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

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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

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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 Dec 13 15:25:53 2020

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