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Iron in PDB 6ac4: Rat Xanthine Oxidoreductase, D428N Variant

Enzymatic activity of Rat Xanthine Oxidoreductase, D428N Variant

All present enzymatic activity of Rat Xanthine Oxidoreductase, D428N Variant:
1.17.1.4; 1.17.3.2;

Protein crystallography data

The structure of Rat Xanthine Oxidoreductase, D428N Variant, PDB code: 6ac4 was solved by K.Okamoto, Y.Kawaguchi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.63 / 2.19
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 98.296, 138.648, 221.865, 90.00, 90.00, 90.00
R / Rfree (%) 17.5 / 23.5

Iron Binding Sites:

The binding sites of Iron atom in the Rat Xanthine Oxidoreductase, D428N Variant (pdb code 6ac4). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 8 binding sites of Iron where determined in the Rat Xanthine Oxidoreductase, D428N Variant, PDB code: 6ac4:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iron binding site 1 out of 8 in 6ac4

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Iron binding site 1 out of 8 in the Rat Xanthine Oxidoreductase, D428N Variant


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Rat Xanthine Oxidoreductase, D428N Variant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe1402

b:26.7
occ:1.00
 FE1 A:FES1402 0.0 26.7 1.0
S1 A:FES1402 2.2 23.7 1.0
S2 A:FES1402 2.2 26.3 1.0
SG A:CYS112 2.2 23.7 1.0
FE2 A:FES1402 2.8 24.2 1.0
SG A:CYS149 2.8 28.7 1.0
CB A:CYS112 3.3 24.4 1.0
CB A:CYS149 3.4 29.4 1.0
O A:HOH1981 3.5 18.2 1.0
N A:CYS112 3.7 23.4 1.0
CA A:CYS112 3.9 23.6 1.0
N A:GLY113 4.0 21.6 1.0
N A:CYS149 4.2 24.8 1.0
C A:CYS112 4.4 22.5 1.0
SG A:CYS147 4.5 27.5 1.0
CA A:CYS149 4.5 24.9 1.0
N A:PHE114 4.5 19.1 1.0
SG A:CYS115 4.6 23.6 1.0
N A:ARG148 4.7 23.4 1.0
C A:GLN111 4.8 22.8 1.0
N A:CYS115 5.0 20.8 1.0

Iron binding site 2 out of 8 in 6ac4

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Iron binding site 2 out of 8 in the Rat Xanthine Oxidoreductase, D428N Variant


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Rat Xanthine Oxidoreductase, D428N Variant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe1402

b:24.2
occ:1.00
 FE2 A:FES1402 0.0 24.2 1.0
S2 A:FES1402 2.2 26.3 1.0
SG A:CYS115 2.2 23.6 1.0
S1 A:FES1402 2.3 23.7 1.0
SG A:CYS147 2.4 27.5 1.0
FE1 A:FES1402 2.8 26.7 1.0
O A:HOH1930 2.8 96.7 1.0
CB A:CYS147 3.3 24.6 1.0
CB A:CYS115 3.4 22.5 1.0
CA A:CYS147 3.7 23.2 1.0
N A:ARG148 4.1 23.4 1.0
O A:HOH2107 4.3 85.4 1.0
N A:CYS115 4.3 20.8 1.0
C A:CYS147 4.3 21.9 1.0
O A:HOH1617 4.3 17.3 1.0
N A:CYS149 4.4 24.8 1.0
CA A:CYS115 4.4 20.8 1.0
CB A:CYS149 4.5 29.4 1.0
CG2 A:THR150 4.5 24.4 1.0
SG A:CYS112 4.6 23.7 1.0
SG A:CYS149 4.9 28.7 1.0
N A:CYS147 4.9 21.8 1.0
O A:LEU146 5.0 25.9 1.0

Iron binding site 3 out of 8 in 6ac4

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Iron binding site 3 out of 8 in the Rat Xanthine Oxidoreductase, D428N Variant


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Rat Xanthine Oxidoreductase, D428N Variant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe1403

b:25.7
occ:1.00
 FE1 A:FES1403 0.0 25.7 1.0
S1 A:FES1403 2.2 25.0 1.0
S2 A:FES1403 2.3 24.4 1.0
SG A:CYS48 2.3 22.9 1.0
SG A:CYS43 2.4 24.7 1.0
FE2 A:FES1403 2.8 23.7 1.0
CB A:CYS48 3.4 21.7 1.0
N A:CYS43 3.4 22.5 1.0
CB A:CYS43 3.4 24.0 1.0
N A:CYS48 3.6 22.1 1.0
N A:GLY44 3.7 25.6 1.0
N A:GLY49 3.8 21.0 1.0
CA A:CYS48 3.8 21.3 1.0
CA A:CYS43 3.8 23.6 1.0
C A:GLY42 4.0 23.5 1.0
C A:CYS48 4.1 21.0 1.0
C A:CYS43 4.2 24.9 1.0
CA A:GLY42 4.2 23.4 1.0
N A:GLY42 4.3 22.8 1.0
N A:GLY46 4.4 23.0 1.0
N A:ALA50 4.5 19.3 1.0
N A:GLY47 4.5 24.9 1.0
N A:GLU45 4.5 28.5 1.0
SG A:CYS73 4.6 27.4 1.0
SG A:CYS51 4.6 20.9 1.0
CA A:GLY44 4.7 26.6 1.0
C A:GLY47 4.8 23.2 1.0
CA A:GLY49 4.9 21.6 1.0
O A:GLY42 4.9 21.0 1.0
C A:GLY46 4.9 27.9 1.0
CA A:GLY46 4.9 24.9 1.0

Iron binding site 4 out of 8 in 6ac4

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Iron binding site 4 out of 8 in the Rat Xanthine Oxidoreductase, D428N Variant


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Rat Xanthine Oxidoreductase, D428N Variant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe1403

b:23.7
occ:1.00
 FE2 A:FES1403 0.0 23.7 1.0
SG A:CYS51 2.2 20.9 1.0
S2 A:FES1403 2.2 24.4 1.0
S1 A:FES1403 2.2 25.0 1.0
SG A:CYS73 2.4 27.4 1.0
FE1 A:FES1403 2.8 25.7 1.0
CB A:CYS73 3.3 23.0 1.0
CB A:CYS51 3.4 19.7 1.0
CB A:ASN71 4.2 22.2 1.0
N A:CYS73 4.3 22.0 1.0
N A:GLY46 4.3 23.0 1.0
N A:CYS51 4.3 20.0 1.0
CA A:CYS73 4.3 24.2 1.0
N A:GLY44 4.4 25.6 1.0
ND2 A:ASN71 4.4 21.5 1.0
CA A:CYS51 4.5 21.0 1.0
SG A:CYS43 4.5 24.7 1.0
CA A:GLY44 4.5 26.6 1.0
CG A:ASN71 4.5 24.2 1.0
CA A:GLY46 4.6 24.9 1.0
N A:GLU45 4.7 28.5 1.0
SG A:CYS48 4.8 22.9 1.0
N A:GLY49 4.8 21.0 1.0
CA A:ASN71 4.8 21.1 1.0
C A:GLY44 4.9 27.8 1.0

Iron binding site 5 out of 8 in 6ac4

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Iron binding site 5 out of 8 in the Rat Xanthine Oxidoreductase, D428N Variant


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Rat Xanthine Oxidoreductase, D428N Variant within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe3001

b:27.5
occ:1.00
 FE1 B:FES3001 0.0 27.5 1.0
O B:HOH3631 2.0 24.5 1.0
S1 B:FES3001 2.2 25.5 1.0
S2 B:FES3001 2.2 27.7 1.0
SG B:CYS112 2.3 24.0 1.0
FE2 B:FES3001 2.8 26.9 1.0
O B:HOH3220 3.0 32.4 1.0
SG B:CYS149 3.2 29.4 1.0
CB B:CYS112 3.4 25.8 1.0
O B:HOH3542 3.4 24.2 1.0
CB B:CYS149 3.5 25.3 1.0
N B:CYS112 3.6 25.8 1.0
CA B:CYS112 3.9 26.1 1.0
N B:GLY113 3.9 23.6 1.0
C B:CYS112 4.3 26.0 1.0
N B:CYS149 4.3 25.2 1.0
SG B:CYS147 4.4 24.8 1.0
N B:PHE114 4.4 20.0 1.0
CA B:CYS149 4.6 25.7 1.0
SG B:CYS115 4.6 28.0 1.0
C B:GLN111 4.7 25.5 1.0
N B:ARG148 4.8 24.6 1.0
CB B:GLN111 4.9 26.7 1.0
CA B:GLY113 5.0 21.6 1.0

Iron binding site 6 out of 8 in 6ac4

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Iron binding site 6 out of 8 in the Rat Xanthine Oxidoreductase, D428N Variant


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Rat Xanthine Oxidoreductase, D428N Variant within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe3001

b:26.9
occ:1.00
 FE2 B:FES3001 0.0 26.9 1.0
SG B:CYS115 2.2 28.0 1.0
S2 B:FES3001 2.2 27.7 1.0
S1 B:FES3001 2.3 25.5 1.0
SG B:CYS147 2.3 24.8 1.0
FE1 B:FES3001 2.8 27.5 1.0
CB B:CYS147 3.3 23.1 1.0
CB B:CYS115 3.4 22.5 1.0
CA B:CYS147 3.6 23.3 1.0
N B:ARG148 4.1 24.6 1.0
N B:CYS115 4.2 19.8 1.0
O B:HOH3631 4.2 24.5 1.0
O B:HOH3282 4.3 30.0 1.0
C B:CYS147 4.3 24.8 1.0
CA B:CYS115 4.4 20.3 1.0
N B:CYS149 4.5 25.2 1.0
CB B:CYS149 4.6 25.3 1.0
SG B:CYS112 4.8 24.0 1.0
CG2 B:THR150 4.8 25.4 1.0
O B:LEU146 4.9 24.8 1.0
N B:CYS147 4.9 23.1 1.0
N B:PHE114 5.0 20.0 1.0

Iron binding site 7 out of 8 in 6ac4

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Iron binding site 7 out of 8 in the Rat Xanthine Oxidoreductase, D428N Variant


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Rat Xanthine Oxidoreductase, D428N Variant within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe3002

b:27.7
occ:1.00
 FE1 B:FES3002 0.0 27.7 1.0
S2 B:FES3002 2.2 28.0 1.0
S1 B:FES3002 2.3 29.2 1.0
SG B:CYS48 2.3 24.9 1.0
SG B:CYS43 2.3 30.1 1.0
FE2 B:FES3002 2.8 28.1 1.0
CB B:CYS48 3.4 26.2 1.0
N B:CYS43 3.4 26.3 1.0
N B:CYS48 3.5 27.6 1.0
CB B:CYS43 3.5 29.7 1.0
N B:GLY49 3.7 28.1 1.0
N B:GLY44 3.8 29.2 1.0
CA B:CYS48 3.8 27.2 1.0
CA B:CYS43 3.9 29.2 1.0
C B:GLY42 4.1 30.1 1.0
C B:CYS48 4.2 28.1 1.0
C B:CYS43 4.3 28.3 1.0
N B:GLY42 4.3 30.4 1.0
N B:GLY47 4.4 30.3 1.0
CA B:GLY42 4.4 28.9 1.0
N B:GLY46 4.4 29.5 1.0
N B:ALA50 4.5 22.9 1.0
SG B:CYS73 4.6 27.2 1.0
SG B:CYS51 4.6 23.9 1.0
C B:GLY47 4.7 32.0 1.0
N B:GLU45 4.7 30.6 1.0
CA B:GLY49 4.7 27.2 1.0
C B:GLY46 4.7 30.6 1.0
CA B:GLY46 4.8 28.1 1.0
CA B:GLY44 4.8 30.4 1.0

Iron binding site 8 out of 8 in 6ac4

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Iron binding site 8 out of 8 in the Rat Xanthine Oxidoreductase, D428N Variant


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Rat Xanthine Oxidoreductase, D428N Variant within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe3002

b:28.1
occ:1.00
 FE2 B:FES3002 0.0 28.1 1.0
S1 B:FES3002 2.2 29.2 1.0
S2 B:FES3002 2.2 28.0 1.0
SG B:CYS51 2.3 23.9 1.0
SG B:CYS73 2.4 27.2 1.0
FE1 B:FES3002 2.8 27.7 1.0
CB B:CYS73 3.2 27.5 1.0
CB B:CYS51 3.5 21.4 1.0
CB B:ASN71 4.3 26.0 1.0
N B:CYS73 4.3 21.8 1.0
N B:CYS51 4.3 21.9 1.0
CA B:CYS73 4.3 25.0 1.0
N B:GLY44 4.4 29.2 1.0
N B:GLY46 4.4 29.5 1.0
ND2 B:ASN71 4.4 25.1 1.0
CA B:CYS51 4.5 22.2 1.0
SG B:CYS43 4.5 30.1 1.0
CA B:GLY46 4.6 28.1 1.0
CG B:ASN71 4.6 29.5 1.0
CA B:GLY44 4.6 30.4 1.0
SG B:CYS48 4.7 24.9 1.0
N B:GLY49 4.8 28.1 1.0
N B:GLU45 5.0 30.6 1.0
CA B:ASN71 5.0 23.9 1.0

Reference:

K.Okamoto, Y.Kawaguchi. Rat Xanthine Oxidoreductase, D428A Variant, Nad Bound Form To Be Published.
Page generated: Wed Aug 6 03:42:24 2025

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