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

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

All present enzymatic activity of Reduced and Carbonmonoxide-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 Carbonmonoxide-Bound Cytochrome C-Dependent Nitric Oxide Reductase (Cnor) From Pseudomonas Aeruginosa in Complex with Antibody Fragment, PDB code: 3wfc 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) 33.37 / 2.50
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 90.672, 107.072, 196.922, 90.00, 90.00, 90.00
R / Rfree (%) 19.1 / 23.2

Other elements in 3wfc:

The structure of Reduced and Carbonmonoxide-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 Carbonmonoxide-Bound Cytochrome C-Dependent Nitric Oxide Reductase (Cnor) From Pseudomonas Aeruginosa in Complex with Antibody Fragment (pdb code 3wfc). 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 Carbonmonoxide-Bound Cytochrome C-Dependent Nitric Oxide Reductase (Cnor) From Pseudomonas Aeruginosa in Complex with Antibody Fragment, PDB code: 3wfc:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 3wfc

Go back to Iron Binding Sites List in 3wfc
Iron binding site 1 out of 4 in the Reduced and Carbonmonoxide-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 Carbonmonoxide-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:40.1
occ:1.00
 FE B:HEM801 0.0 40.1 1.0
NE2 B:HIS60 2.0 37.3 1.0
NE2 B:HIS349 2.0 39.1 1.0
NB B:HEM801 2.0 41.2 1.0
NA B:HEM801 2.0 38.7 1.0
NC B:HEM801 2.1 41.2 1.0
ND B:HEM801 2.1 39.5 1.0
CE1 B:HIS349 2.8 39.1 1.0
CE1 B:HIS60 2.9 37.8 1.0
C4A B:HEM801 3.0 39.7 1.0
C1D B:HEM801 3.0 39.3 1.0
C1B B:HEM801 3.0 41.4 1.0
C4C B:HEM801 3.0 41.2 1.0
C4B B:HEM801 3.0 42.6 1.0
CD2 B:HIS60 3.1 37.4 1.0
C4D B:HEM801 3.1 39.8 1.0
CD2 B:HIS349 3.1 38.6 1.0
C1A B:HEM801 3.1 38.7 1.0
C1C B:HEM801 3.2 41.7 1.0
CHB B:HEM801 3.3 40.5 1.0
CHD B:HEM801 3.3 40.2 1.0
CHA B:HEM801 3.5 38.8 1.0
CHC B:HEM801 3.5 42.1 1.0
ND1 B:HIS349 3.9 39.1 1.0
ND1 B:HIS60 4.0 38.6 1.0
CG B:HIS349 4.1 39.5 1.0
CG B:HIS60 4.1 38.1 1.0
O B:HOH916 4.2 44.9 1.0
C3B B:HEM801 4.2 43.3 1.0
C2D B:HEM801 4.2 39.3 1.0
C2B B:HEM801 4.3 42.7 1.0
C3C B:HEM801 4.3 41.9 1.0
C3A B:HEM801 4.3 38.6 1.0
C3D B:HEM801 4.3 40.0 1.0
C2A B:HEM801 4.3 38.0 1.0
C2C B:HEM801 4.4 41.9 1.0
OE1 B:GLN30 4.8 56.4 1.0

Iron binding site 2 out of 4 in 3wfc

Go back to Iron Binding Sites List in 3wfc
Iron binding site 2 out of 4 in the Reduced and Carbonmonoxide-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 Carbonmonoxide-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:41.0
occ:1.00
 FE B:HEM802 0.0 41.0 1.0
ND B:HEM802 2.0 41.8 1.0
NC B:HEM802 2.0 40.5 1.0
NB B:HEM802 2.1 38.4 1.0
NE2 B:HIS347 2.1 42.6 1.0
C B:CMO804 2.1 40.9 1.0
NA B:HEM802 2.1 39.5 1.0
O B:CMO805 2.3 39.2 1.0
C4D B:HEM802 3.0 42.0 1.0
C1C B:HEM802 3.0 39.7 1.0
CE1 B:HIS347 3.0 42.7 1.0
C4C B:HEM802 3.0 41.7 1.0
C1D B:HEM802 3.0 43.0 1.0
CD2 B:HIS347 3.1 42.2 1.0
C4B B:HEM802 3.1 38.2 1.0
C1B B:HEM802 3.1 38.4 1.0
C4A B:HEM802 3.1 39.0 1.0
C1A B:HEM802 3.2 40.0 1.0
O B:CMO804 3.3 41.3 1.0
CHB B:HEM802 3.3 39.1 1.0
CHA B:HEM802 3.4 41.2 1.0
CHD B:HEM802 3.4 43.2 1.0
CHC B:HEM802 3.4 38.8 1.0
C B:CMO805 3.4 40.4 1.0
ND1 B:HIS347 4.1 42.5 1.0
CG B:HIS347 4.2 42.0 1.0
C3D B:HEM802 4.2 42.1 1.0
C2C B:HEM802 4.2 40.9 1.0
C3C B:HEM802 4.2 41.5 1.0
C2D B:HEM802 4.3 42.5 1.0
C3B B:HEM802 4.3 37.5 1.0
C2B B:HEM802 4.3 37.4 1.0
OE1 B:GLU211 4.3 48.2 1.0
C3A B:HEM802 4.4 38.9 1.0
OE2 B:GLU211 4.4 52.7 1.0
FE B:FE803 4.4 42.8 1.0
C2A B:HEM802 4.4 39.7 1.0
CD B:GLU211 4.5 49.8 1.0
CE1 B:HIS259 4.9 40.4 1.0

Iron binding site 3 out of 4 in 3wfc

Go back to Iron Binding Sites List in 3wfc
Iron binding site 3 out of 4 in the Reduced and Carbonmonoxide-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 Carbonmonoxide-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:42.8
occ:1.00
 C B:CMO805 2.0 40.4 1.0
ND1 B:HIS207 2.0 47.5 1.0
OE1 B:GLU211 2.1 48.2 1.0
NE2 B:HIS258 2.1 43.0 1.0
NE2 B:HIS259 2.2 40.7 1.0
O B:CMO805 2.2 39.2 1.0
OE2 B:GLU211 2.3 52.7 1.0
CD B:GLU211 2.6 49.8 1.0
CE1 B:HIS207 2.7 47.7 1.0
CE1 B:HIS258 2.9 43.5 1.0
CE1 B:HIS259 3.1 40.4 1.0
CD2 B:HIS259 3.2 41.0 1.0
CG B:HIS207 3.2 47.7 1.0
CD2 B:HIS258 3.3 44.2 1.0
O B:CMO804 3.6 41.3 1.0
C B:CMO804 3.7 40.9 1.0
CB B:HIS207 3.8 45.8 1.0
NE2 B:HIS207 4.0 50.1 1.0
CG B:GLU211 4.1 49.4 1.0
ND1 B:HIS258 4.1 44.6 1.0
ND1 B:HIS259 4.2 41.0 1.0
CD2 B:HIS207 4.2 48.3 1.0
CG B:HIS259 4.2 42.0 1.0
NC B:HEM802 4.3 40.5 1.0
CG B:HIS258 4.3 44.8 1.0
FE B:HEM802 4.4 41.0 1.0
ND B:HEM802 4.5 41.8 1.0
C4C B:HEM802 4.5 41.7 1.0
CA B:HIS207 4.5 44.4 1.0
C1D B:HEM802 4.6 43.0 1.0
CHD B:HEM802 4.6 43.2 1.0
OE1 B:GLU280 4.6 61.4 1.0
CB B:GLU211 4.7 47.5 1.0
C1C B:HEM802 4.9 39.7 1.0
OE2 B:GLU280 5.0 62.2 1.0
C4D B:HEM802 5.0 42.0 1.0

Iron binding site 4 out of 4 in 3wfc

Go back to Iron Binding Sites List in 3wfc
Iron binding site 4 out of 4 in the Reduced and Carbonmonoxide-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 Carbonmonoxide-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:37.4
occ:1.00
 FE C:HEC201 0.0 37.4 1.0
NA C:HEC201 1.9 36.8 1.0
NC C:HEC201 2.0 37.5 1.0
NE2 C:HIS65 2.0 38.2 1.0
NB C:HEC201 2.0 37.7 1.0
ND C:HEC201 2.0 36.4 1.0
SD C:MET112 2.3 40.1 1.0
CE1 C:HIS65 2.8 37.9 1.0
C1A C:HEC201 3.0 36.5 1.0
C1C C:HEC201 3.0 38.0 1.0
C4A C:HEC201 3.0 37.1 1.0
C4B C:HEC201 3.0 38.0 1.0
C4D C:HEC201 3.0 36.4 1.0
C4C C:HEC201 3.0 37.9 1.0
C1B C:HEC201 3.0 37.9 1.0
C1D C:HEC201 3.1 36.9 1.0
CD2 C:HIS65 3.1 38.1 1.0
CE C:MET112 3.3 40.6 1.0
CHA C:HEC201 3.3 36.6 1.0
CHC C:HEC201 3.4 38.0 1.0
CHB C:HEC201 3.4 37.4 1.0
CHD C:HEC201 3.4 37.2 1.0
CG C:MET112 3.5 39.4 1.0
ND1 C:HIS65 4.0 38.1 1.0
CG C:HIS65 4.2 38.3 1.0
C2A C:HEC201 4.2 36.3 1.0
CB C:MET112 4.2 39.6 1.0
C3A C:HEC201 4.2 36.4 1.0
C2C C:HEC201 4.2 38.3 1.0
C3B C:HEC201 4.3 38.5 1.0
C2B C:HEC201 4.3 38.2 1.0
C3C C:HEC201 4.3 37.9 1.0
C3D C:HEC201 4.3 36.5 1.0
C2D C:HEC201 4.3 36.8 1.0
NE1 C:TRP98 4.8 39.7 1.0
CB C:ALA75 4.8 34.1 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 22:36:52 2024

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