Iron in PDB 6adj: Rat Xanthine Oxidoreductase, D428E Variant

Enzymatic activity of Rat Xanthine Oxidoreductase, D428E Variant

All present enzymatic activity of Rat Xanthine Oxidoreductase, D428E Variant:
1.17.1.4; 1.17.3.2;

Protein crystallography data

The structure of Rat Xanthine Oxidoreductase, D428E Variant, PDB code: 6adj 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) 42.40 / 2.18
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 98.836, 138.665, 222.463, 90.00, 90.00, 90.00
R / Rfree (%) 16.7 / 21

Other elements in 6adj:

The structure of Rat Xanthine Oxidoreductase, D428E Variant also contains other interesting chemical elements:

Calcium (Ca) 2 atoms

Iron Binding Sites:

The binding sites of Iron atom in the Rat Xanthine Oxidoreductase, D428E Variant (pdb code 6adj). 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, D428E Variant, PDB code: 6adj:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iron binding site 1 out of 8 in 6adj

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Iron binding site 1 out of 8 in the Rat Xanthine Oxidoreductase, D428E 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, D428E Variant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe3001

b:21.8
occ:1.00
 FE1 A:FES3001 0.0 21.8 1.0
S2 A:FES3001 2.3 20.5 1.0
S1 A:FES3001 2.3 22.8 1.0
SG A:CYS112 2.3 16.2 1.0
FE2 A:FES3001 2.7 19.5 1.0
SG A:CYS149 2.8 23.0 1.0
CB A:CYS112 3.3 16.4 1.0
CB A:CYS149 3.5 19.1 1.0
O A:HOH3473 3.5 18.9 1.0
N A:CYS112 3.6 16.4 1.0
CA A:CYS112 3.9 15.7 1.0
N A:GLY113 4.0 14.0 1.0
N A:CYS149 4.2 16.9 1.0
C A:CYS112 4.3 14.7 1.0
SG A:CYS147 4.4 18.4 1.0
N A:PHE114 4.4 13.9 1.0
CA A:CYS149 4.5 18.9 1.0
SG A:CYS115 4.5 16.3 1.0
N A:ARG148 4.7 16.2 1.0
C A:GLN111 4.8 16.3 1.0
N A:CYS115 4.9 13.8 1.0

Iron binding site 2 out of 8 in 6adj

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Iron binding site 2 out of 8 in the Rat Xanthine Oxidoreductase, D428E 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, D428E Variant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe3001

b:19.5
occ:1.00
 FE2 A:FES3001 0.0 19.5 1.0
SG A:CYS115 2.2 16.3 1.0
S2 A:FES3001 2.3 20.5 1.0
S1 A:FES3001 2.3 22.8 1.0
SG A:CYS147 2.3 18.4 1.0
FE1 A:FES3001 2.7 21.8 1.0
CB A:CYS147 3.3 17.5 1.0
CB A:CYS115 3.4 15.0 1.0
CA A:CYS147 3.7 16.3 1.0
N A:ARG148 4.1 16.2 1.0
N A:CYS115 4.2 13.8 1.0
C A:CYS147 4.3 15.9 1.0
O A:HOH3172 4.4 14.1 1.0
N A:CYS149 4.4 16.9 1.0
CA A:CYS115 4.4 13.9 1.0
CB A:CYS149 4.6 19.1 1.0
SG A:CYS112 4.7 16.2 1.0
CG2 A:THR150 4.7 21.2 1.0
SG A:CYS149 4.9 23.0 1.0
O A:LEU146 4.9 17.5 1.0
N A:CYS147 4.9 14.9 1.0

Iron binding site 3 out of 8 in 6adj

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Iron binding site 3 out of 8 in the Rat Xanthine Oxidoreductase, D428E 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, D428E Variant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe3002

b:18.5
occ:1.00
 FE1 A:FES3002 0.0 18.5 1.0
S1 A:FES3002 2.2 15.5 1.0
S2 A:FES3002 2.2 18.2 1.0
SG A:CYS51 2.3 16.4 1.0
SG A:CYS73 2.4 17.8 1.0
FE2 A:FES3002 2.7 17.6 1.0
CB A:CYS73 3.1 18.4 1.0
CB A:CYS51 3.4 15.1 1.0
N A:GLY46 4.3 22.1 1.0
N A:CYS73 4.3 16.6 1.0
CB A:ASN71 4.3 19.7 1.0
CA A:CYS73 4.3 18.2 1.0
N A:CYS51 4.3 13.6 1.0
OD1 A:ASN71 4.4 20.8 1.0
N A:GLY44 4.4 19.9 1.0
SG A:CYS43 4.4 19.7 1.0
CA A:CYS51 4.5 14.9 1.0
CA A:GLY46 4.5 21.1 1.0
CG A:ASN71 4.6 21.1 1.0
SG A:CYS48 4.6 16.6 1.0
CA A:GLY44 4.7 19.2 1.0
N A:GLU45 4.8 22.1 1.0
N A:GLY49 4.8 15.4 1.0

Iron binding site 4 out of 8 in 6adj

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Iron binding site 4 out of 8 in the Rat Xanthine Oxidoreductase, D428E 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, D428E Variant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe3002

b:17.6
occ:1.00
 FE2 A:FES3002 0.0 17.6 1.0
S1 A:FES3002 2.2 15.5 1.0
S2 A:FES3002 2.3 18.2 1.0
SG A:CYS48 2.3 16.6 1.0
SG A:CYS43 2.4 19.7 1.0
FE1 A:FES3002 2.7 18.5 1.0
N A:CYS43 3.4 18.7 1.0
CB A:CYS43 3.5 17.1 1.0
CB A:CYS48 3.5 17.3 1.0
N A:CYS48 3.5 17.1 1.0
N A:GLY49 3.8 15.4 1.0
CA A:CYS43 3.8 19.6 1.0
N A:GLY44 3.9 19.9 1.0
CA A:CYS48 3.9 16.4 1.0
C A:GLY42 4.1 19.7 1.0
C A:CYS48 4.2 15.8 1.0
C A:CYS43 4.3 18.7 1.0
N A:GLY42 4.3 19.4 1.0
CA A:GLY42 4.4 17.9 1.0
N A:GLY47 4.4 20.9 1.0
N A:ALA50 4.4 14.3 1.0
N A:GLY46 4.4 22.1 1.0
SG A:CYS73 4.5 17.8 1.0
SG A:CYS51 4.6 16.4 1.0
N A:GLU45 4.6 22.1 1.0
C A:GLY47 4.7 20.4 1.0
C A:GLY46 4.8 20.1 1.0
CA A:GLY49 4.8 15.6 1.0
CA A:GLY46 4.8 21.1 1.0
CA A:GLY44 4.9 19.2 1.0

Iron binding site 5 out of 8 in 6adj

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Iron binding site 5 out of 8 in the Rat Xanthine Oxidoreductase, D428E 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, D428E Variant within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe4001

b:19.3
occ:1.00
 FE1 B:FES4001 0.0 19.3 1.0
SG B:CYS112 2.3 14.7 1.0
S1 B:FES4001 2.3 21.2 1.0
S2 B:FES4001 2.3 17.9 1.0
FE2 B:FES4001 2.7 18.7 1.0
SG B:CYS149 2.9 23.0 1.0
CB B:CYS112 3.3 16.1 1.0
CB B:CYS149 3.4 18.8 1.0
O B:HOH4568 3.5 12.6 1.0
N B:CYS112 3.7 15.6 1.0
CA B:CYS112 3.9 15.8 1.0
N B:GLY113 4.0 13.7 1.0
N B:CYS149 4.2 14.9 1.0
C B:CYS112 4.4 15.7 1.0
N B:PHE114 4.4 13.4 1.0
SG B:CYS147 4.4 18.6 1.0
CA B:CYS149 4.5 17.3 1.0
SG B:CYS115 4.5 14.8 1.0
N B:ARG148 4.8 15.7 1.0
C B:GLN111 4.8 15.8 1.0
N B:CYS115 4.9 13.3 1.0

Iron binding site 6 out of 8 in 6adj

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Iron binding site 6 out of 8 in the Rat Xanthine Oxidoreductase, D428E 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, D428E Variant within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe4001

b:18.7
occ:1.00
 FE2 B:FES4001 0.0 18.7 1.0
S1 B:FES4001 2.2 21.2 1.0
SG B:CYS115 2.2 14.8 1.0
S2 B:FES4001 2.3 17.9 1.0
SG B:CYS147 2.4 18.6 1.0
FE1 B:FES4001 2.7 19.3 1.0
CB B:CYS147 3.3 16.3 1.0
CB B:CYS115 3.4 14.3 1.0
CA B:CYS147 3.7 14.7 1.0
N B:ARG148 4.1 15.7 1.0
N B:CYS115 4.2 13.3 1.0
O B:HOH4260 4.3 14.2 1.0
C B:CYS147 4.3 14.7 1.0
CA B:CYS115 4.4 12.4 1.0
N B:CYS149 4.4 14.9 1.0
CB B:CYS149 4.4 18.8 1.0
SG B:CYS112 4.6 14.7 1.0
CG2 B:THR150 4.7 19.4 1.0
SG B:CYS149 4.9 23.0 1.0
N B:CYS147 5.0 14.1 1.0

Iron binding site 7 out of 8 in 6adj

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Iron binding site 7 out of 8 in the Rat Xanthine Oxidoreductase, D428E 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, D428E Variant within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe4002

b:14.6
occ:1.00
 FE1 B:FES4002 0.0 14.6 1.0
S1 B:FES4002 2.2 14.3 1.0
S2 B:FES4002 2.2 14.3 1.0
SG B:CYS51 2.3 13.7 1.0
SG B:CYS73 2.3 17.1 1.0
FE2 B:FES4002 2.8 15.5 1.0
CB B:CYS73 3.2 14.9 1.0
CB B:CYS51 3.5 13.2 1.0
N B:CYS73 4.3 13.7 1.0
CB B:ASN71 4.3 13.7 1.0
CA B:CYS73 4.3 14.8 1.0
N B:GLY44 4.3 17.0 1.0
N B:GLY46 4.3 18.5 1.0
OD1 B:ASN71 4.4 15.5 1.0
N B:CYS51 4.4 12.1 1.0
SG B:CYS43 4.4 15.6 1.0
CG B:ASN71 4.5 15.1 1.0
CA B:CYS51 4.5 12.7 1.0
CA B:GLY44 4.6 17.3 1.0
CA B:GLY46 4.6 19.4 1.0
SG B:CYS48 4.7 15.3 1.0
N B:GLU45 4.8 19.7 1.0
N B:GLY49 4.8 13.2 1.0
C B:GLY44 4.9 18.7 1.0
CA B:ASN71 4.9 13.9 1.0

Iron binding site 8 out of 8 in 6adj

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Iron binding site 8 out of 8 in the Rat Xanthine Oxidoreductase, D428E 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, D428E Variant within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe4002

b:15.5
occ:1.00
 FE2 B:FES4002 0.0 15.5 1.0
S2 B:FES4002 2.3 14.3 1.0
S1 B:FES4002 2.3 14.3 1.0
SG B:CYS48 2.3 15.3 1.0
SG B:CYS43 2.4 15.6 1.0
FE1 B:FES4002 2.8 14.6 1.0
N B:CYS43 3.3 15.1 1.0
CB B:CYS48 3.4 14.4 1.0
CB B:CYS43 3.4 15.6 1.0
N B:CYS48 3.6 16.1 1.0
N B:GLY44 3.7 17.0 1.0
CA B:CYS43 3.8 16.0 1.0
CA B:CYS48 3.9 14.1 1.0
N B:GLY49 3.9 13.2 1.0
C B:GLY42 4.0 15.6 1.0
C B:CYS43 4.2 16.2 1.0
C B:CYS48 4.2 13.5 1.0
CA B:GLY42 4.3 15.6 1.0
N B:GLY42 4.3 13.5 1.0
N B:ALA50 4.4 12.9 1.0
N B:GLY46 4.4 18.5 1.0
SG B:CYS73 4.5 17.1 1.0
N B:GLY47 4.5 19.3 1.0
N B:GLU45 4.6 19.7 1.0
SG B:CYS51 4.7 13.7 1.0
CA B:GLY44 4.8 17.3 1.0
C B:GLY47 4.8 20.1 1.0
C B:GLY46 4.8 20.9 1.0
CA B:GLY46 4.9 19.4 1.0
CA B:GLY49 4.9 13.0 1.0
O B:GLY42 4.9 15.5 1.0

Reference:

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

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