Atomistry » Iron » PDB 5g6f-5h8y » 5gux
Atomistry »
  Iron »
    PDB 5g6f-5h8y »
      5gux »

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

Last articles

Ca in 5NQ2
Ca in 5N97
Ca in 5N8P
Ca in 5NMR
Ca in 5NN9
Ca in 5NM8
Ca in 5NH8
Ca in 5NL7
Ca in 5NIN
Ca in 5NGQ
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy