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Iron in PDB 6aju: Rat Xanthine Oxidoreductase

Enzymatic activity of Rat Xanthine Oxidoreductase

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

Protein crystallography data

The structure of Rat Xanthine Oxidoreductase, PDB code: 6aju 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) 38.89 / 1.94
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 98.717, 138.084, 222.255, 90.00, 90.00, 90.00
R / Rfree (%) 17.2 / 20.8

Iron Binding Sites:

The binding sites of Iron atom in the Rat Xanthine Oxidoreductase (pdb code 6aju). 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, PDB code: 6aju:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iron binding site 1 out of 8 in 6aju

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


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe3001

b:17.4
occ:1.00
 FE1 A:FES3001 0.0 17.4 1.0
S2 A:FES3001 2.2 15.2 1.0
S1 A:FES3001 2.3 17.9 1.0
SG A:CYS112 2.3 13.7 1.0
FE2 A:FES3001 2.7 16.1 1.0
SG A:CYS149 2.8 23.2 1.0
CB A:CYS112 3.3 14.2 1.0
CB A:CYS149 3.4 18.1 1.0
O A:HOH3544 3.6 11.7 1.0
N A:CYS112 3.6 12.9 1.0
CA A:CYS112 3.9 15.0 1.0
N A:GLY113 3.9 13.3 1.0
N A:CYS149 4.2 13.4 1.0
C A:CYS112 4.3 13.8 1.0
N A:PHE114 4.4 12.6 1.0
SG A:CYS147 4.4 15.4 1.0
CA A:CYS149 4.4 15.4 1.0
SG A:CYS115 4.5 16.1 1.0
N A:ARG148 4.7 13.6 1.0
C A:GLN111 4.8 15.1 1.0
N A:CYS115 4.9 13.2 1.0
CA A:GLY113 5.0 13.5 1.0
CB A:GLN111 5.0 15.6 1.0

Iron binding site 2 out of 8 in 6aju

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


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe3001

b:16.1
occ:1.00
 FE2 A:FES3001 0.0 16.1 1.0
S1 A:FES3001 2.2 17.9 1.0
S2 A:FES3001 2.2 15.2 1.0
SG A:CYS115 2.3 16.1 1.0
SG A:CYS147 2.4 15.4 1.0
FE1 A:FES3001 2.7 17.4 1.0
CB A:CYS147 3.3 15.7 1.0
CB A:CYS115 3.4 14.5 1.0
CA A:CYS147 3.7 14.0 1.0
N A:ARG148 4.1 13.6 1.0
N A:CYS115 4.2 13.2 1.0
O A:HOH3147 4.3 16.0 1.0
C A:CYS147 4.3 13.6 1.0
N A:CYS149 4.4 13.4 1.0
CA A:CYS115 4.4 13.2 1.0
CB A:CYS149 4.5 18.1 1.0
SG A:CYS112 4.6 13.7 1.0
CG2 A:THR150 4.8 15.3 1.0
SG A:CYS149 4.8 23.2 1.0
O A:LEU146 5.0 14.8 1.0
CA A:CYS149 5.0 15.4 1.0

Iron binding site 3 out of 8 in 6aju

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


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe3002

b:13.9
occ:1.00
 FE1 A:FES3002 0.0 13.9 1.0
S1 A:FES3002 2.2 13.8 1.0
S2 A:FES3002 2.2 13.3 1.0
SG A:CYS51 2.3 12.8 1.0
SG A:CYS73 2.3 14.4 1.0
FE2 A:FES3002 2.8 14.6 1.0
CB A:CYS73 3.2 15.0 1.0
CB A:CYS51 3.4 12.0 1.0
CB A:ASN71 4.2 14.7 1.0
N A:CYS73 4.3 12.6 1.0
CA A:CYS73 4.3 14.4 1.0
N A:GLY46 4.3 15.5 1.0
N A:CYS51 4.3 11.6 1.0
N A:GLY44 4.4 14.4 1.0
OD1 A:ASN71 4.4 18.6 1.0
SG A:CYS43 4.4 14.7 1.0
CA A:GLY46 4.4 16.2 1.0
CG A:ASN71 4.5 17.1 1.0
CA A:CYS51 4.5 12.0 1.0
CA A:GLY44 4.6 14.6 1.0
SG A:CYS48 4.7 12.8 1.0
N A:GLU45 4.8 16.0 1.0
N A:GLY49 4.8 14.5 1.0
CA A:ASN71 4.9 14.5 1.0
C A:GLY44 5.0 17.0 1.0
N A:ALA50 5.0 12.0 1.0

Iron binding site 4 out of 8 in 6aju

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


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe3002

b:14.6
occ:1.00
 FE2 A:FES3002 0.0 14.6 1.0
S1 A:FES3002 2.3 13.8 1.0
S2 A:FES3002 2.3 13.3 1.0
SG A:CYS43 2.3 14.7 1.0
SG A:CYS48 2.3 12.8 1.0
FE1 A:FES3002 2.8 13.9 1.0
CB A:CYS48 3.3 13.8 1.0
N A:CYS43 3.4 13.3 1.0
CB A:CYS43 3.5 14.2 1.0
N A:CYS48 3.6 15.2 1.0
N A:GLY44 3.8 14.4 1.0
CA A:CYS48 3.8 13.8 1.0
CA A:CYS43 3.8 14.2 1.0
N A:GLY49 3.9 14.5 1.0
C A:GLY42 4.1 13.4 1.0
C A:CYS48 4.2 14.1 1.0
C A:CYS43 4.3 14.0 1.0
N A:GLY42 4.3 11.8 1.0
CA A:GLY42 4.4 13.5 1.0
N A:GLY47 4.4 15.8 1.0
N A:GLY46 4.4 15.5 1.0
N A:ALA50 4.4 12.0 1.0
SG A:CYS73 4.5 14.4 1.0
SG A:CYS51 4.6 12.8 1.0
N A:GLU45 4.6 16.0 1.0
C A:GLY47 4.7 18.8 1.0
CA A:GLY46 4.8 16.2 1.0
C A:GLY46 4.8 16.7 1.0
CA A:GLY44 4.8 14.6 1.0
CA A:GLY49 4.9 13.0 1.0
O A:GLY42 5.0 13.8 1.0

Iron binding site 5 out of 8 in 6aju

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


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Fe3001

b:18.2
occ:1.00
 FE1 F:FES3001 0.0 18.2 1.0
S2 F:FES3001 2.2 17.0 1.0
S1 F:FES3001 2.2 19.3 1.0
SG F:CYS112 2.3 14.1 1.0
FE2 F:FES3001 2.7 17.1 1.0
SG F:CYS149 2.8 21.6 1.0
CB F:CYS112 3.3 13.9 1.0
CB F:CYS149 3.5 16.3 1.0
O F:HOH3583 3.5 16.6 1.0
N F:CYS112 3.7 14.2 1.0
CA F:CYS112 3.9 13.8 1.0
N F:GLY113 4.0 13.3 1.0
N F:CYS149 4.2 15.1 1.0
C F:CYS112 4.3 13.2 1.0
SG F:CYS147 4.4 15.6 1.0
N F:PHE114 4.4 13.2 1.0
CA F:CYS149 4.5 15.2 1.0
SG F:CYS115 4.5 17.2 1.0
N F:ARG148 4.7 14.8 1.0
C F:GLN111 4.8 14.4 1.0
N F:CYS115 4.9 12.3 1.0
CB F:GLN111 5.0 14.9 1.0

Iron binding site 6 out of 8 in 6aju

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


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Fe3001

b:17.1
occ:1.00
 FE2 F:FES3001 0.0 17.1 1.0
SG F:CYS115 2.2 17.2 1.0
S1 F:FES3001 2.2 19.3 1.0
S2 F:FES3001 2.3 17.0 1.0
SG F:CYS147 2.4 15.6 1.0
FE1 F:FES3001 2.7 18.2 1.0
CB F:CYS147 3.3 14.7 1.0
CB F:CYS115 3.4 14.3 1.0
CA F:CYS147 3.7 14.6 1.0
N F:ARG148 4.0 14.8 1.0
N F:CYS115 4.2 12.3 1.0
C F:CYS147 4.3 14.5 1.0
N F:CYS149 4.4 15.1 1.0
CA F:CYS115 4.4 12.8 1.0
O F:HOH3217 4.4 15.0 1.0
CB F:CYS149 4.6 16.3 1.0
SG F:CYS112 4.7 14.1 1.0
CG2 F:THR150 4.8 14.4 1.0
SG F:CYS149 4.8 21.6 1.0
O F:LEU146 4.9 15.6 1.0
N F:CYS147 4.9 14.1 1.0
C F:CYS115 5.0 13.2 1.0

Iron binding site 7 out of 8 in 6aju

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


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Fe3002

b:15.6
occ:1.00
 FE1 F:FES3002 0.0 15.6 1.0
S1 F:FES3002 2.2 15.7 1.0
S2 F:FES3002 2.2 15.2 1.0
SG F:CYS51 2.3 15.6 1.0
SG F:CYS73 2.4 15.7 1.0
FE2 F:FES3002 2.8 15.8 1.0
CB F:CYS73 3.1 15.3 1.0
CB F:CYS51 3.5 13.5 1.0
N F:CYS73 4.3 14.4 1.0
CA F:CYS73 4.3 16.5 1.0
CB F:ASN71 4.3 17.7 1.0
N F:GLY46 4.3 17.7 1.0
OD1 F:ASN71 4.4 22.1 1.0
N F:CYS51 4.4 13.1 1.0
N F:GLY44 4.4 16.2 1.0
SG F:CYS43 4.4 17.0 1.0
CA F:GLY46 4.5 17.3 1.0
CA F:CYS51 4.5 13.3 1.0
CG F:ASN71 4.6 20.7 1.0
SG F:CYS48 4.6 15.1 1.0
CA F:GLY44 4.7 16.2 1.0
N F:GLU45 4.9 16.4 1.0
N F:GLY49 4.9 14.7 1.0
CA F:ASN71 5.0 16.2 1.0
N F:ALA50 5.0 12.9 1.0

Iron binding site 8 out of 8 in 6aju

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Iron binding site 8 out of 8 in the Rat Xanthine Oxidoreductase


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Fe3002

b:15.8
occ:1.00
 FE2 F:FES3002 0.0 15.8 1.0
S2 F:FES3002 2.3 15.2 1.0
S1 F:FES3002 2.3 15.7 1.0
SG F:CYS48 2.3 15.1 1.0
SG F:CYS43 2.3 17.0 1.0
FE1 F:FES3002 2.8 15.6 1.0
CB F:CYS48 3.4 16.2 1.0
N F:CYS43 3.4 17.1 1.0
CB F:CYS43 3.5 16.1 1.0
N F:CYS48 3.5 16.2 1.0
CA F:CYS48 3.8 14.5 1.0
CA F:CYS43 3.9 17.2 1.0
N F:GLY44 3.9 16.2 1.0
N F:GLY49 3.9 14.7 1.0
C F:GLY42 4.1 16.9 1.0
C F:CYS48 4.2 15.2 1.0
C F:CYS43 4.3 17.2 1.0
N F:GLY47 4.3 15.4 1.0
CA F:GLY42 4.4 15.6 1.0
N F:GLY42 4.4 15.9 1.0
N F:ALA50 4.4 12.9 1.0
N F:GLY46 4.4 17.7 1.0
SG F:CYS73 4.5 15.7 1.0
SG F:CYS51 4.6 15.6 1.0
N F:GLU45 4.7 16.4 1.0
C F:GLY47 4.7 17.7 1.0
C F:GLY46 4.8 16.9 1.0
CA F:GLY46 4.8 17.3 1.0
CA F:GLY44 4.9 16.2 1.0
O F:GLY42 4.9 18.1 1.0
CA F:GLY49 4.9 15.0 1.0
CB F:ALA50 5.0 14.5 1.0

Reference:

K.Okamoto, Y.Kawaguchi. Rat Xanthine Oxidoreductase, D428A Variant, Nad Bound Form To Be Published.
Page generated: Sun Dec 13 16:20:25 2020

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