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Iron in PDB 3o0r: Crystal Structure of Nitric Oxide Reductase From Pseudomonas Aeruginosa in Complex with Antibody Fragment

Enzymatic activity of Crystal Structure of Nitric Oxide Reductase From Pseudomonas Aeruginosa in Complex with Antibody Fragment

All present enzymatic activity of Crystal Structure of Nitric Oxide Reductase From Pseudomonas Aeruginosa in Complex with Antibody Fragment:
1.7.99.7;

Protein crystallography data

The structure of Crystal Structure of Nitric Oxide Reductase From Pseudomonas Aeruginosa in Complex with Antibody Fragment, PDB code: 3o0r was solved by T.Hino, Y.Matsumoto, S.Nagano, H.Sugimoto, Y.Fukumori, T.Murata, S.Iwata, Y.Shiro, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 2.70
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 90.470, 104.520, 195.360, 90.00, 90.00, 90.00
R / Rfree (%) 18.5 / 24.7

Other elements in 3o0r:

The structure of Crystal Structure of Nitric Oxide Reductase 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 Crystal Structure of Nitric Oxide Reductase From Pseudomonas Aeruginosa in Complex with Antibody Fragment (pdb code 3o0r). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Crystal Structure of Nitric Oxide Reductase From Pseudomonas Aeruginosa in Complex with Antibody Fragment, PDB code: 3o0r:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 3o0r

Go back to Iron Binding Sites List in 3o0r
Iron binding site 1 out of 4 in the Crystal Structure of Nitric Oxide Reductase 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 Crystal Structure of Nitric Oxide Reductase From Pseudomonas Aeruginosa in Complex with Antibody Fragment within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe801

b:60.0
occ:1.00
 FE B:HEM801 0.0 60.0 1.0
NB B:HEM801 2.0 60.1 1.0
NE2 B:HIS349 2.0 64.5 1.0
NE2 B:HIS60 2.0 65.2 1.0
NA B:HEM801 2.0 54.7 1.0
ND B:HEM801 2.0 56.4 1.0
NC B:HEM801 2.1 59.8 1.0
CE1 B:HIS60 2.7 70.3 1.0
CD2 B:HIS349 2.9 65.2 1.0
CE1 B:HIS349 3.0 62.2 1.0
C1B B:HEM801 3.0 62.7 1.0
C4C B:HEM801 3.0 60.6 1.0
C1D B:HEM801 3.0 59.1 1.0
C4A B:HEM801 3.1 58.3 1.0
C4B B:HEM801 3.1 66.5 1.0
C1A B:HEM801 3.1 56.6 1.0
C4D B:HEM801 3.1 57.4 1.0
CD2 B:HIS60 3.2 67.1 1.0
C1C B:HEM801 3.2 59.2 1.0
CHD B:HEM801 3.3 61.8 1.0
CHB B:HEM801 3.4 62.1 1.0
CHA B:HEM801 3.4 58.0 1.0
CHC B:HEM801 3.6 60.9 1.0
ND1 B:HIS60 3.9 70.3 1.0
ND1 B:HIS349 4.0 62.3 1.0
CG B:HIS349 4.1 64.0 1.0
CG B:HIS60 4.2 66.7 1.0
C3B B:HEM801 4.2 68.1 1.0
C2B B:HEM801 4.2 64.8 1.0
C3C B:HEM801 4.2 63.8 1.0
C2D B:HEM801 4.3 58.2 1.0
C3A B:HEM801 4.3 58.9 1.0
C2A B:HEM801 4.3 57.0 1.0
C3D B:HEM801 4.3 57.1 1.0
C2C B:HEM801 4.4 63.9 1.0
OE1 B:GLN30 4.5 75.3 1.0
O B:HOH919 4.7 80.0 1.0

Iron binding site 2 out of 4 in 3o0r

Go back to Iron Binding Sites List in 3o0r
Iron binding site 2 out of 4 in the Crystal Structure of Nitric Oxide Reductase 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 Crystal Structure of Nitric Oxide Reductase From Pseudomonas Aeruginosa in Complex with Antibody Fragment within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe802

b:67.8
occ:1.00
 FE B:HEM802 0.0 67.8 1.0
O B:O805 1.8 60.2 1.0
NC B:HEM802 1.9 70.5 1.0
NA B:HEM802 2.0 65.2 1.0
NB B:HEM802 2.0 68.3 1.0
ND B:HEM802 2.1 66.5 1.0
NE2 B:HIS347 2.3 70.8 1.0
C4C B:HEM802 3.0 71.7 1.0
C1C B:HEM802 3.0 69.9 1.0
C4B B:HEM802 3.0 69.2 1.0
C1D B:HEM802 3.0 68.8 1.0
C1A B:HEM802 3.0 63.2 1.0
C4A B:HEM802 3.1 64.3 1.0
C1B B:HEM802 3.1 67.2 1.0
C4D B:HEM802 3.1 63.9 1.0
CD2 B:HIS347 3.2 71.6 1.0
CE1 B:HIS347 3.3 74.0 1.0
CHD B:HEM802 3.4 71.1 1.0
CHC B:HEM802 3.4 70.3 1.0
CHB B:HEM802 3.4 66.7 1.0
CHA B:HEM802 3.5 61.7 1.0
FE B:FE803 3.8 64.8 1.0
OE1 B:GLU211 4.0 77.5 1.0
C3C B:HEM802 4.2 73.9 1.0
C2C B:HEM802 4.2 72.4 1.0
C3B B:HEM802 4.2 68.8 1.0
C2A B:HEM802 4.2 60.8 1.0
C2B B:HEM802 4.2 67.4 1.0
C3A B:HEM802 4.3 61.1 1.0
C2D B:HEM802 4.3 68.6 1.0
CD B:GLU211 4.3 73.8 1.0
OE2 B:GLU211 4.3 73.5 1.0
C3D B:HEM802 4.4 64.9 1.0
CG B:HIS347 4.4 71.2 1.0
ND1 B:HIS347 4.4 74.2 1.0
CE1 B:HIS259 4.6 59.9 1.0
NE2 B:HIS259 4.8 59.8 1.0
CE1 B:HIS258 4.9 67.5 1.0
NE2 B:HIS258 4.9 68.6 1.0

Iron binding site 3 out of 4 in 3o0r

Go back to Iron Binding Sites List in 3o0r
Iron binding site 3 out of 4 in the Crystal Structure of Nitric Oxide Reductase 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 Crystal Structure of Nitric Oxide Reductase From Pseudomonas Aeruginosa in Complex with Antibody Fragment within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe803

b:64.8
occ:1.00
 O B:O805 2.0 60.2 1.0
OE2 B:GLU211 2.0 73.5 1.0
NE2 B:HIS259 2.1 59.8 1.0
NE2 B:HIS258 2.1 68.6 1.0
ND1 B:HIS207 2.2 67.9 1.0
OE1 B:GLU211 2.5 77.5 1.0
CD B:GLU211 2.6 73.8 1.0
CE1 B:HIS207 3.0 70.1 1.0
CE1 B:HIS258 3.0 67.5 1.0
CE1 B:HIS259 3.0 59.9 1.0
CD2 B:HIS259 3.1 61.4 1.0
CD2 B:HIS258 3.2 70.0 1.0
CG B:HIS207 3.3 68.5 1.0
CB B:HIS207 3.8 68.0 1.0
FE B:HEM802 3.8 67.8 1.0
CG B:GLU211 4.1 75.3 1.0
NC B:HEM802 4.1 70.5 1.0
ND1 B:HIS259 4.1 61.1 1.0
ND1 B:HIS258 4.1 68.4 1.0
ND B:HEM802 4.1 66.5 1.0
NE2 B:HIS207 4.2 68.6 1.0
CG B:HIS259 4.2 62.3 1.0
CG B:HIS258 4.2 68.6 1.0
C4C B:HEM802 4.4 71.7 1.0
CD2 B:HIS207 4.4 68.5 1.0
C1D B:HEM802 4.4 68.8 1.0
CHD B:HEM802 4.5 71.1 1.0
CA B:HIS207 4.5 67.3 1.0
OE1 B:GLU280 4.6 79.9 1.0
C1C B:HEM802 4.7 69.9 1.0
CB B:GLU211 4.7 74.5 1.0
C4D B:HEM802 4.8 63.9 1.0
NB B:HEM802 4.9 68.3 1.0
NA B:HEM802 4.9 65.2 1.0

Iron binding site 4 out of 4 in 3o0r

Go back to Iron Binding Sites List in 3o0r
Iron binding site 4 out of 4 in the Crystal Structure of Nitric Oxide Reductase 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 Crystal Structure of Nitric Oxide Reductase From Pseudomonas Aeruginosa in Complex with Antibody Fragment within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe201

b:54.8
occ:1.00
 FE C:HEC201 0.0 54.8 1.0
NE2 C:HIS65 2.0 64.1 1.0
NB C:HEC201 2.0 56.7 1.0
NC C:HEC201 2.0 58.5 1.0
NA C:HEC201 2.1 56.9 1.0
ND C:HEC201 2.1 57.5 1.0
SD C:MET112 2.3 59.7 1.0
CE1 C:HIS65 2.9 62.7 1.0
C1B C:HEC201 2.9 59.7 1.0
C4C C:HEC201 3.0 59.0 1.0
CD2 C:HIS65 3.0 63.9 1.0
C4A C:HEC201 3.0 57.2 1.0
C1D C:HEC201 3.1 60.3 1.0
C1C C:HEC201 3.1 59.8 1.0
C4B C:HEC201 3.1 57.8 1.0
C1A C:HEC201 3.1 57.1 1.0
C4D C:HEC201 3.2 58.1 1.0
CHB C:HEC201 3.3 59.9 1.0
CE C:MET112 3.4 56.2 1.0
CHD C:HEC201 3.4 60.0 1.0
CHC C:HEC201 3.5 58.5 1.0
CHA C:HEC201 3.5 60.5 1.0
CG C:MET112 3.5 60.0 1.0
ND1 C:HIS65 4.0 62.6 1.0
CG C:HIS65 4.1 59.2 1.0
CB C:MET112 4.2 59.1 1.0
C2B C:HEC201 4.2 58.9 1.0
C3C C:HEC201 4.2 57.8 1.0
C3A C:HEC201 4.3 57.1 1.0
C2C C:HEC201 4.3 58.1 1.0
C3B C:HEC201 4.3 57.9 1.0
C2A C:HEC201 4.3 57.3 1.0
C2D C:HEC201 4.4 59.1 1.0
C3D C:HEC201 4.4 57.3 1.0
NE1 C:TRP98 4.8 50.5 1.0
CB C:ALA75 4.9 50.8 1.0

Reference:

T.Hino, Y.Matsumoto, S.Nagano, H.Sugimoto, Y.Fukumori, T.Murata, S.Iwata, Y.Shiro. Structural Basis of Biological N2O Generation By Bacterial Nitric Oxide Reductase Science V. 330 1666 2010.
ISSN: ISSN 0036-8075
PubMed: 21109633
DOI: 10.1126/SCIENCE.1195591
Page generated: Sun Aug 4 16:56:14 2024

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