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Xenon in PDB 5gux: Cytochrome C-Dependent Nitric Oxide Reductase (Cnor) From Pseudomonas Aeruginosa in Complex with Xenon

Enzymatic activity of Cytochrome C-Dependent Nitric Oxide Reductase (Cnor) From Pseudomonas Aeruginosa in Complex with Xenon

All present enzymatic activity of Cytochrome C-Dependent Nitric Oxide Reductase (Cnor) From Pseudomonas Aeruginosa in Complex with Xenon:
1.7.2.5;

Protein crystallography data

The structure of Cytochrome C-Dependent Nitric Oxide Reductase (Cnor) From Pseudomonas Aeruginosa in Complex with Xenon, PDB code: 5gux was solved by S.Ishii, E.Terasaka, H.Sugimoto, Y.Shiro, T.Tosha, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.39 / 3.30
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 89.843, 105.379, 192.577, 90.00, 90.00, 90.00
R / Rfree (%) 20.9 / 26.8

Other elements in 5gux:

The structure of Cytochrome C-Dependent Nitric Oxide Reductase (Cnor) From Pseudomonas Aeruginosa in Complex with Xenon also contains other interesting chemical elements:

Iron (Fe) 4 atoms
Calcium (Ca) 1 atom

Xenon Binding Sites:

The binding sites of Xenon atom in the Cytochrome C-Dependent Nitric Oxide Reductase (Cnor) From Pseudomonas Aeruginosa in Complex with Xenon (pdb code 5gux). This binding sites where shown within 5.0 Angstroms radius around Xenon atom.
In total 7 binding sites of Xenon where determined in the Cytochrome C-Dependent Nitric Oxide Reductase (Cnor) From Pseudomonas Aeruginosa in Complex with Xenon, PDB code: 5gux:
Jump to Xenon binding site number: 1; 2; 3; 4; 5; 6; 7;

Xenon binding site 1 out of 7 in 5gux

Go back to Xenon Binding Sites List in 5gux
Xenon binding site 1 out of 7 in the Cytochrome C-Dependent Nitric Oxide Reductase (Cnor) From Pseudomonas Aeruginosa 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 Cytochrome C-Dependent Nitric Oxide Reductase (Cnor) From Pseudomonas Aeruginosa in Complex with Xenon within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Xe805

b:98.3
occ:0.70
 O B:LEU178 3.8 90.1 1.0
CD2 B:PHE154 4.1 77.1 1.0
CE2 B:PHE154 4.1 73.2 1.0
CB B:ALA182 4.2 80.2 1.0
CD2 B:LEU181 4.2 86.5 1.0
CB B:ALA151 4.4 89.9 1.0
XE B:XE808 4.4 93.7 0.6
CD2 B:LEU155 4.4 71.7 1.0
CD2 B:LEU178 4.6 86.1 1.0
C B:LEU178 4.6 84.5 1.0
CD1 B:LEU181 4.7 78.1 1.0
N B:ALA182 4.7 81.6 1.0
CG B:LEU155 4.7 74.1 1.0
XE B:XE807 4.8 94.1 0.6
CB B:LEU178 4.8 81.4 1.0
CA B:ALA151 4.8 86.3 1.0
CG B:LEU181 4.8 83.0 1.0
CB B:LEU181 4.8 81.3 1.0
CA B:LEU178 4.8 81.0 1.0
CA B:ALA182 4.8 81.8 1.0
CE B:MET73 4.9 92.8 1.0
O B:ALA151 5.0 94.2 1.0

Xenon binding site 2 out of 7 in 5gux

Go back to Xenon Binding Sites List in 5gux
Xenon binding site 2 out of 7 in the Cytochrome C-Dependent Nitric Oxide Reductase (Cnor) From Pseudomonas Aeruginosa 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 Cytochrome C-Dependent Nitric Oxide Reductase (Cnor) From Pseudomonas Aeruginosa in Complex with Xenon within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Xe806

b:91.8
occ:0.70
 CD1 B:ILE65 3.9 90.4 1.0
CE3 B:TRP209 4.0 83.5 1.0
CD2 B:PHE136 4.0 73.0 1.0
CG2 B:VAL206 4.0 77.8 1.0
CG1 B:ILE65 4.2 82.1 1.0
CZ3 B:TRP209 4.2 88.2 1.0
CZ B:PHE352 4.2 67.8 1.0
CG1 B:VAL206 4.2 76.9 1.0
CG B:PHE136 4.2 76.4 1.0
CB B:PHE136 4.3 79.2 1.0
XE B:XE809 4.3 85.8 0.6
CB B:VAL206 4.5 82.0 1.0
CA B:VAL206 4.6 83.9 1.0
CE2 B:PHE136 4.6 71.5 1.0
CG2 B:VAL210 4.9 70.9 1.0
CE2 B:PHE352 5.0 73.6 1.0
CD1 B:PHE136 5.0 76.9 1.0
O B:VAL206 5.0 75.1 1.0

Xenon binding site 3 out of 7 in 5gux

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Xenon binding site 3 out of 7 in the Cytochrome C-Dependent Nitric Oxide Reductase (Cnor) From Pseudomonas Aeruginosa 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 Cytochrome C-Dependent Nitric Oxide Reductase (Cnor) From Pseudomonas Aeruginosa in Complex with Xenon within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Xe807

b:94.1
occ:0.60
 CD2 B:LEU181 3.6 86.5 1.0
CG B:PHE185 3.6 90.7 1.0
CD2 B:PHE185 3.8 94.7 1.0
CG2 B:ILE147 3.9 0.8 1.0
XE B:XE808 3.9 93.7 0.6
CB B:PHE185 3.9 89.5 1.0
CD1 B:PHE185 4.0 98.7 1.0
CE2 B:PHE185 4.3 91.8 1.0
CB B:ALA151 4.4 89.9 1.0
CE1 B:PHE185 4.5 0.8 1.0
CZ2 B:TRP209 4.5 81.5 1.0
CZ B:PHE185 4.6 96.8 1.0
CA B:ALA182 4.6 81.8 1.0
XE B:XE805 4.8 98.3 0.7
CD2 B:LEU69 4.8 77.3 1.0
O B:ILE147 4.9 95.4 1.0
O B:LEU181 4.9 79.6 1.0
CH2 B:TRP209 4.9 83.5 1.0

Xenon binding site 4 out of 7 in 5gux

Go back to Xenon Binding Sites List in 5gux
Xenon binding site 4 out of 7 in the Cytochrome C-Dependent Nitric Oxide Reductase (Cnor) From Pseudomonas Aeruginosa 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 Cytochrome C-Dependent Nitric Oxide Reductase (Cnor) From Pseudomonas Aeruginosa in Complex with Xenon within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Xe808

b:93.7
occ:0.55
 CE B:MET73 2.9 92.8 1.0
CZ B:PHE101 3.7 96.3 1.0
CE2 B:PHE101 3.9 95.1 1.0
XE B:XE807 3.9 94.1 0.6
CG2 B:ILE147 3.9 0.8 1.0
CB B:ALA151 4.0 89.9 1.0
CG1 B:VAL150 4.1 91.2 1.0
O B:ILE147 4.1 95.4 1.0
CA B:ALA151 4.2 86.3 1.0
N B:ALA151 4.2 85.3 1.0
CE1 B:PHE101 4.4 93.4 1.0
XE B:XE805 4.4 98.3 0.7
SD B:MET73 4.6 85.5 1.0
CD2 B:PHE101 4.6 96.7 1.0
CB B:VAL150 4.8 97.7 1.0
CD2 B:LEU69 4.8 77.3 1.0
C B:VAL150 4.8 91.4 1.0
CD1 B:LEU69 4.8 84.5 1.0
CB B:LEU69 5.0 74.0 1.0

Xenon binding site 5 out of 7 in 5gux

Go back to Xenon Binding Sites List in 5gux
Xenon binding site 5 out of 7 in the Cytochrome C-Dependent Nitric Oxide Reductase (Cnor) From Pseudomonas Aeruginosa in Complex with Xenon


Mono view


Stereo pair view

A full contact list of Xenon with other atoms in the Xe binding site number 5 of Cytochrome C-Dependent Nitric Oxide Reductase (Cnor) From Pseudomonas Aeruginosa in Complex with Xenon within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Xe809

b:85.8
occ:0.55
 CE1 B:PHE136 3.3 72.1 1.0
CD1 B:PHE136 3.5 76.9 1.0
CMD B:HEM801 3.7 70.3 1.0
CZ B:PHE136 3.8 68.7 1.0
CD2 B:LEU64 3.9 65.0 1.0
CZ B:PHE352 4.0 67.8 1.0
O B:THR61 4.0 73.1 1.0
CG1 B:ILE65 4.0 82.1 1.0
CE2 B:PHE352 4.1 73.6 1.0
CG B:PHE136 4.1 76.4 1.0
CB B:THR61 4.1 64.2 1.0
CD1 B:ILE65 4.2 90.4 1.0
CG2 B:THR61 4.2 60.4 1.0
XE B:XE806 4.3 91.8 0.7
CE2 B:PHE136 4.4 71.5 1.0
C2D B:HEM801 4.4 69.3 1.0
CE1 B:PHE352 4.5 70.0 1.0
CD2 B:PHE136 4.5 73.0 1.0
CA B:THR61 4.6 66.3 1.0
CG B:LEU64 4.7 66.3 1.0
CD2 B:PHE352 4.7 70.4 1.0
C B:THR61 4.7 68.6 1.0
CB B:LEU64 4.8 64.4 1.0
CAD B:HEM801 4.8 64.1 1.0
C3D B:HEM801 4.9 64.4 1.0
CB B:PHE136 5.0 79.2 1.0

Xenon binding site 6 out of 7 in 5gux

Go back to Xenon Binding Sites List in 5gux
Xenon binding site 6 out of 7 in the Cytochrome C-Dependent Nitric Oxide Reductase (Cnor) From Pseudomonas Aeruginosa in Complex with Xenon


Mono view


Stereo pair view

A full contact list of Xenon with other atoms in the Xe binding site number 6 of Cytochrome C-Dependent Nitric Oxide Reductase (Cnor) From Pseudomonas Aeruginosa in Complex with Xenon within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Xe810

b:87.7
occ:0.45
 CB B:THR108 3.8 95.1 1.0
CG2 B:THR108 3.9 92.6 1.0
CG2 B:VAL66 3.9 75.5 1.0
CB B:ASN62 4.2 77.3 1.0
ND2 B:ASN62 4.2 86.0 1.0
CD1 B:ILE109 4.2 77.3 1.0
O B:GLY105 4.3 0.1 1.0
OG1 B:THR108 4.4 0.3 1.0
CG1 B:ILE109 4.5 78.8 1.0
CB B:GLN139 4.6 93.3 1.0
CA B:GLY105 4.6 96.9 1.0
N B:ILE109 4.6 85.8 1.0
CG B:ASN62 4.7 86.9 1.0
OH B:TYR112 4.8 60.0 1.0
CE2 B:TYR112 4.9 61.6 1.0
OE1 B:GLN139 4.9 73.3 1.0
C B:GLY105 4.9 93.9 1.0

Xenon binding site 7 out of 7 in 5gux

Go back to Xenon Binding Sites List in 5gux
Xenon binding site 7 out of 7 in the Cytochrome C-Dependent Nitric Oxide Reductase (Cnor) From Pseudomonas Aeruginosa in Complex with Xenon


Mono view


Stereo pair view

A full contact list of Xenon with other atoms in the Xe binding site number 7 of Cytochrome C-Dependent Nitric Oxide Reductase (Cnor) From Pseudomonas Aeruginosa in Complex with Xenon within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Xe811

b:89.9
occ:0.40
 OE1 B:GLN139 4.2 73.3 1.0
CD B:GLN139 4.2 85.4 1.0
CG2 B:ILE65 4.2 74.3 1.0
NE2 B:GLN139 4.3 83.5 1.0
CE1 B:PHE185 4.3 0.8 1.0
CD1 B:ILE147 4.3 0.8 1.0
CG2 B:VAL66 4.5 75.5 1.0
CZ B:PHE185 4.6 96.8 1.0
CD1 B:LEU69 4.6 84.5 1.0
CB B:ILE65 4.7 78.1 1.0
CG B:GLN139 4.7 91.2 1.0
CD1 B:ILE65 5.0 90.4 1.0

Reference:

E.Terasaka, K.Yamada, P.H.Wang, K.Hosokawa, R.Yamagiwa, K.Matsumoto, S.Ishii, T.Mori, K.Yagi, H.Sawai, H.Arai, H.Sugimoto, Y.Sugita, Y.Shiro, T.Tosha. Dynamics of Nitric Oxide Controlled By Protein Complex in Bacterial System. Proc. Natl. Acad. Sci. V. 114 9888 2017U.S.A..
ISSN: ESSN 1091-6490
PubMed: 28847930
DOI: 10.1073/PNAS.1621301114
Page generated: Sat Oct 12 19:33:05 2024

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