Atomistry » Xenon, Xe » PDB 4zzc-7tsj » 5gux
Atomistry »
  Xenon, Xe »
    PDB 4zzc-7tsj »
      5gux »

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

Go back to Xenon Binding Sites List in 5gux
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

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy