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

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

All present enzymatic activity of Reduced 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 Cytochrome C-Dependent Nitric Oxide Reductase (Cnor) From Pseudomonas Aeruginosa in Complex with Antibody Fragment, PDB code: 3wfb 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) 41.07 / 2.70
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 90.763, 110.644, 193.546, 90.00, 90.00, 90.00
R / Rfree (%) 20.2 / 25

Other elements in 3wfb:

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

Chlorine (Cl) 1 atom
Calcium (Ca) 1 atom

Iron Binding Sites:

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

Iron binding site 1 out of 4 in 3wfb

Go back to Iron Binding Sites List in 3wfb
Iron binding site 1 out of 4 in the Reduced 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 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:63.9
occ:1.00
 FE B:HEM801 0.0 63.9 1.0
NA B:HEM801 1.9 67.1 1.0
ND B:HEM801 2.0 62.5 1.0
NE2 B:HIS60 2.0 62.4 1.0
NC B:HEM801 2.0 66.2 1.0
NE2 B:HIS349 2.1 55.9 1.0
NB B:HEM801 2.1 68.7 1.0
CD2 B:HIS349 2.9 57.7 1.0
C4A B:HEM801 3.0 66.2 1.0
C1D B:HEM801 3.0 61.7 1.0
CE1 B:HIS60 3.0 66.9 1.0
C4D B:HEM801 3.0 61.5 1.0
C1A B:HEM801 3.0 64.6 1.0
C4C B:HEM801 3.0 65.9 1.0
CD2 B:HIS60 3.1 63.5 1.0
C1B B:HEM801 3.1 68.3 1.0
C1C B:HEM801 3.1 70.3 1.0
C4B B:HEM801 3.1 73.1 1.0
CE1 B:HIS349 3.2 58.1 1.0
CHD B:HEM801 3.3 63.9 1.0
CHB B:HEM801 3.4 69.0 1.0
CHA B:HEM801 3.4 62.9 1.0
CHC B:HEM801 3.5 70.3 1.0
ND1 B:HIS60 4.1 67.9 1.0
CG B:HIS349 4.1 57.7 1.0
CG B:HIS60 4.2 63.9 1.0
C2D B:HEM801 4.2 60.6 1.0
C3D B:HEM801 4.2 60.9 1.0
C3A B:HEM801 4.2 62.7 1.0
C2A B:HEM801 4.2 64.2 1.0
ND1 B:HIS349 4.2 59.4 1.0
C3C B:HEM801 4.3 70.6 1.0
C2C B:HEM801 4.3 70.9 1.0
C2B B:HEM801 4.3 73.5 1.0
C3B B:HEM801 4.4 77.1 1.0
NE2 B:GLN30 4.6 66.8 1.0

Iron binding site 2 out of 4 in 3wfb

Go back to Iron Binding Sites List in 3wfb
Iron binding site 2 out of 4 in the Reduced 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 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:76.4
occ:1.00
 FE B:HEM802 0.0 76.4 1.0
NE2 B:HIS347 2.0 67.6 1.0
ND B:HEM802 2.0 77.3 1.0
NC B:HEM802 2.0 84.1 1.0
NA B:HEM802 2.0 79.5 1.0
NB B:HEM802 2.1 79.0 1.0
CL B:CL804 2.8 68.0 1.0
CD2 B:HIS347 3.0 63.5 1.0
C4D B:HEM802 3.0 77.2 1.0
C1D B:HEM802 3.0 79.3 1.0
CE1 B:HIS347 3.0 69.4 1.0
C1A B:HEM802 3.0 78.4 1.0
C1C B:HEM802 3.0 83.3 1.0
C4C B:HEM802 3.1 83.5 1.0
C4A B:HEM802 3.1 75.9 1.0
C4B B:HEM802 3.1 76.8 1.0
C1B B:HEM802 3.1 77.3 1.0
CHA B:HEM802 3.3 75.0 1.0
CHD B:HEM802 3.4 84.2 1.0
CHC B:HEM802 3.4 80.9 1.0
CHB B:HEM802 3.5 75.2 1.0
ND1 B:HIS347 4.1 69.0 1.0
CG B:HIS347 4.1 64.1 1.0
FE B:FE803 4.2 74.7 1.0
C2D B:HEM802 4.2 83.4 1.0
C3D B:HEM802 4.2 79.0 1.0
C2A B:HEM802 4.2 78.2 1.0
C2C B:HEM802 4.3 86.7 1.0
C3C B:HEM802 4.3 84.4 1.0
C3A B:HEM802 4.3 79.0 1.0
C3B B:HEM802 4.3 77.9 1.0
C2B B:HEM802 4.3 74.7 1.0
OE2 B:GLU211 4.4 75.1 1.0
CD B:GLU211 4.4 76.8 1.0
OE1 B:GLU211 4.5 84.8 1.0
CE1 B:HIS259 4.9 72.6 1.0
NE2 B:HIS329 5.0 0.2 1.0

Iron binding site 3 out of 4 in 3wfb

Go back to Iron Binding Sites List in 3wfb
Iron binding site 3 out of 4 in the Reduced 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 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:74.7
occ:1.00
 NE2 B:HIS258 2.1 80.2 1.0
NE2 B:HIS259 2.1 75.3 1.0
ND1 B:HIS207 2.3 74.5 1.0
OE1 B:GLU211 2.3 84.8 1.0
OE2 B:GLU211 2.4 75.1 1.0
CL B:CL804 2.5 68.0 1.0
CD B:GLU211 2.6 76.8 1.0
CE1 B:HIS259 2.9 72.6 1.0
CE1 B:HIS258 2.9 79.2 1.0
CE1 B:HIS207 3.0 71.5 1.0
CD2 B:HIS259 3.2 73.3 1.0
CD2 B:HIS258 3.2 84.6 1.0
CG B:HIS207 3.4 75.8 1.0
CB B:HIS207 3.9 77.1 1.0
ND1 B:HIS259 4.0 73.9 1.0
ND1 B:HIS258 4.1 84.0 1.0
NC B:HEM802 4.1 84.1 1.0
CG B:GLU211 4.1 71.3 1.0
FE B:HEM802 4.2 76.4 1.0
NE2 B:HIS207 4.2 71.8 1.0
CG B:HIS259 4.2 74.9 1.0
ND B:HEM802 4.2 77.3 1.0
CG B:HIS258 4.3 83.6 1.0
C4C B:HEM802 4.3 83.5 1.0
C1D B:HEM802 4.3 79.3 1.0
CD2 B:HIS207 4.4 74.8 1.0
CHD B:HEM802 4.4 84.2 1.0
CA B:HIS207 4.6 73.4 1.0
C1C B:HEM802 4.7 83.3 1.0
C4D B:HEM802 4.8 77.2 1.0
OE1 B:GLU280 4.8 85.5 1.0
CB B:GLU211 4.8 70.6 1.0
C2D B:HEM802 4.9 83.4 1.0

Iron binding site 4 out of 4 in 3wfb

Go back to Iron Binding Sites List in 3wfb
Iron binding site 4 out of 4 in the Reduced 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 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:62.6
occ:1.00
 FE C:HEC201 0.0 62.6 1.0
NC C:HEC201 1.9 64.0 1.0
ND C:HEC201 2.0 61.0 1.0
NA C:HEC201 2.0 59.9 1.0
NE2 C:HIS65 2.1 61.2 1.0
NB C:HEC201 2.1 63.0 1.0
SD C:MET112 2.3 59.5 1.0
C4C C:HEC201 3.0 65.5 1.0
CE1 C:HIS65 3.0 62.9 1.0
C1C C:HEC201 3.0 66.9 1.0
C1D C:HEC201 3.0 60.3 1.0
C1A C:HEC201 3.1 60.4 1.0
C4A C:HEC201 3.1 61.1 1.0
C4D C:HEC201 3.1 61.6 1.0
C1B C:HEC201 3.1 63.9 1.0
CD2 C:HIS65 3.1 59.5 1.0
C4B C:HEC201 3.1 65.6 1.0
CHD C:HEC201 3.3 63.8 1.0
CG C:MET112 3.3 56.7 1.0
CE C:MET112 3.4 52.3 1.0
CHB C:HEC201 3.5 64.1 1.0
CHA C:HEC201 3.5 60.4 1.0
CHC C:HEC201 3.5 68.2 1.0
ND1 C:HIS65 4.1 61.5 1.0
CB C:MET112 4.2 57.5 1.0
C2C C:HEC201 4.2 65.5 1.0
CG C:HIS65 4.2 60.3 1.0
C3C C:HEC201 4.2 65.4 1.0
C2A C:HEC201 4.3 58.6 1.0
C3A C:HEC201 4.3 61.5 1.0
C2D C:HEC201 4.3 58.7 1.0
C2B C:HEC201 4.3 65.3 1.0
C3D C:HEC201 4.3 60.3 1.0
C3B C:HEC201 4.4 65.2 1.0
NE1 C:TRP98 4.8 55.4 1.0
CB C:ALA75 4.9 49.7 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 22:36:31 2024

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