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:
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
![](/pictures/XE/pdb/bv/3bvd-XE-sphere_01.jpg) Mono view
![](/pictures/XE/pdb/bv/3bvd-XE-sphere_01_stereo.jpg) 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
![](/pictures/XE/pdb/bv/3bvd-XE-sphere_02.jpg) Mono view
![](/pictures/XE/pdb/bv/3bvd-XE-sphere_02_stereo.jpg) 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
![](/pictures/XE/pdb/bv/3bvd-XE-sphere_03.jpg) Mono view
![](/pictures/XE/pdb/bv/3bvd-XE-sphere_03_stereo.jpg) 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
![](/pictures/XE/pdb/bv/3bvd-XE-sphere_04.jpg) Mono view
![](/pictures/XE/pdb/bv/3bvd-XE-sphere_04_stereo.jpg) 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
![](/pictures/XE/pdb/bv/3bvd-XE-sphere_05.jpg) Mono view
![](/pictures/XE/pdb/bv/3bvd-XE-sphere_05_stereo.jpg) 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
![](/pictures/XE/pdb/bv/3bvd-XE-sphere_06.jpg) Mono view
![](/pictures/XE/pdb/bv/3bvd-XE-sphere_06_stereo.jpg) 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
![](/pictures/XE/pdb/bv/3bvd-XE-sphere_07.jpg) Mono view
![](/pictures/XE/pdb/bv/3bvd-XE-sphere_07_stereo.jpg) 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
|