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Iron 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:

Xenon (Xe) 7 atoms
Calcium (Ca) 1 atom

Iron Binding Sites:

The binding sites of Iron 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 Iron atom.
In total 4 binding sites of Iron where determined in the Cytochrome C-Dependent Nitric Oxide Reductase (Cnor) From Pseudomonas Aeruginosa in Complex with Xenon, PDB code: 5gux:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 5gux

Go back to Iron Binding Sites List in 5gux
Iron binding site 1 out of 4 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 Iron with other atoms in the Fe 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:Fe801

b:73.0
occ:1.00
 FE B:HEM801 0.0 73.0 1.0
NE2 B:HIS349 2.0 75.1 1.0
NB B:HEM801 2.0 74.7 1.0
NE2 B:HIS60 2.0 60.6 1.0
ND B:HEM801 2.0 67.5 1.0
NA B:HEM801 2.0 73.1 1.0
NC B:HEM801 2.1 71.4 1.0
CE1 B:HIS349 2.7 72.7 1.0
CE1 B:HIS60 2.9 57.6 1.0
C1D B:HEM801 3.0 68.1 1.0
CD2 B:HIS349 3.0 79.1 1.0
C4A B:HEM801 3.0 75.2 1.0
C4B B:HEM801 3.0 77.7 1.0
C1B B:HEM801 3.0 78.0 1.0
C4D B:HEM801 3.1 69.1 1.0
C4C B:HEM801 3.1 70.3 1.0
C1A B:HEM801 3.1 71.5 1.0
CD2 B:HIS60 3.1 58.4 1.0
C1C B:HEM801 3.2 72.8 1.0
CHB B:HEM801 3.3 81.1 1.0
CHD B:HEM801 3.4 68.5 1.0
CHA B:HEM801 3.5 73.5 1.0
CHC B:HEM801 3.5 75.0 1.0
ND1 B:HIS349 3.8 81.2 1.0
CG B:HIS349 4.0 78.4 1.0
ND1 B:HIS60 4.0 60.0 1.0
CG B:HIS60 4.2 59.4 1.0
C3B B:HEM801 4.2 84.1 1.0
C2D B:HEM801 4.2 69.3 1.0
C3A B:HEM801 4.3 67.9 1.0
C2B B:HEM801 4.3 83.0 1.0
C2A B:HEM801 4.3 67.9 1.0
C3D B:HEM801 4.3 64.4 1.0
C3C B:HEM801 4.3 74.7 1.0
C2C B:HEM801 4.5 74.5 1.0
OE1 B:GLN30 4.8 70.7 1.0

Iron binding site 2 out of 4 in 5gux

Go back to Iron Binding Sites List in 5gux
Iron binding site 2 out of 4 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 Iron with other atoms in the Fe 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:Fe802

b:84.2
occ:1.00
 FE B:HEM802 0.0 84.2 1.0
ND B:HEM802 1.9 82.7 1.0
NC B:HEM802 2.0 89.7 1.0
NB B:HEM802 2.0 83.5 1.0
NE2 B:HIS347 2.0 83.8 1.0
O B:O804 2.0 80.3 1.0
NA B:HEM802 2.1 92.0 1.0
CE1 B:HIS347 2.9 87.2 1.0
C1D B:HEM802 2.9 83.4 1.0
C4D B:HEM802 3.0 85.1 1.0
C1C B:HEM802 3.1 89.6 1.0
C4C B:HEM802 3.1 87.4 1.0
C1B B:HEM802 3.1 86.6 1.0
C4B B:HEM802 3.1 85.9 1.0
CD2 B:HIS347 3.1 80.9 1.0
C4A B:HEM802 3.1 93.2 1.0
C1A B:HEM802 3.2 87.0 1.0
CHD B:HEM802 3.3 85.4 1.0
CHC B:HEM802 3.4 89.1 1.0
CHA B:HEM802 3.4 85.3 1.0
CHB B:HEM802 3.4 92.1 1.0
OE2 B:GLU211 3.7 0.6 1.0
FE B:FE803 4.0 80.8 1.0
ND1 B:HIS347 4.0 85.1 1.0
CD B:GLU211 4.0 96.0 1.0
OE1 B:GLU211 4.1 89.5 1.0
CG B:HIS347 4.2 83.4 1.0
C3D B:HEM802 4.2 83.3 1.0
C2D B:HEM802 4.2 84.3 1.0
C2C B:HEM802 4.3 85.7 1.0
C3C B:HEM802 4.3 85.8 1.0
C2B B:HEM802 4.3 83.1 1.0
C3B B:HEM802 4.3 84.2 1.0
C3A B:HEM802 4.4 89.0 1.0
C2A B:HEM802 4.4 86.6 1.0
CE1 B:HIS258 4.7 81.5 1.0
CE1 B:HIS259 4.8 91.7 1.0

Iron binding site 3 out of 4 in 5gux

Go back to Iron Binding Sites List in 5gux
Iron binding site 3 out of 4 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 Iron with other atoms in the Fe 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:Fe803

b:80.8
occ:1.00
 O B:O804 2.0 80.3 1.0
OE1 B:GLU211 2.1 89.5 1.0
NE2 B:HIS259 2.1 90.9 1.0
NE2 B:HIS258 2.2 79.3 1.0
ND1 B:HIS207 2.2 73.9 1.0
OE2 B:GLU211 2.4 0.6 1.0
CD B:GLU211 2.5 96.0 1.0
CE1 B:HIS259 2.9 91.7 1.0
CE1 B:HIS258 2.9 81.5 1.0
CE1 B:HIS207 3.0 78.2 1.0
CD2 B:HIS259 3.2 93.6 1.0
CD2 B:HIS258 3.3 82.8 1.0
CG B:HIS207 3.3 75.5 1.0
CB B:HIS207 3.8 75.7 1.0
CG B:GLU211 4.0 83.0 1.0
FE B:HEM802 4.0 84.2 1.0
ND1 B:HIS259 4.0 86.0 1.0
ND1 B:HIS258 4.1 78.0 1.0
ND B:HEM802 4.1 82.7 1.0
NC B:HEM802 4.2 89.7 1.0
NE2 B:HIS207 4.2 77.3 1.0
CG B:HIS259 4.2 83.8 1.0
CG B:HIS258 4.3 79.4 1.0
C1D B:HEM802 4.3 83.4 1.0
CD2 B:HIS207 4.4 77.3 1.0
C4C B:HEM802 4.5 87.4 1.0
CB B:GLU211 4.5 79.6 1.0
CHD B:HEM802 4.5 85.4 1.0
CA B:HIS207 4.6 74.9 1.0
C4D B:HEM802 4.7 85.1 1.0
OE1 B:GLU280 4.8 0.2 1.0
C1C B:HEM802 4.8 89.6 1.0
NB B:HEM802 4.9 83.5 1.0
C2D B:HEM802 4.9 84.3 1.0
NA B:HEM802 5.0 92.0 1.0
O B:GLY255 5.0 78.4 1.0

Iron binding site 4 out of 4 in 5gux

Go back to Iron Binding Sites List in 5gux
Iron binding site 4 out of 4 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 Iron with other atoms in the Fe 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
C:Fe201

b:64.0
occ:1.00
 FE C:HEC201 0.0 64.0 1.0
NB C:HEC201 2.0 62.5 1.0
NE2 C:HIS65 2.0 68.0 1.0
NA C:HEC201 2.0 62.1 1.0
ND C:HEC201 2.0 59.2 1.0
NC C:HEC201 2.0 63.2 1.0
SD C:MET112 2.3 76.0 1.0
CE1 C:HIS65 3.0 66.2 1.0
C4D C:HEC201 3.0 56.6 1.0
C1A C:HEC201 3.0 64.9 1.0
C4B C:HEC201 3.0 62.4 1.0
CD2 C:HIS65 3.0 63.6 1.0
C1B C:HEC201 3.0 64.7 1.0
C4A C:HEC201 3.0 63.5 1.0
C1C C:HEC201 3.0 66.0 1.0
C1D C:HEC201 3.1 58.0 1.0
C4C C:HEC201 3.1 63.9 1.0
CHA C:HEC201 3.3 60.4 1.0
CHB C:HEC201 3.4 67.2 1.0
CHC C:HEC201 3.4 62.3 1.0
CHD C:HEC201 3.5 57.7 1.0
CG C:MET112 3.5 67.0 1.0
CE C:MET112 3.5 73.6 1.0
ND1 C:HIS65 4.1 64.8 1.0
CG C:HIS65 4.1 62.8 1.0
CB C:MET112 4.2 69.5 1.0
C3D C:HEC201 4.2 61.1 1.0
C3B C:HEC201 4.2 64.8 1.0
C2B C:HEC201 4.2 67.8 1.0
C2A C:HEC201 4.3 67.3 1.0
C3A C:HEC201 4.3 63.5 1.0
C2D C:HEC201 4.3 57.7 1.0
C2C C:HEC201 4.3 65.5 1.0
C3C C:HEC201 4.3 69.5 1.0
CB C:ALA75 4.8 58.2 1.0
NE1 C:TRP98 4.9 79.3 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: Tue Aug 6 01:37:47 2024

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