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Xenon in PDB 3bvd: Structure of Surface-Engineered Cytochrome BA3 Oxidase From Thermus Thermophilus Under Xenon Pressure, 100PSI 5MIN

Enzymatic activity of Structure of Surface-Engineered Cytochrome BA3 Oxidase From Thermus Thermophilus Under Xenon Pressure, 100PSI 5MIN

All present enzymatic activity of Structure of Surface-Engineered Cytochrome BA3 Oxidase From Thermus Thermophilus Under Xenon Pressure, 100PSI 5MIN:
1.9.3.1;

Protein crystallography data

The structure of Structure of Surface-Engineered Cytochrome BA3 Oxidase From Thermus Thermophilus Under Xenon Pressure, 100PSI 5MIN, PDB code: 3bvd was solved by V.M.Luna, Y.Chen, J.A.Fee, C.D.Stout, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 26.96 / 3.37
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 119.726, 119.726, 153.535, 90.00, 90.00, 90.00
R / Rfree (%) 29.2 / 33.6

Other elements in 3bvd:

The structure of Structure of Surface-Engineered Cytochrome BA3 Oxidase From Thermus Thermophilus Under Xenon Pressure, 100PSI 5MIN also contains other interesting chemical elements:

Iron (Fe) 2 atoms
Copper (Cu) 3 atoms

Xenon Binding Sites:

The binding sites of Xenon atom in the Structure of Surface-Engineered Cytochrome BA3 Oxidase From Thermus Thermophilus Under Xenon Pressure, 100PSI 5MIN (pdb code 3bvd). This binding sites where shown within 5.0 Angstroms radius around Xenon atom.
In total 7 binding sites of Xenon where determined in the Structure of Surface-Engineered Cytochrome BA3 Oxidase From Thermus Thermophilus Under Xenon Pressure, 100PSI 5MIN, PDB code: 3bvd:
Jump to Xenon binding site number: 1; 2; 3; 4; 5; 6; 7;

Xenon binding site 1 out of 7 in 3bvd

Go back to Xenon Binding Sites List in 3bvd
Xenon binding site 1 out of 7 in the Structure of Surface-Engineered Cytochrome BA3 Oxidase From Thermus Thermophilus Under Xenon Pressure, 100PSI 5MIN


Mono view


Stereo pair view

A full contact list of Xenon with other atoms in the Xe binding site number 1 of Structure of Surface-Engineered Cytochrome BA3 Oxidase From Thermus Thermophilus Under Xenon Pressure, 100PSI 5MIN within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Xe805

b:85.5
occ:0.96
 O A:GLY232 3.6 85.5 1.0
OH A:TYR133 3.6 85.5 1.0
CZ3 A:TRP229 3.7 85.5 1.0
CE2 A:TYR133 3.8 85.5 1.0
CH2 A:TRP229 3.9 85.5 1.0
CZ A:TYR133 4.0 85.5 1.0
CG2 A:ILE235 4.1 85.5 1.0
CH2 A:TRP239 4.4 85.5 1.0
CA A:GLY232 4.4 85.5 1.0
C A:GLY232 4.4 85.5 1.0
CBA A:HAS801 4.4 85.5 1.0
CZ2 A:TRP239 4.5 85.5 1.0
CE2 A:PHE228 4.5 85.5 1.0
CG1 A:VAL236 4.7 85.5 1.0
CZ A:PHE228 4.7 85.5 1.0
CE3 A:TRP229 4.8 85.5 1.0
CD2 A:TYR133 4.9 85.5 1.0
CMA A:HAS801 4.9 85.5 1.0
XE A:XE810 4.9 85.5 0.3

Xenon binding site 2 out of 7 in 3bvd

Go back to Xenon Binding Sites List in 3bvd
Xenon binding site 2 out of 7 in the Structure of Surface-Engineered Cytochrome BA3 Oxidase From Thermus Thermophilus Under Xenon Pressure, 100PSI 5MIN


Mono view


Stereo pair view

A full contact list of Xenon with other atoms in the Xe binding site number 2 of Structure of Surface-Engineered Cytochrome BA3 Oxidase From Thermus Thermophilus Under Xenon Pressure, 100PSI 5MIN within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Xe806

b:85.5
occ:0.80
 CB A:ALA120 3.8 85.5 1.0
CG1 A:VAL74 3.9 85.5 1.0
CG2 A:VAL79 4.0 85.5 1.0
CA A:ALA149 4.1 85.5 1.0
CB A:ALA149 4.2 85.5 1.0
CG A:PHE152 4.3 85.5 1.0
CD1 A:LEU117 4.4 85.5 1.0
CB A:PHE152 4.4 85.5 1.0
CD1 A:PHE152 4.4 85.5 1.0
CA A:LEU117 4.5 85.5 1.0
N A:ALA149 4.5 85.5 1.0
CD2 A:PHE152 4.8 85.5 1.0
XE A:XE811 4.8 85.5 0.3
O A:GLY116 4.8 85.5 1.0
O A:LEU117 4.9 85.5 1.0
CE1 A:PHE152 4.9 85.5 1.0
C A:GLY148 5.0 85.5 1.0

Xenon binding site 3 out of 7 in 3bvd

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Xenon binding site 3 out of 7 in the Structure of Surface-Engineered Cytochrome BA3 Oxidase From Thermus Thermophilus Under Xenon Pressure, 100PSI 5MIN


Mono view


Stereo pair view

A full contact list of Xenon with other atoms in the Xe binding site number 3 of Structure of Surface-Engineered Cytochrome BA3 Oxidase From Thermus Thermophilus Under Xenon Pressure, 100PSI 5MIN within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Xe807

b:85.5
occ:0.73
 CD1 A:LEU208 3.6 85.5 1.0
CZ A:PHE135 3.7 85.5 1.0
OG A:SER150 3.9 85.5 1.0
O A:TYR146 3.9 85.5 1.0
CE1 A:PHE135 4.2 85.5 1.0
CE2 A:PHE135 4.2 85.5 1.0
CB A:ALA149 4.3 85.5 1.0
CB A:ALA204 4.3 85.5 1.0
N A:SER150 4.4 85.5 1.0
CD1 A:LEU200 4.5 85.5 1.0
CD2 A:TYR146 4.6 85.5 1.0
CG A:LEU200 4.6 85.5 1.0
CA A:TYR146 4.7 85.5 1.0
CA A:SER150 4.7 85.5 1.0
CD2 A:LEU200 4.8 85.5 1.0
C A:TYR146 4.8 85.5 1.0
C A:ALA149 4.8 85.5 1.0
CB A:SER150 4.9 85.5 1.0

Xenon binding site 4 out of 7 in 3bvd

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Xenon binding site 4 out of 7 in the Structure of Surface-Engineered Cytochrome BA3 Oxidase From Thermus Thermophilus Under Xenon Pressure, 100PSI 5MIN


Mono view


Stereo pair view

A full contact list of Xenon with other atoms in the Xe binding site number 4 of Structure of Surface-Engineered Cytochrome BA3 Oxidase From Thermus Thermophilus Under Xenon Pressure, 100PSI 5MIN within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Xe808

b:85.5
occ:0.61
 CG2 A:VAL201 3.2 85.5 1.0
CA A:VAL201 3.7 85.5 1.0
CG1 A:VAL153 3.7 85.5 1.0
N A:VAL201 3.8 85.5 1.0
CB A:VAL153 3.9 85.5 1.0
O A:SER150 4.0 85.5 1.0
CB A:VAL201 4.0 85.5 1.0
C A:LEU200 4.2 85.5 1.0
CD2 A:LEU200 4.3 85.5 1.0
O A:LEU200 4.3 85.5 1.0
CA A:SER150 4.3 85.5 1.0
CG A:LEU200 4.4 85.5 1.0
CB A:LEU200 4.6 85.5 1.0
C A:SER150 4.6 85.5 1.0
CG2 A:VAL153 4.7 85.5 1.0
CG A:LEU154 4.7 85.5 1.0
CB A:ALA204 4.7 85.5 1.0
OG A:SER150 4.7 85.5 1.0
CB A:SER150 4.8 85.5 1.0
CD1 A:LEU154 4.9 85.5 1.0
CG1 A:VAL201 5.0 85.5 1.0
C A:VAL153 5.0 85.5 1.0
C A:VAL201 5.0 85.5 1.0
O A:SER197 5.0 85.5 1.0
CA A:VAL153 5.0 85.5 1.0

Xenon binding site 5 out of 7 in 3bvd

Go back to Xenon Binding Sites List in 3bvd
Xenon binding site 5 out of 7 in the Structure of Surface-Engineered Cytochrome BA3 Oxidase From Thermus Thermophilus Under Xenon Pressure, 100PSI 5MIN


Mono view


Stereo pair view

A full contact list of Xenon with other atoms in the Xe binding site number 5 of Structure of Surface-Engineered Cytochrome BA3 Oxidase From Thermus Thermophilus Under Xenon Pressure, 100PSI 5MIN within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Xe809

b:85.5
occ:0.60
 XE A:XE810 2.7 85.5 0.3
CE1 A:PHE228 3.7 85.5 1.0
CZ A:PHE228 3.8 85.5 1.0
CD2 A:LEU200 3.8 85.5 1.0
CD1 A:ILE78 3.9 85.5 1.0
CD1 A:LEU200 4.2 85.5 1.0
CD1 A:ILE235 4.4 85.5 1.0
CZ A:PHE135 4.4 85.5 1.0
O A:TYR133 4.5 85.5 1.0
CE2 A:PHE135 4.6 85.5 1.0
CG A:LEU200 4.6 85.5 1.0
CD1 A:PHE228 4.6 85.5 1.0
CG1 A:ILE78 4.7 85.5 1.0
CE2 A:PHE228 4.8 85.5 1.0

Xenon binding site 6 out of 7 in 3bvd

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Xenon binding site 6 out of 7 in the Structure of Surface-Engineered Cytochrome BA3 Oxidase From Thermus Thermophilus Under Xenon Pressure, 100PSI 5MIN


Mono view


Stereo pair view

A full contact list of Xenon with other atoms in the Xe binding site number 6 of Structure of Surface-Engineered Cytochrome BA3 Oxidase From Thermus Thermophilus Under Xenon Pressure, 100PSI 5MIN within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Xe810

b:85.5
occ:0.27
 XE A:XE809 2.7 85.5 0.6
O A:PHE228 3.5 85.5 1.0
CZ A:PHE228 3.7 85.5 1.0
CA A:GLY232 3.7 85.5 1.0
N A:GLY232 3.7 85.5 1.0
CE1 A:PHE228 3.8 85.5 1.0
C A:THR231 3.9 85.5 1.0
CB A:THR231 3.9 85.5 1.0
CE2 A:PHE228 3.9 85.5 1.0
CD1 A:PHE228 4.1 85.5 1.0
O A:THR231 4.1 85.5 1.0
CG2 A:THR231 4.2 85.5 1.0
CD2 A:PHE228 4.2 85.5 1.0
CD1 A:LEU200 4.3 85.5 1.0
CG A:PHE228 4.3 85.5 1.0
CD2 A:LEU200 4.4 85.5 1.0
CA A:THR231 4.5 85.5 1.0
CG2 A:ILE235 4.5 85.5 1.0
C A:PHE228 4.5 85.5 1.0
CD1 A:ILE235 4.6 85.5 1.0
CG A:LEU200 4.7 85.5 1.0
CB A:LEU200 4.7 85.5 1.0
XE A:XE805 4.9 85.5 1.0
OG1 A:THR231 4.9 85.5 1.0
C A:GLY232 4.9 85.5 1.0
CB A:ILE235 5.0 85.5 1.0
CA A:PHE228 5.0 85.5 1.0

Xenon binding site 7 out of 7 in 3bvd

Go back to Xenon Binding Sites List in 3bvd
Xenon binding site 7 out of 7 in the Structure of Surface-Engineered Cytochrome BA3 Oxidase From Thermus Thermophilus Under Xenon Pressure, 100PSI 5MIN


Mono view


Stereo pair view

A full contact list of Xenon with other atoms in the Xe binding site number 7 of Structure of Surface-Engineered Cytochrome BA3 Oxidase From Thermus Thermophilus Under Xenon Pressure, 100PSI 5MIN within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Xe811

b:85.5
occ:0.32
 CB A:ALA149 3.7 85.5 1.0
CE2 A:PHE135 3.7 85.5 1.0
CE1 A:PHE145 3.8 85.5 1.0
CZ A:PHE145 4.1 85.5 1.0
CG1 A:VAL74 4.3 85.5 1.0
CD2 A:PHE135 4.3 85.5 1.0
CG2 A:VAL74 4.3 85.5 1.0
CG2 A:ILE78 4.7 85.5 1.0
CG1 A:ILE78 4.7 85.5 1.0
CZ A:PHE135 4.8 85.5 1.0
XE A:XE806 4.8 85.5 0.8
CD1 A:PHE145 4.8 85.5 1.0
O A:TYR133 4.8 85.5 1.0
CB A:VAL74 4.9 85.5 1.0
CB A:ILE78 4.9 85.5 1.0
CA A:ALA149 5.0 85.5 1.0

Reference:

V.M.Luna, Y.Chen, J.A.Fee, C.D.Stout. Crystallographic Studies of Xe and Kr Binding Within the Large Internal Cavity of Cytochrome BA3 From Thermus Thermophilus: Structural Analysis and Role of Oxygen Transport Channels in the Heme-Cu Oxidases. Biochemistry V. 47 4657 2008.
ISSN: ISSN 0006-2960
PubMed: 18376849
DOI: 10.1021/BI800045Y
Page generated: Sat Oct 12 18:34:51 2024

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