Atomistry » Xenon, Xe » PDB 1w53-3pk4 » 3bvd
Atomistry »
  Xenon, Xe »
    PDB 1w53-3pk4 »
      3bvd »

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

Go back to Xenon Binding Sites List in 3bvd
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

Go back to Xenon Binding Sites List in 3bvd
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

Go back to Xenon Binding Sites List in 3bvd
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: Wed Dec 16 02:39:43 2020

Last articles

Mg in 4Y52
Mg in 4Y30
Mg in 4Y2V
Mg in 4Y2X
Mg in 4Y2Y
Mg in 4Y2U
Mg in 4Y2T
Mg in 4Y2Q
Mg in 4Y2R
Mg in 4Y2S
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy