Iron in PDB 8j79: Bovine Xanthine Oxidoreductase Crystallized with Oxypurinol

Enzymatic activity of Bovine Xanthine Oxidoreductase Crystallized with Oxypurinol

All present enzymatic activity of Bovine Xanthine Oxidoreductase Crystallized with Oxypurinol:
1.17.1.4; 1.17.3.2;

Protein crystallography data

The structure of Bovine Xanthine Oxidoreductase Crystallized with Oxypurinol, PDB code: 8j79 was solved by K.Okamoto, M.Sekine, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.72 / 1.99
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 167.678, 123.47, 150.059, 90, 90.89, 90
R / Rfree (%) 16.3 / 19.7

Other elements in 8j79:

The structure of Bovine Xanthine Oxidoreductase Crystallized with Oxypurinol also contains other interesting chemical elements:

Molybdenum (Mo) 2 atoms
Calcium (Ca) 4 atoms

Iron Binding Sites:

The binding sites of Iron atom in the Bovine Xanthine Oxidoreductase Crystallized with Oxypurinol (pdb code 8j79). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 8 binding sites of Iron where determined in the Bovine Xanthine Oxidoreductase Crystallized with Oxypurinol, PDB code: 8j79:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iron binding site 1 out of 8 in 8j79

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Iron binding site 1 out of 8 in the Bovine Xanthine Oxidoreductase Crystallized with Oxypurinol


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Bovine Xanthine Oxidoreductase Crystallized with Oxypurinol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe1401

b:22.0
occ:1.00
 FE1 A:FES1401 0.0 22.0 1.0
S2 A:FES1401 2.2 20.8 1.0
S1 A:FES1401 2.2 22.2 1.0
SG A:CYS113 2.3 20.8 1.0
SG A:CYS150 2.3 20.4 1.0
FE2 A:FES1401 2.8 21.5 1.0
CB A:CYS150 3.2 23.3 1.0
CB A:CYS113 3.3 21.3 1.0
N A:CYS113 3.5 21.2 1.0
O A:HOH2165 3.6 21.8 1.0
CA A:CYS113 3.8 20.8 1.0
N A:GLY114 3.9 20.3 1.0
N A:CYS150 4.1 22.5 1.0
C A:CYS113 4.2 20.8 1.0
CA A:CYS150 4.3 22.7 1.0
N A:PHE115 4.4 23.9 1.0
SG A:CYS148 4.5 22.1 1.0
SG A:CYS116 4.6 24.1 1.0
C A:GLN112 4.7 21.1 1.0
CB A:GLN112 4.8 20.6 1.0
N A:ARG149 4.8 23.7 1.0
CA A:GLY114 4.9 21.8 1.0
N A:CYS116 4.9 24.2 1.0

Iron binding site 2 out of 8 in 8j79

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Iron binding site 2 out of 8 in the Bovine Xanthine Oxidoreductase Crystallized with Oxypurinol


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Bovine Xanthine Oxidoreductase Crystallized with Oxypurinol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe1401

b:21.5
occ:1.00
 FE2 A:FES1401 0.0 21.5 1.0
S2 A:FES1401 2.2 20.8 1.0
S1 A:FES1401 2.2 22.2 1.0
SG A:CYS116 2.3 24.1 1.0
SG A:CYS148 2.4 22.1 1.0
FE1 A:FES1401 2.8 22.0 1.0
CB A:CYS148 3.3 19.7 1.0
CB A:CYS116 3.5 23.2 1.0
CA A:CYS148 3.7 20.4 1.0
N A:ARG149 4.1 23.7 1.0
N A:CYS116 4.2 24.2 1.0
C A:CYS148 4.3 21.2 1.0
CB A:CYS150 4.3 23.3 1.0
N A:CYS150 4.3 22.5 1.0
O A:HOH1786 4.4 19.0 1.0
CA A:CYS116 4.4 22.6 1.0
SG A:CYS150 4.4 20.4 1.0
SG A:CYS113 4.7 20.8 1.0
CG2 A:THR151 4.7 19.9 1.0
CA A:CYS150 4.9 22.7 1.0
N A:CYS148 5.0 21.1 1.0
O A:LEU147 5.0 23.9 1.0

Iron binding site 3 out of 8 in 8j79

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Iron binding site 3 out of 8 in the Bovine Xanthine Oxidoreductase Crystallized with Oxypurinol


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Bovine Xanthine Oxidoreductase Crystallized with Oxypurinol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe1402

b:23.0
occ:1.00
 FE1 A:FES1402 0.0 23.0 1.0
S1 A:FES1402 2.2 24.5 1.0
S2 A:FES1402 2.2 25.3 1.0
SG A:CYS73 2.3 22.7 1.0
SG A:CYS51 2.3 22.7 1.0
FE2 A:FES1402 2.8 23.8 1.0
CB A:CYS73 3.2 23.6 1.0
CB A:CYS51 3.4 20.5 1.0
N A:CYS73 4.2 20.6 1.0
CB A:ASN71 4.2 24.7 1.0
CA A:CYS73 4.3 23.9 1.0
N A:GLY46 4.3 21.2 1.0
N A:GLY44 4.3 25.1 1.0
N A:CYS51 4.3 21.1 1.0
OD1 A:ASN71 4.4 31.6 1.0
SG A:CYS43 4.4 25.1 1.0
CA A:CYS51 4.5 20.6 1.0
CA A:GLY46 4.5 24.1 1.0
CG A:ASN71 4.6 23.9 1.0
CA A:GLY44 4.6 24.5 1.0
SG A:CYS48 4.7 22.6 1.0
N A:GLU45 4.8 22.9 1.0
N A:GLY49 4.8 22.4 1.0
CA A:ASN71 5.0 22.2 1.0

Iron binding site 4 out of 8 in 8j79

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Iron binding site 4 out of 8 in the Bovine Xanthine Oxidoreductase Crystallized with Oxypurinol


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Bovine Xanthine Oxidoreductase Crystallized with Oxypurinol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe1402

b:23.8
occ:1.00
 FE2 A:FES1402 0.0 23.8 1.0
S2 A:FES1402 2.3 25.3 1.0
SG A:CYS48 2.3 22.6 1.0
S1 A:FES1402 2.3 24.5 1.0
SG A:CYS43 2.4 25.1 1.0
FE1 A:FES1402 2.8 23.0 1.0
N A:CYS43 3.4 22.9 1.0
CB A:CYS48 3.4 24.5 1.0
CB A:CYS43 3.5 27.1 1.0
N A:CYS48 3.6 23.1 1.0
N A:GLY44 3.8 25.1 1.0
N A:GLY49 3.8 22.4 1.0
CA A:CYS43 3.8 26.9 1.0
CA A:CYS48 3.9 23.4 1.0
C A:GLY42 4.1 24.2 1.0
C A:CYS43 4.2 25.8 1.0
C A:CYS48 4.2 22.2 1.0
N A:GLY42 4.3 23.1 1.0
CA A:GLY42 4.4 22.3 1.0
N A:GLY47 4.4 25.6 1.0
N A:ALA50 4.4 21.5 1.0
N A:GLY46 4.4 21.2 1.0
SG A:CYS73 4.5 22.7 1.0
SG A:CYS51 4.7 22.7 1.0
N A:GLU45 4.7 22.9 1.0
C A:GLY47 4.7 27.0 1.0
C A:GLY46 4.8 26.5 1.0
CA A:GLY44 4.8 24.5 1.0
CA A:GLY49 4.8 23.8 1.0
CA A:GLY46 4.9 24.1 1.0

Iron binding site 5 out of 8 in 8j79

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Iron binding site 5 out of 8 in the Bovine Xanthine Oxidoreductase Crystallized with Oxypurinol


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Bovine Xanthine Oxidoreductase Crystallized with Oxypurinol within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe1401

b:21.4
occ:1.00
 FE1 B:FES1401 0.0 21.4 1.0
S2 B:FES1401 2.2 21.0 1.0
S1 B:FES1401 2.3 24.3 1.0
SG B:CYS113 2.3 21.0 1.0
SG B:CYS150 2.3 21.7 1.0
FE2 B:FES1401 2.7 21.4 1.0
CB B:CYS150 3.2 20.4 1.0
CB B:CYS113 3.3 19.1 1.0
N B:CYS113 3.5 20.3 1.0
O B:HOH2056 3.5 20.1 1.0
CA B:CYS113 3.9 19.3 1.0
N B:GLY114 3.9 19.6 1.0
N B:CYS150 4.1 21.5 1.0
CA B:CYS150 4.3 21.4 1.0
C B:CYS113 4.3 18.6 1.0
SG B:CYS148 4.4 20.9 1.0
N B:PHE115 4.4 24.6 1.0
SG B:CYS116 4.6 23.0 1.0
C B:GLN112 4.6 21.4 1.0
CB B:GLN112 4.8 19.4 1.0
N B:ARG149 4.8 22.3 1.0
CA B:GLY114 4.9 20.8 1.0
N B:CYS116 5.0 20.7 1.0
N B:GLN112 5.0 19.8 1.0

Iron binding site 6 out of 8 in 8j79

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Iron binding site 6 out of 8 in the Bovine Xanthine Oxidoreductase Crystallized with Oxypurinol


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Bovine Xanthine Oxidoreductase Crystallized with Oxypurinol within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe1401

b:21.4
occ:1.00
 FE2 B:FES1401 0.0 21.4 1.0
S1 B:FES1401 2.2 24.3 1.0
S2 B:FES1401 2.2 21.0 1.0
SG B:CYS116 2.3 23.0 1.0
SG B:CYS148 2.3 20.9 1.0
FE1 B:FES1401 2.7 21.4 1.0
CB B:CYS148 3.3 20.2 1.0
CB B:CYS116 3.4 21.6 1.0
CA B:CYS148 3.6 20.2 1.0
N B:ARG149 4.0 22.3 1.0
C B:CYS148 4.2 18.3 1.0
N B:CYS116 4.3 20.7 1.0
N B:CYS150 4.3 21.5 1.0
CB B:CYS150 4.3 20.4 1.0
O B:HOH1902 4.4 19.6 1.0
CA B:CYS116 4.4 18.2 1.0
SG B:CYS150 4.5 21.7 1.0
SG B:CYS113 4.7 21.0 1.0
CG2 B:THR151 4.7 23.6 1.0
CA B:CYS150 4.9 21.4 1.0
N B:CYS148 4.9 22.5 1.0
O B:LEU147 4.9 19.8 1.0

Iron binding site 7 out of 8 in 8j79

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Iron binding site 7 out of 8 in the Bovine Xanthine Oxidoreductase Crystallized with Oxypurinol


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Bovine Xanthine Oxidoreductase Crystallized with Oxypurinol within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe1402

b:22.3
occ:1.00
 FE1 B:FES1402 0.0 22.3 1.0
S1 B:FES1402 2.2 22.0 1.0
S2 B:FES1402 2.2 23.0 1.0
SG B:CYS73 2.3 21.5 1.0
SG B:CYS51 2.4 22.2 1.0
FE2 B:FES1402 2.8 21.9 1.0
CB B:CYS73 3.1 23.3 1.0
CB B:CYS51 3.4 20.3 1.0
CA B:CYS73 4.2 23.1 1.0
N B:CYS73 4.2 21.6 1.0
CB B:ASN71 4.3 22.8 1.0
N B:GLY46 4.3 23.3 1.0
SG B:CYS43 4.4 22.1 1.0
N B:CYS51 4.4 19.8 1.0
N B:GLY44 4.4 19.9 1.0
ND2 B:ASN71 4.4 22.8 1.0
CA B:CYS51 4.5 19.9 1.0
CA B:GLY46 4.6 22.2 1.0
SG B:CYS48 4.6 20.9 1.0
CG B:ASN71 4.6 24.6 1.0
CA B:GLY44 4.7 22.4 1.0
N B:GLU45 4.8 22.8 1.0
N B:GLY49 4.9 19.9 1.0
CA B:ASN71 4.9 21.3 1.0

Iron binding site 8 out of 8 in 8j79

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Iron binding site 8 out of 8 in the Bovine Xanthine Oxidoreductase Crystallized with Oxypurinol


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Bovine Xanthine Oxidoreductase Crystallized with Oxypurinol within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe1402

b:21.9
occ:1.00
 FE2 B:FES1402 0.0 21.9 1.0
SG B:CYS48 2.2 20.9 1.0
S1 B:FES1402 2.3 22.0 1.0
S2 B:FES1402 2.3 23.0 1.0
SG B:CYS43 2.3 22.1 1.0
FE1 B:FES1402 2.8 22.3 1.0
CB B:CYS48 3.4 19.9 1.0
N B:CYS43 3.4 22.2 1.0
CB B:CYS43 3.5 25.3 1.0
N B:CYS48 3.6 21.4 1.0
N B:GLY49 3.9 19.9 1.0
N B:GLY44 3.9 19.9 1.0
CA B:CYS48 3.9 20.1 1.0
CA B:CYS43 3.9 25.3 1.0
C B:GLY42 4.1 22.1 1.0
N B:GLY42 4.3 21.7 1.0
C B:CYS48 4.3 21.4 1.0
CA B:GLY42 4.3 21.4 1.0
C B:CYS43 4.3 24.6 1.0
N B:GLY47 4.4 25.3 1.0
N B:GLY46 4.4 23.3 1.0
N B:ALA50 4.5 20.2 1.0
SG B:CYS73 4.5 21.5 1.0
N B:GLU45 4.7 22.8 1.0
SG B:CYS51 4.7 22.2 1.0
C B:GLY47 4.7 25.0 1.0
C B:GLY46 4.8 23.4 1.0
CA B:GLY44 4.9 22.4 1.0
CA B:GLY49 4.9 20.5 1.0
CA B:GLY46 4.9 22.2 1.0
O B:GLY42 5.0 22.9 1.0

Reference:

K.Okamoto, M.Sekine. Bovine Xanthine Oxidoreductase Crystallized with Oxypurinol To Be Published.
Page generated: Thu Jul 27 17:30:15 2023

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