Atomistry » Iron » PDB 3vtj-3wg7 » 3wfe
Atomistry »
  Iron »
    PDB 3vtj-3wg7 »
      3wfe »

Iron in PDB 3wfe: Reduced and Cyanide-Bound Cytochrome C-Dependent Nitric Oxide Reductase (Cnor) From Pseudomonas Aeruginosa in Complex with Antibody Fragment

Enzymatic activity of Reduced and Cyanide-Bound Cytochrome C-Dependent Nitric Oxide Reductase (Cnor) From Pseudomonas Aeruginosa in Complex with Antibody Fragment

All present enzymatic activity of Reduced and Cyanide-Bound Cytochrome C-Dependent Nitric Oxide Reductase (Cnor) From Pseudomonas Aeruginosa in Complex with Antibody Fragment:
1.7.2.5;

Protein crystallography data

The structure of Reduced and Cyanide-Bound Cytochrome C-Dependent Nitric Oxide Reductase (Cnor) From Pseudomonas Aeruginosa in Complex with Antibody Fragment, PDB code: 3wfe was solved by N.Sato, S.Ishii, T.Hino, H.Sugimoto, Y.Fukumori, Y.Shiro, T.Tosha, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 35.16 / 2.49
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 90.688, 107.381, 195.288, 90.00, 90.00, 90.00
R / Rfree (%) 18.9 / 22.7

Other elements in 3wfe:

The structure of Reduced and Cyanide-Bound Cytochrome C-Dependent Nitric Oxide Reductase (Cnor) From Pseudomonas Aeruginosa in Complex with Antibody Fragment also contains other interesting chemical elements:

Calcium (Ca) 1 atom

Iron Binding Sites:

The binding sites of Iron atom in the Reduced and Cyanide-Bound Cytochrome C-Dependent Nitric Oxide Reductase (Cnor) From Pseudomonas Aeruginosa in Complex with Antibody Fragment (pdb code 3wfe). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Reduced and Cyanide-Bound Cytochrome C-Dependent Nitric Oxide Reductase (Cnor) From Pseudomonas Aeruginosa in Complex with Antibody Fragment, PDB code: 3wfe:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 3wfe

Go back to Iron Binding Sites List in 3wfe
Iron binding site 1 out of 4 in the Reduced and Cyanide-Bound Cytochrome C-Dependent Nitric Oxide Reductase (Cnor) From Pseudomonas Aeruginosa in Complex with Antibody Fragment


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Reduced and Cyanide-Bound Cytochrome C-Dependent Nitric Oxide Reductase (Cnor) From Pseudomonas Aeruginosa in Complex with Antibody Fragment within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe801

b:48.7
occ:1.00
 FE B:HEM801 0.0 48.7 1.0
NA B:HEM801 1.9 45.0 1.0
NC B:HEM801 2.0 49.3 1.0
NE2 B:HIS60 2.0 47.8 1.0
NE2 B:HIS349 2.0 47.7 1.0
NB B:HEM801 2.0 49.4 1.0
ND B:HEM801 2.1 46.5 1.0
CE1 B:HIS349 2.8 46.6 1.0
CE1 B:HIS60 2.9 49.1 1.0
C4A B:HEM801 2.9 47.1 1.0
C4C B:HEM801 3.0 48.8 1.0
C4D B:HEM801 3.0 47.0 1.0
C1D B:HEM801 3.0 46.7 1.0
C1A B:HEM801 3.0 44.9 1.0
C4B B:HEM801 3.0 51.8 1.0
C1C B:HEM801 3.1 49.9 1.0
CD2 B:HIS60 3.1 48.1 1.0
CD2 B:HIS349 3.1 46.5 1.0
C1B B:HEM801 3.1 50.3 1.0
CHB B:HEM801 3.4 48.5 1.0
CHD B:HEM801 3.4 48.6 1.0
CHA B:HEM801 3.4 44.4 1.0
CHC B:HEM801 3.4 50.0 1.0
ND1 B:HIS349 3.9 47.1 1.0
ND1 B:HIS60 4.0 50.7 1.0
CG B:HIS349 4.1 47.8 1.0
CG B:HIS60 4.1 48.3 1.0
C3A B:HEM801 4.2 44.0 1.0
C3C B:HEM801 4.2 49.7 1.0
C2D B:HEM801 4.2 47.3 1.0
O B:HOH916 4.3 49.8 1.0
C3B B:HEM801 4.3 54.4 1.0
C2A B:HEM801 4.3 42.9 1.0
C2C B:HEM801 4.3 48.9 1.0
C3D B:HEM801 4.3 48.3 1.0
C2B B:HEM801 4.3 52.9 1.0
OE1 B:GLN30 4.6 64.0 1.0

Iron binding site 2 out of 4 in 3wfe

Go back to Iron Binding Sites List in 3wfe
Iron binding site 2 out of 4 in the Reduced and Cyanide-Bound Cytochrome C-Dependent Nitric Oxide Reductase (Cnor) From Pseudomonas Aeruginosa in Complex with Antibody Fragment


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Reduced and Cyanide-Bound Cytochrome C-Dependent Nitric Oxide Reductase (Cnor) From Pseudomonas Aeruginosa in Complex with Antibody Fragment within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe802

b:47.6
occ:1.00
 FE B:HEM802 0.0 47.6 1.0
ND B:HEM802 1.9 45.3 1.0
NC B:HEM802 2.0 45.5 1.0
NB B:HEM802 2.0 43.3 1.0
C B:CYN804 2.1 49.1 1.0
NA B:HEM802 2.1 43.9 1.0
NE2 B:HIS347 2.1 48.4 1.0
N B:CYN805 2.2 39.5 1.0
C4D B:HEM802 2.9 46.6 1.0
C1C B:HEM802 3.0 44.2 1.0
C1D B:HEM802 3.0 46.7 1.0
C4C B:HEM802 3.0 46.9 1.0
CE1 B:HIS347 3.0 48.1 1.0
C4B B:HEM802 3.0 43.5 1.0
C1A B:HEM802 3.1 44.4 1.0
C1B B:HEM802 3.1 43.2 1.0
C B:CYN805 3.1 42.4 1.0
C4A B:HEM802 3.1 43.8 1.0
CD2 B:HIS347 3.2 45.6 1.0
CHA B:HEM802 3.2 45.7 1.0
N B:CYN804 3.3 47.6 1.0
CHC B:HEM802 3.4 43.6 1.0
CHD B:HEM802 3.4 46.8 1.0
CHB B:HEM802 3.4 44.0 1.0
C3D B:HEM802 4.1 44.0 1.0
ND1 B:HIS347 4.2 46.3 1.0
C2C B:HEM802 4.2 45.8 1.0
C2D B:HEM802 4.2 45.4 1.0
C3C B:HEM802 4.2 45.5 1.0
CG B:HIS347 4.3 45.6 1.0
C3B B:HEM802 4.3 41.9 1.0
C2B B:HEM802 4.3 41.8 1.0
C2A B:HEM802 4.3 44.8 1.0
C3A B:HEM802 4.4 43.4 1.0
OE1 B:GLU211 4.4 46.7 1.0
FE B:FE803 4.4 47.4 1.0
CD B:GLU211 4.6 49.1 1.0
OE2 B:GLU211 4.8 52.6 1.0
NE2 B:HIS329 4.9 52.3 1.0
CE1 B:HIS258 4.9 53.6 1.0

Iron binding site 3 out of 4 in 3wfe

Go back to Iron Binding Sites List in 3wfe
Iron binding site 3 out of 4 in the Reduced and Cyanide-Bound Cytochrome C-Dependent Nitric Oxide Reductase (Cnor) From Pseudomonas Aeruginosa in Complex with Antibody Fragment


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Reduced and Cyanide-Bound Cytochrome C-Dependent Nitric Oxide Reductase (Cnor) From Pseudomonas Aeruginosa in Complex with Antibody Fragment within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe803

b:47.4
occ:1.00
 C B:CYN805 2.0 42.4 1.0
OE1 B:GLU211 2.1 46.7 1.0
NE2 B:HIS258 2.1 51.8 1.0
NE2 B:HIS259 2.2 45.4 1.0
OE2 B:GLU211 2.2 52.6 1.0
ND1 B:HIS207 2.2 53.1 1.0
N B:CYN805 2.3 39.5 1.0
CD B:GLU211 2.5 49.1 1.0
CE1 B:HIS258 2.9 53.6 1.0
CE1 B:HIS207 3.0 52.1 1.0
CE1 B:HIS259 3.0 45.4 1.0
CD2 B:HIS259 3.2 46.4 1.0
CD2 B:HIS258 3.3 53.2 1.0
CG B:HIS207 3.3 52.8 1.0
N B:CYN804 3.6 47.6 1.0
C B:CYN804 3.6 49.1 1.0
CB B:HIS207 3.8 50.4 1.0
CG B:GLU211 4.0 50.1 1.0
ND1 B:HIS258 4.1 55.1 1.0
ND1 B:HIS259 4.2 44.9 1.0
NE2 B:HIS207 4.2 57.0 1.0
CG B:HIS259 4.3 46.5 1.0
NC B:HEM802 4.3 45.5 1.0
CG B:HIS258 4.3 52.4 1.0
CD2 B:HIS207 4.4 54.6 1.0
FE B:HEM802 4.4 47.6 1.0
ND B:HEM802 4.5 45.3 1.0
CA B:HIS207 4.5 49.8 1.0
C4C B:HEM802 4.6 46.9 1.0
C1D B:HEM802 4.6 46.7 1.0
OE1 B:GLU280 4.7 59.1 1.0
CHD B:HEM802 4.7 46.8 1.0
CB B:GLU211 4.8 50.0 1.0
C1C B:HEM802 4.8 44.2 1.0
C4D B:HEM802 5.0 46.6 1.0

Iron binding site 4 out of 4 in 3wfe

Go back to Iron Binding Sites List in 3wfe
Iron binding site 4 out of 4 in the Reduced and Cyanide-Bound Cytochrome C-Dependent Nitric Oxide Reductase (Cnor) From Pseudomonas Aeruginosa in Complex with Antibody Fragment


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Reduced and Cyanide-Bound Cytochrome C-Dependent Nitric Oxide Reductase (Cnor) From Pseudomonas Aeruginosa in Complex with Antibody Fragment within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe201

b:43.1
occ:1.00
 FE C:HEC201 0.0 43.1 1.0
NA C:HEC201 1.9 41.3 1.0
NC C:HEC201 1.9 40.8 1.0
NE2 C:HIS65 2.0 48.9 1.0
ND C:HEC201 2.0 42.9 1.0
NB C:HEC201 2.0 44.1 1.0
SD C:MET112 2.3 48.5 1.0
CE1 C:HIS65 2.8 46.5 1.0
C1A C:HEC201 2.9 40.1 1.0
C1C C:HEC201 2.9 43.3 1.0
C4A C:HEC201 3.0 48.5 1.0
C4D C:HEC201 3.0 38.7 1.0
C4B C:HEC201 3.0 40.0 1.0
C4C C:HEC201 3.1 49.8 1.0
C1B C:HEC201 3.1 44.8 1.0
C1D C:HEC201 3.1 44.6 1.0
CD2 C:HIS65 3.1 45.1 1.0
CHA C:HEC201 3.3 38.6 1.0
CE C:MET112 3.3 50.6 1.0
CHC C:HEC201 3.3 41.5 1.0
CHB C:HEC201 3.5 47.5 1.0
CG C:MET112 3.5 45.7 1.0
CHD C:HEC201 3.5 53.5 1.0
ND1 C:HIS65 4.0 45.7 1.0
C2A C:HEC201 4.1 38.6 1.0
C3A C:HEC201 4.1 37.9 1.0
CB C:MET112 4.2 44.7 1.0
CG C:HIS65 4.2 44.2 1.0
C2C C:HEC201 4.2 45.1 1.0
C3D C:HEC201 4.3 44.5 1.0
C3B C:HEC201 4.3 42.1 1.0
C3C C:HEC201 4.3 41.9 1.0
C2D C:HEC201 4.3 44.7 1.0
C2B C:HEC201 4.3 41.0 1.0
NE1 C:TRP98 4.8 44.1 1.0
CB C:ALA75 4.9 39.8 1.0

Reference:

N.Sato, S.Ishii, H.Sugimoto, T.Hino, Y.Fukumori, Y.Sako, Y.Shiro, T.Tosha. Structures of Reduced and Ligand-Bound Nitric Oxide Reductase Provide Insights Into Functional Differences in Respiratory Enzymes Proteins 2013.
ISSN: ESSN 1097-0134
PubMed: 24338896
DOI: 10.1002/PROT.24492
Page generated: Sun Aug 4 22:37:05 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