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

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

All present enzymatic activity of Reduced and Acetaldoxime-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 Acetaldoxime-Bound Cytochrome C-Dependent Nitric Oxide Reductase (Cnor) From Pseudomonas Aeruginosa in Complex with Antibody Fragment, PDB code: 3wfd 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) 33.38 / 2.30
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 90.927, 106.747, 196.437, 90.00, 90.00, 90.00
R / Rfree (%) 19.1 / 23.2

Other elements in 3wfd:

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

Iron binding site 1 out of 4 in 3wfd

Go back to Iron Binding Sites List in 3wfd
Iron binding site 1 out of 4 in the Reduced and Acetaldoxime-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 Acetaldoxime-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:47.1
occ:1.00
 FE B:HEM801 0.0 47.1 1.0
NA B:HEM801 2.0 43.4 1.0
NE2 B:HIS349 2.0 48.4 1.0
NC B:HEM801 2.0 48.4 1.0
NE2 B:HIS60 2.0 44.2 1.0
NB B:HEM801 2.0 48.7 1.0
ND B:HEM801 2.0 45.0 1.0
CE1 B:HIS349 2.8 48.3 1.0
CE1 B:HIS60 2.8 46.2 1.0
C1D B:HEM801 3.0 46.4 1.0
C4A B:HEM801 3.0 48.4 1.0
C4C B:HEM801 3.0 49.5 1.0
C4B B:HEM801 3.0 50.9 1.0
CD2 B:HIS349 3.1 46.4 1.0
C4D B:HEM801 3.1 46.3 1.0
C1A B:HEM801 3.1 44.0 1.0
C1B B:HEM801 3.1 51.6 1.0
C1C B:HEM801 3.1 50.6 1.0
CD2 B:HIS60 3.1 45.5 1.0
CHD B:HEM801 3.3 46.9 1.0
CHB B:HEM801 3.4 50.8 1.0
CHC B:HEM801 3.4 50.3 1.0
CHA B:HEM801 3.5 44.5 1.0
ND1 B:HIS349 3.9 47.1 1.0
ND1 B:HIS60 4.0 49.2 1.0
CG B:HIS349 4.1 49.1 1.0
CG B:HIS60 4.2 46.6 1.0
O B:HOH918 4.2 56.0 1.0
C2D B:HEM801 4.2 45.3 1.0
C3C B:HEM801 4.2 49.9 1.0
C3B B:HEM801 4.3 53.7 1.0
C3A B:HEM801 4.3 45.2 1.0
C2A B:HEM801 4.3 44.7 1.0
C3D B:HEM801 4.3 43.7 1.0
C2B B:HEM801 4.3 52.8 1.0
C2C B:HEM801 4.4 48.3 1.0
OE1 B:GLN30 4.9 57.4 1.0

Iron binding site 2 out of 4 in 3wfd

Go back to Iron Binding Sites List in 3wfd
Iron binding site 2 out of 4 in the Reduced and Acetaldoxime-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 Acetaldoxime-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:46.8
occ:1.00
 FE B:HEM802 0.0 46.8 1.0
ND B:HEM802 1.9 45.0 1.0
N B:AXO804 1.9 45.3 1.0
NB B:HEM802 2.0 44.2 1.0
NC B:HEM802 2.0 45.9 1.0
NA B:HEM802 2.1 43.1 1.0
NE2 B:HIS347 2.1 48.4 1.0
O1 B:AXO804 2.4 49.2 1.0
C4D B:HEM802 3.0 46.2 1.0
C1D B:HEM802 3.0 48.5 1.0
C1C B:HEM802 3.0 45.4 1.0
CE1 B:HIS347 3.0 46.9 1.0
C4C B:HEM802 3.0 46.0 1.0
C1B B:HEM802 3.0 44.7 1.0
C4B B:HEM802 3.1 44.4 1.0
C4A B:HEM802 3.1 43.2 1.0
C1A B:HEM802 3.1 43.5 1.0
C1 B:AXO804 3.1 47.1 1.0
CD2 B:HIS347 3.2 47.7 1.0
CHB B:HEM802 3.3 45.4 1.0
CHD B:HEM802 3.4 47.5 1.0
CHA B:HEM802 3.4 42.5 1.0
CHC B:HEM802 3.5 43.7 1.0
C2 B:AXO804 3.9 53.6 1.0
ND1 B:HIS347 4.2 47.1 1.0
C3D B:HEM802 4.2 43.2 1.0
C2C B:HEM802 4.2 46.8 1.0
C2D B:HEM802 4.3 45.0 1.0
C3B B:HEM802 4.3 42.5 1.0
CG B:HIS347 4.3 49.2 1.0
C3C B:HEM802 4.3 46.4 1.0
C2B B:HEM802 4.3 41.7 1.0
C3A B:HEM802 4.3 43.6 1.0
C2A B:HEM802 4.4 43.9 1.0
FE B:FE803 4.4 48.0 1.0
OE2 B:GLU211 4.5 55.0 1.0
CD B:GLU211 4.6 49.4 1.0
OE1 B:GLU211 4.6 49.8 1.0
NE2 B:HIS329 5.0 56.7 1.0

Iron binding site 3 out of 4 in 3wfd

Go back to Iron Binding Sites List in 3wfd
Iron binding site 3 out of 4 in the Reduced and Acetaldoxime-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 Acetaldoxime-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:48.0
occ:1.00
 O1 B:AXO804 2.0 49.2 1.0
OE2 B:GLU211 2.0 55.0 1.0
NE2 B:HIS259 2.2 42.2 1.0
NE2 B:HIS258 2.2 48.1 1.0
ND1 B:HIS207 2.2 51.3 1.0
OE1 B:GLU211 2.2 49.8 1.0
CD B:GLU211 2.5 49.4 1.0
C1 B:AXO804 2.9 47.1 1.0
CE1 B:HIS258 3.0 49.8 1.0
CE1 B:HIS207 3.0 53.4 1.0
CE1 B:HIS259 3.0 41.7 1.0
N B:AXO804 3.0 45.3 1.0
CD2 B:HIS259 3.2 42.8 1.0
CD2 B:HIS258 3.3 50.5 1.0
CG B:HIS207 3.3 53.8 1.0
CB B:HIS207 3.8 50.1 1.0
CG B:GLU211 4.0 47.6 1.0
ND1 B:HIS259 4.1 41.9 1.0
ND1 B:HIS258 4.2 51.3 1.0
NE2 B:HIS207 4.2 55.8 1.0
C2 B:AXO804 4.2 53.6 1.0
CG B:HIS259 4.3 44.6 1.0
CD2 B:HIS207 4.4 54.6 1.0
CG B:HIS258 4.4 50.4 1.0
FE B:HEM802 4.4 46.8 1.0
NC B:HEM802 4.4 45.9 1.0
ND B:HEM802 4.5 45.0 1.0
CA B:HIS207 4.5 50.0 1.0
C4C B:HEM802 4.6 46.0 1.0
C1D B:HEM802 4.6 48.5 1.0
CHD B:HEM802 4.7 47.5 1.0
OE1 B:GLU280 4.7 56.4 1.0
CB B:GLU211 4.8 48.1 1.0
C1C B:HEM802 4.9 45.4 1.0
OE2 B:GLU280 4.9 61.5 1.0
C4D B:HEM802 5.0 46.2 1.0

Iron binding site 4 out of 4 in 3wfd

Go back to Iron Binding Sites List in 3wfd
Iron binding site 4 out of 4 in the Reduced and Acetaldoxime-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 Acetaldoxime-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:44.6
occ:1.00
 FE C:HEC201 0.0 44.6 1.0
NC C:HEC201 1.9 45.7 1.0
NA C:HEC201 1.9 44.2 1.0
NE2 C:HIS65 2.0 44.9 1.0
NB C:HEC201 2.0 44.8 1.0
ND C:HEC201 2.0 44.9 1.0
SD C:MET112 2.3 45.7 1.0
CE1 C:HIS65 2.9 43.9 1.0
C1C C:HEC201 3.0 44.8 1.0
C4A C:HEC201 3.0 44.8 1.0
C4C C:HEC201 3.0 46.5 1.0
C1A C:HEC201 3.0 43.0 1.0
C4B C:HEC201 3.0 43.7 1.0
C1B C:HEC201 3.0 45.3 1.0
C1D C:HEC201 3.0 45.8 1.0
CD2 C:HIS65 3.1 42.1 1.0
C4D C:HEC201 3.1 42.1 1.0
CE C:MET112 3.3 44.5 1.0
CHC C:HEC201 3.4 44.0 1.0
CHD C:HEC201 3.4 45.8 1.0
CHB C:HEC201 3.4 43.6 1.0
CHA C:HEC201 3.4 43.2 1.0
CG C:MET112 3.4 45.2 1.0
ND1 C:HIS65 4.0 43.9 1.0
CG C:HIS65 4.1 44.5 1.0
CB C:MET112 4.2 44.0 1.0
C2C C:HEC201 4.2 46.7 1.0
C3A C:HEC201 4.2 42.4 1.0
C2A C:HEC201 4.2 40.8 1.0
C3B C:HEC201 4.3 44.2 1.0
C2B C:HEC201 4.3 43.3 1.0
C3C C:HEC201 4.3 45.5 1.0
C3D C:HEC201 4.3 43.4 1.0
C2D C:HEC201 4.3 44.9 1.0
NE1 C:TRP98 4.8 45.9 1.0
CB C:ALA75 4.8 38.0 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 22:36:54 2024

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