding site 1 out of 5 in the Sperm Whale Myoglobin Under Xenon Pressure 30 Bar


Mono view


Stereo pair view

A full contact list of Xenon with other atoms in the Xe binding site number 1 of Sperm Whale Myoglobin Under Xenon Pressure 30 Bar within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Xe207

b:26.2
occ:0.80
CG A:HIS93 3.8 14.5 1.0
CD2 A:HIS93 3.9 14.4 1.0
ND1 A:HIS93 3.9 15.7 1.0
C4B A:HEM201 4.0 13.0 1.0
C3B A:HEM201 4.0 13.7 1.0
NE2 A:HIS93 4.1 13.7 1.0
CD1 A:ILE142 4.1 21.4 1.0
CE1 A:HIS93 4.1 15.3 1.0
C2B A:HEM201 4.2 13.4 1.0
CZ A:PHE138 4.2 30.7 1.0
NB A:HEM201 4.2 13.5 1.0
CD2 A:LEU104 4.2 20.8 1.0
C1B A:HEM201 4.2 13.2 1.0
CB A:HIS93 4.3 14.8 1.0
CHC A:HEM201 4.4 13.1 1.0
O A:LEU89 4.4 18.6 1.0
CD2 A:LEU89 4.5 27.1 1.0
CAB A:HEM201 4.5 14.5 1.0
CB A:LEU89 4.5 21.8 1.0
CE2 A:PHE138 4.5 30.5 1.0
CD1 A:LEU104 4.6 22.1 1.0
C A:LEU89 4.8 19.0 1.0
CMB A:HEM201 4.9 15.5 1.0
CG1 A:ILE142 4.9 20.2 1.0

Xenon binding site 2 out of 5 in 4nxa

Go back to Xenon Binding Sites List in 4nxa
Xenon binding site 2 out of 5 in the Sperm Whale Myoglobin Under Xenon Pressure 30 Bar


Mono view


Stereo pair view

A full contact list of Xenon with other atoms in the Xe binding site number 2 of Sperm Whale Myoglobin Under Xenon Pressure 30 Bar within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Xe208

b:25.4
occ:0.15
CD2 A:PHE138 2.4 29.8 1.0
CE2 A:PHE138 2.7 30.5 1.0
OG A:SER108 3.4 15.4 1.0
CG A:PHE138 3.6 26.0 1.0
CG A:ARG139 4.0 19.8 1.0
CZ A:PHE138 4.0 30.7 1.0
O A:LEU104 4.1 16.0 1.0
O A:LEU135 4.1 16.4 1.0
CB A:PHE138 4.2 21.4 1.0
CAB A:HEM201 4.4 14.5 1.0
CBB A:HEM201 4.4 15.7 1.0
CB A:LEU104 4.4 16.4 1.0
CD2 A:LEU135 4.5 17.2 1.0
N A:ARG139 4.7 16.4 1.0
CD1 A:PHE138 4.7 27.4 1.0
CG2 A:ILE107 4.8 13.2 1.0
C A:LEU104 4.8 14.9 1.0
CB A:SER108 4.8 13.4 1.0
CB A:LEU135 4.8 15.2 1.0
CE1 A:PHE138 4.9 31.1 1.0
CD A:ARG139 4.9 19.5 1.0
CA A:LEU104 4.9 15.4 1.0
C A:LEU135 5.0 14.8 1.0
CA A:LEU135 5.0 14.8 1.0

Xenon binding site 3 out of 5 in 4nxa

Go back to Xenon Binding Sites List in 4nxa
Xenon binding site 3 out of 5 in the Sperm Whale Myoglobin Under Xenon Pressure 30 Bar


Mono view


Stereo pair view

A full contact list of Xenon with other atoms in the Xe binding site number 3 of Sperm Whale Myoglobin Under Xenon Pressure 30 Bar within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Xe209

b:33.9
occ:0.30
O A:HOH318 3.2 34.6 1.0
O A:ALA134 3.4 14.6 1.0
CE1 A:HIS82 3.5 27.3 1.0
ND1 A:HIS82 3.6 27.7 1.0
CB A:PHE138 3.9 21.4 1.0
N A:PHE138 3.9 17.1 1.0
CA A:PHE138 4.0 19.4 1.0
CG2 A:ILE75 4.1 21.4 1.0
CD2 A:LEU137 4.1 22.1 1.0
CD2 A:LEU76 4.2 24.8 1.0
CH2 A:TRP7 4.2 30.6 1.0
C A:ALA134 4.3 13.9 1.0
CG A:LEU137 4.4 21.7 1.0
CB A:LEU137 4.4 19.2 1.0
C A:LEU137 4.6 17.8 1.0
CD1 A:PHE138 4.6 27.4 1.0
NE2 A:HIS82 4.6 25.6 1.0
CG A:PHE138 4.7 26.0 1.0
CG A:HIS82 4.8 26.2 1.0
CA A:ALA134 4.8 15.2 1.0
CZ3 A:TRP7 5.0 29.7 1.0
CB A:ALA134 5.0 15.0 1.0
O A:ILE75 5.0 21.8 1.0

Xenon binding site 4 out of 5 in 4nxa

Go back to Xenon Binding Sites List in 4nxa
Xenon binding site 4 out of 5 in the Sperm Whale Myoglobin Under Xenon Pressure 30 Bar


Mono view


Stereo pair view

A full contact list of Xenon with other atoms in the Xe binding site number 4 of Sperm Whale Myoglobin Under Xenon Pressure 30 Bar within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Xe210

b:27.4
occ:0.25
CG1 A:VAL68 3.4 14.4 1.0
CB A:VAL68 3.6 13.2 1.0
CG2 A:ILE28 3.6 14.5 1.0
O A:GLY25 3.8 15.2 1.0
CG A:LEU29 3.9 13.9 1.0
CB A:ILE28 3.9 13.3 1.0
CD2 A:LEU69 4.0 18.8 1.0
CG A:LEU69 4.0 16.4 1.0
CD2 A:LEU29 4.0 15.9 1.0
O A:GLY65 4.0 12.9 1.0
CA A:GLY25 4.2 14.0 1.0
CA A:GLY65 4.3 12.8 1.0
CG2 A:VAL68 4.4 14.4 1.0
C A:GLY25 4.4 15.2 1.0
CD1 A:ILE28 4.5 15.4 1.0
CD1 A:LEU29 4.5 14.6 1.0
N A:LEU69 4.5 14.2 1.0
N A:LEU29 4.6 12.6 1.0
C A:GLY65 4.6 13.1 1.0
CD1 A:ILE107 4.7 14.6 1.0
CA A:VAL68 4.8 13.3 1.0
CD1 A:LEU69 4.8 16.5 1.0
C A:VAL68 4.9 13.4 1.0
CG1 A:ILE28 4.9 14.8 1.0
C A:ILE28 5.0 13.2 1.0
CA A:ILE28 5.0 13.6 1.0

Xenon binding site 5 out of 5 in 4nxa

Go back to Xenon Binding Sites List in 4nxa
Xenon binding site 5 out of 5 in the Sperm Whale Myoglobin Under Xenon Pressure 30 Bar


Mono view


Stereo pair view

A full contact list of Xenon with other atoms in the Xe binding site number 5 of Sperm Whale Myoglobin Under Xenon Pressure 30 Bar within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Xe211

b:31.6
occ:0.15
CD1 A:ILE28 2.8 15.4 1.0
CD2 A:LEU115 3.8 19.9 1.0
CG A:LEU115 3.9 17.9 1.0
CG2 A:ILE111 3.9 13.6 1.0
CG1 A:ILE28 4.0 14.8 1.0
CG2 A:VAL17 4.0 19.6 1.0
CD2 A:HIS24 4.1 15.4 1.0
CB A:HIS24 4.2 13.7 1.0
CG1 A:VAL17 4.2 19.6 1.0
CZ3 A:TRP14 4.4 25.7 1.0
O A:ILE111 4.4 13.8 1.0
CG A:HIS24 4.5 14.3 1.0
CD1 A:LEU115 4.5 19.4 1.0
CD1 A:LEU69 4.5 16.5 1.0
CD2 A:LEU69 4.5 18.8 1.0
CH2 A:TRP14 4.6 26.1 1.0
CB A:ILE111 4.7 12.7 1.0
CA A:ILE111 4.8 12.7 1.0
CB A:VAL17 4.8 19.0 1.0
CG1 A:ILE111 4.8 13.9 1.0
CG1 A:VAL114 4.9 15.4 1.0

Reference:

J.H.Abraini, G.Marassio, H.N.David, B.Vallone, T.Prange, N.Colloc'h. Crystallographic Studies with Xenon and Nitrous Oxide Provide Evidence For Protein-Dependent Processes in the Mechanisms of General Anesthesia Anesthesiology 2014.
ISSN: ESSN 1528-1175
PubMed: 25211169
DOI: 10.1097/ALN.0000000000000435
Page generated: Wed Dec 16 02:40:06 2020

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