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Iron in PDB 6ad4: Rat Xanthine Oxidoreductase, D428A Variant, Nadh Bound Form

Enzymatic activity of Rat Xanthine Oxidoreductase, D428A Variant, Nadh Bound Form

All present enzymatic activity of Rat Xanthine Oxidoreductase, D428A Variant, Nadh Bound Form:
1.17.1.4; 1.17.3.2;

Protein crystallography data

The structure of Rat Xanthine Oxidoreductase, D428A Variant, Nadh Bound Form, PDB code: 6ad4 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) 49.36 / 1.80
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 98.718, 138.334, 222.513, 90.00, 90.00, 90.00
R / Rfree (%) 16.4 / 19.8

Iron Binding Sites:

The binding sites of Iron atom in the Rat Xanthine Oxidoreductase, D428A Variant, Nadh Bound Form (pdb code 6ad4). 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, D428A Variant, Nadh Bound Form, PDB code: 6ad4:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iron binding site 1 out of 8 in 6ad4

Go back to Iron Binding Sites List in 6ad4
Iron binding site 1 out of 8 in the Rat Xanthine Oxidoreductase, D428A Variant, Nadh Bound Form


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, D428A Variant, Nadh Bound Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe1503

b:14.2
occ:1.00
 FE1 A:FES1503 0.0 14.2 1.0
S2 A:FES1503 2.2 14.8 1.0
S1 A:FES1503 2.3 14.2 1.0
SG A:CYS48 2.3 14.1 1.0
SG A:CYS43 2.4 15.3 1.0
FE2 A:FES1503 2.8 14.0 1.0
N A:CYS43 3.4 14.8 1.0
CB A:CYS48 3.5 15.5 1.0
CB A:CYS43 3.5 13.9 1.0
N A:CYS48 3.5 15.3 1.0
CA A:CYS43 3.8 15.2 1.0
N A:GLY44 3.9 14.9 1.0
N A:GLY49 3.9 13.7 1.0
CA A:CYS48 3.9 15.3 1.0
C A:GLY42 4.1 14.1 1.0
C A:CYS48 4.2 13.7 1.0
C A:CYS43 4.3 15.7 1.0
N A:ALA50 4.3 12.4 1.0
N A:GLY42 4.4 13.6 1.0
CA A:GLY42 4.4 13.7 1.0
N A:GLY47 4.4 17.5 1.0
N A:GLY46 4.4 19.6 1.0
SG A:CYS73 4.5 14.2 1.0
SG A:CYS51 4.6 13.4 1.0
N A:GLU45 4.6 19.6 1.0
C A:GLY47 4.7 18.4 1.0
C A:GLY46 4.8 17.7 1.0
CA A:GLY49 4.8 12.8 1.0
CA A:GLY46 4.9 19.8 1.0
CA A:GLY44 4.9 15.1 1.0
O A:GLY42 5.0 15.0 1.0
CB A:ALA50 5.0 14.2 1.0

Iron binding site 2 out of 8 in 6ad4

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Iron binding site 2 out of 8 in the Rat Xanthine Oxidoreductase, D428A Variant, Nadh Bound Form


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, D428A Variant, Nadh Bound Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe1503

b:14.0
occ:1.00
 FE2 A:FES1503 0.0 14.0 1.0
S1 A:FES1503 2.2 14.2 1.0
S2 A:FES1503 2.2 14.8 1.0
SG A:CYS51 2.3 13.4 1.0
SG A:CYS73 2.3 14.2 1.0
FE1 A:FES1503 2.8 14.2 1.0
CB A:CYS73 3.2 13.7 1.0
CB A:CYS51 3.4 12.0 1.0
N A:CYS73 4.2 13.7 1.0
CB A:ASN71 4.2 14.1 1.0
CA A:CYS73 4.2 14.3 1.0
ND2 A:ASN71 4.3 14.7 1.0
N A:CYS51 4.3 11.3 1.0
N A:GLY46 4.3 19.6 1.0
N A:GLY44 4.4 14.9 1.0
SG A:CYS43 4.4 15.3 1.0
CA A:CYS51 4.5 12.0 1.0
CA A:GLY46 4.6 19.8 1.0
CG A:ASN71 4.6 16.9 1.0
CA A:GLY44 4.6 15.1 1.0
SG A:CYS48 4.7 14.1 1.0
N A:GLU45 4.8 19.6 1.0
N A:GLY49 4.9 13.7 1.0
CA A:ASN71 4.9 14.4 1.0
N A:ALA50 5.0 12.4 1.0
C A:GLY44 5.0 17.5 1.0

Iron binding site 3 out of 8 in 6ad4

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Iron binding site 3 out of 8 in the Rat Xanthine Oxidoreductase, D428A Variant, Nadh Bound Form


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, D428A Variant, Nadh Bound Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe1504

b:16.8
occ:1.00
 FE1 A:FES1504 0.0 16.8 1.0
S2 A:FES1504 2.2 18.1 1.0
SG A:CYS115 2.2 17.0 1.0
S1 A:FES1504 2.3 17.5 1.0
SG A:CYS147 2.3 15.4 1.0
FE2 A:FES1504 2.7 17.8 1.0
CB A:CYS147 3.3 14.4 1.0
CB A:CYS115 3.4 13.3 1.0
CA A:CYS147 3.7 13.8 1.0
N A:ARG148 4.1 12.7 1.0
N A:CYS115 4.2 12.2 1.0
C A:CYS147 4.3 14.2 1.0
N A:CYS149 4.3 14.4 1.0
O A:HOH1637 4.4 14.5 1.0
CA A:CYS115 4.4 12.4 1.0
CB A:CYS149 4.4 16.7 1.0
SG A:CYS112 4.6 14.1 1.0
SG A:CYS149 4.7 24.6 1.0
CG2 A:THR150 4.8 15.1 1.0
O A:LEU146 4.9 15.5 1.0
CD2 A:LEU744 4.9 35.2 1.0
CA A:CYS149 5.0 16.4 1.0
N A:CYS147 5.0 13.6 1.0

Iron binding site 4 out of 8 in 6ad4

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Iron binding site 4 out of 8 in the Rat Xanthine Oxidoreductase, D428A Variant, Nadh Bound Form


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, D428A Variant, Nadh Bound Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe1504

b:17.8
occ:1.00
 FE2 A:FES1504 0.0 17.8 1.0
S1 A:FES1504 2.2 17.5 1.0
SG A:CYS112 2.3 14.1 1.0
S2 A:FES1504 2.3 18.1 1.0
FE1 A:FES1504 2.7 16.8 1.0
SG A:CYS149 2.8 24.6 1.0
CB A:CYS112 3.3 14.2 1.0
CB A:CYS149 3.5 16.7 1.0
O A:HOH2085 3.5 14.8 1.0
N A:CYS112 3.7 15.0 1.0
CA A:CYS112 3.8 13.7 1.0
N A:GLY113 3.9 12.8 1.0
N A:CYS149 4.2 14.4 1.0
C A:CYS112 4.2 13.2 1.0
SG A:CYS147 4.3 15.4 1.0
N A:PHE114 4.4 12.3 1.0
CA A:CYS149 4.4 16.4 1.0
SG A:CYS115 4.5 17.0 1.0
N A:ARG148 4.7 12.7 1.0
C A:GLN111 4.8 15.0 1.0
N A:CYS115 4.9 12.2 1.0
CA A:GLY113 5.0 13.2 1.0

Iron binding site 5 out of 8 in 6ad4

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Iron binding site 5 out of 8 in the Rat Xanthine Oxidoreductase, D428A Variant, Nadh Bound Form


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, D428A Variant, Nadh Bound Form within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe3001

b:17.3
occ:1.00
 FE1 B:FES3001 0.0 17.3 1.0
S1 B:FES3001 2.2 15.8 1.0
S2 B:FES3001 2.2 18.4 1.0
SG B:CYS112 2.3 14.6 1.0
FE2 B:FES3001 2.7 15.8 1.0
SG B:CYS149 2.7 24.4 1.0
CB B:CYS112 3.3 15.2 1.0
CB B:CYS149 3.5 18.1 1.0
O B:HOH3617 3.6 12.5 1.0
N B:CYS112 3.6 13.5 1.0
CA B:CYS112 3.8 13.5 1.0
N B:GLY113 3.9 12.9 1.0
N B:CYS149 4.1 14.7 1.0
C B:CYS112 4.3 14.0 1.0
SG B:CYS147 4.4 14.9 1.0
N B:PHE114 4.4 11.4 1.0
CA B:CYS149 4.4 16.0 1.0
SG B:CYS115 4.5 15.9 1.0
N B:ARG148 4.7 11.9 1.0
C B:GLN111 4.8 14.3 1.0
N B:CYS115 4.9 12.5 1.0
CB B:GLN111 5.0 14.8 1.0
CA B:GLY113 5.0 13.4 1.0

Iron binding site 6 out of 8 in 6ad4

Go back to Iron Binding Sites List in 6ad4
Iron binding site 6 out of 8 in the Rat Xanthine Oxidoreductase, D428A Variant, Nadh Bound Form


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, D428A Variant, Nadh Bound Form within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe3001

b:15.8
occ:1.00
 FE2 B:FES3001 0.0 15.8 1.0
SG B:CYS115 2.2 15.9 1.0
S2 B:FES3001 2.2 18.4 1.0
S1 B:FES3001 2.3 15.8 1.0
SG B:CYS147 2.3 14.9 1.0
FE1 B:FES3001 2.7 17.3 1.0
CB B:CYS147 3.3 13.1 1.0
CB B:CYS115 3.4 12.8 1.0
CA B:CYS147 3.7 12.8 1.0
N B:ARG148 4.1 11.9 1.0
N B:CYS115 4.2 12.5 1.0
N B:CYS149 4.3 14.7 1.0
C B:CYS147 4.3 11.9 1.0
O B:HOH3231 4.3 13.8 1.0
CA B:CYS115 4.4 10.9 1.0
CB B:CYS149 4.5 18.1 1.0
SG B:CYS112 4.6 14.6 1.0
SG B:CYS149 4.7 24.4 1.0
CG2 B:THR150 4.8 15.1 1.0
CD2 B:LEU744 4.8 33.3 1.0
CA B:CYS149 5.0 16.0 1.0
O B:LEU146 5.0 14.4 1.0
N B:THR150 5.0 13.4 1.0

Iron binding site 7 out of 8 in 6ad4

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Iron binding site 7 out of 8 in the Rat Xanthine Oxidoreductase, D428A Variant, Nadh Bound Form


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, D428A Variant, Nadh Bound Form within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe3002

b:11.8
occ:1.00
 FE1 B:FES3002 0.0 11.8 1.0
S2 B:FES3002 2.2 11.9 1.0
S1 B:FES3002 2.3 11.9 1.0
SG B:CYS51 2.3 11.4 1.0
SG B:CYS73 2.3 13.0 1.0
FE2 B:FES3002 2.8 12.1 1.0
CB B:CYS73 3.2 12.1 1.0
CB B:CYS51 3.4 10.4 1.0
CB B:ASN71 4.2 12.5 1.0
N B:CYS73 4.2 12.5 1.0
CA B:CYS73 4.3 13.3 1.0
N B:GLY46 4.3 14.9 1.0
ND2 B:ASN71 4.3 13.1 1.0
N B:CYS51 4.4 10.3 1.0
N B:GLY44 4.4 12.6 1.0
SG B:CYS43 4.4 12.7 1.0
CA B:CYS51 4.5 11.1 1.0
CA B:GLY46 4.6 15.8 1.0
CG B:ASN71 4.6 14.5 1.0
CA B:GLY44 4.6 13.3 1.0
SG B:CYS48 4.7 13.2 1.0
N B:GLU45 4.8 14.5 1.0
N B:GLY49 4.8 11.0 1.0
CA B:ASN71 4.9 11.6 1.0
C B:GLY44 5.0 15.1 1.0
N B:ALA50 5.0 11.3 1.0

Iron binding site 8 out of 8 in 6ad4

Go back to Iron Binding Sites List in 6ad4
Iron binding site 8 out of 8 in the Rat Xanthine Oxidoreductase, D428A Variant, Nadh Bound Form


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, D428A Variant, Nadh Bound Form within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe3002

b:12.1
occ:1.00
 FE2 B:FES3002 0.0 12.1 1.0
S2 B:FES3002 2.3 11.9 1.0
S1 B:FES3002 2.3 11.9 1.0
SG B:CYS48 2.3 13.2 1.0
SG B:CYS43 2.3 12.7 1.0
FE1 B:FES3002 2.8 11.8 1.0
CB B:CYS48 3.4 13.8 1.0
N B:CYS43 3.4 12.7 1.0
CB B:CYS43 3.5 12.8 1.0
N B:CYS48 3.6 13.9 1.0
N B:GLY49 3.8 11.0 1.0
CA B:CYS43 3.8 12.8 1.0
N B:GLY44 3.9 12.6 1.0
CA B:CYS48 3.9 13.2 1.0
C B:GLY42 4.1 12.0 1.0
C B:CYS48 4.2 12.5 1.0
C B:CYS43 4.3 13.6 1.0
N B:GLY42 4.3 11.4 1.0
N B:ALA50 4.4 11.3 1.0
CA B:GLY42 4.4 12.8 1.0
N B:GLY46 4.4 14.9 1.0
N B:GLY47 4.4 14.7 1.0
SG B:CYS73 4.5 13.0 1.0
N B:GLU45 4.6 14.5 1.0
SG B:CYS51 4.6 11.4 1.0
C B:GLY46 4.8 16.0 1.0
C B:GLY47 4.8 16.7 1.0
CA B:GLY46 4.8 15.8 1.0
CA B:GLY49 4.9 11.7 1.0
CA B:GLY44 4.9 13.3 1.0
O B:GLY42 5.0 13.0 1.0

Reference:

K.Okamoto, Y.Kawaguchi. Rat Xanthine Oxidoreductase, D428A Variant, Nad Bound Form To Be Published.
Page generated: Tue Aug 6 13:30:15 2024

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