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Iron in PDB 4ytz: Rat Xanthine Oxidoreductase, C-Terminal Deletion Protein Variant, Crystal Grown Without Dithiothreitol

Enzymatic activity of Rat Xanthine Oxidoreductase, C-Terminal Deletion Protein Variant, Crystal Grown Without Dithiothreitol

All present enzymatic activity of Rat Xanthine Oxidoreductase, C-Terminal Deletion Protein Variant, Crystal Grown Without Dithiothreitol:
1.17.1.4; 1.17.3.2;

Protein crystallography data

The structure of Rat Xanthine Oxidoreductase, C-Terminal Deletion Protein Variant, Crystal Grown Without Dithiothreitol, PDB code: 4ytz was solved by T.Nishino, K.Okamoto, Y.Kawaguchi, T.Matsumura, B.T.Eger, E.F.Pai, T.Nishino, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.87 / 2.30
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 100.172, 139.123, 223.273, 90.00, 90.00, 90.00
R / Rfree (%) 20.8 / 26.5

Other elements in 4ytz:

The structure of Rat Xanthine Oxidoreductase, C-Terminal Deletion Protein Variant, Crystal Grown Without Dithiothreitol also contains other interesting chemical elements:

Calcium (Ca) 4 atoms

Iron Binding Sites:

The binding sites of Iron atom in the Rat Xanthine Oxidoreductase, C-Terminal Deletion Protein Variant, Crystal Grown Without Dithiothreitol (pdb code 4ytz). 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, C-Terminal Deletion Protein Variant, Crystal Grown Without Dithiothreitol, PDB code: 4ytz:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iron binding site 1 out of 8 in 4ytz

Go back to Iron Binding Sites List in 4ytz
Iron binding site 1 out of 8 in the Rat Xanthine Oxidoreductase, C-Terminal Deletion Protein Variant, Crystal Grown Without Dithiothreitol


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, C-Terminal Deletion Protein Variant, Crystal Grown Without Dithiothreitol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe1401

b:34.8
occ:1.00
 FE1 A:FES1401 0.0 34.8 1.0
S2 A:FES1401 2.2 31.7 1.0
S1 A:FES1401 2.2 33.5 1.0
SG A:CYS112 2.2 28.2 1.0
SG A:CYS149 2.8 40.2 1.0
FE2 A:FES1401 2.9 35.5 1.0
CB A:CYS112 3.3 25.9 1.0
O A:HOH1519 3.4 24.8 1.0
CB A:CYS149 3.4 34.8 1.0
N A:CYS112 3.6 27.7 1.0
CA A:CYS112 3.9 25.6 1.0
N A:CYS149 4.0 31.7 1.0
N A:GLY113 4.1 23.6 1.0
CA A:CYS149 4.4 34.6 1.0
C A:CYS112 4.4 24.9 1.0
SG A:CYS147 4.5 30.2 1.0
N A:PHE114 4.5 21.6 1.0
N A:ARG148 4.7 29.5 1.0
SG A:CYS115 4.7 30.9 1.0
C A:GLN111 4.8 27.7 1.0
C A:ARG148 5.0 31.4 1.0
CB A:GLN111 5.0 29.7 1.0

Iron binding site 2 out of 8 in 4ytz

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Iron binding site 2 out of 8 in the Rat Xanthine Oxidoreductase, C-Terminal Deletion Protein Variant, Crystal Grown Without Dithiothreitol


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, C-Terminal Deletion Protein Variant, Crystal Grown Without Dithiothreitol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe1401

b:35.5
occ:1.00
 FE2 A:FES1401 0.0 35.5 1.0
SG A:CYS115 2.1 30.9 1.0
S2 A:FES1401 2.2 31.7 1.0
S1 A:FES1401 2.2 33.5 1.0
SG A:CYS147 2.4 30.2 1.0
FE1 A:FES1401 2.9 34.8 1.0
CB A:CYS147 3.3 28.0 1.0
CB A:CYS115 3.4 23.7 1.0
CA A:CYS147 3.8 27.7 1.0
N A:CYS115 4.1 22.4 1.0
N A:ARG148 4.2 29.5 1.0
CA A:CYS115 4.3 23.3 1.0
C A:CYS147 4.4 29.7 1.0
CG2 A:THR150 4.5 33.1 1.0
N A:CYS149 4.5 31.7 1.0
SG A:CYS112 4.6 28.2 1.0
CB A:CYS149 4.8 34.8 1.0
C A:CYS115 5.0 23.2 1.0
N A:THR116 5.0 22.9 1.0

Iron binding site 3 out of 8 in 4ytz

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Iron binding site 3 out of 8 in the Rat Xanthine Oxidoreductase, C-Terminal Deletion Protein Variant, Crystal Grown Without Dithiothreitol


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, C-Terminal Deletion Protein Variant, Crystal Grown Without Dithiothreitol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe1402

b:26.8
occ:1.00
 FE1 A:FES1402 0.0 26.8 1.0
S1 A:FES1402 2.1 26.2 1.0
S2 A:FES1402 2.2 27.3 1.0
SG A:CYS51 2.2 25.6 1.0
SG A:CYS73 2.3 30.4 1.0
FE2 A:FES1402 2.9 25.7 1.0
CB A:CYS73 3.2 26.9 1.0
CB A:CYS51 3.4 19.9 1.0
CB A:ASN71 4.0 25.0 1.0
ND2 A:ASN71 4.2 22.9 1.0
N A:GLY44 4.2 30.1 1.0
N A:CYS73 4.3 26.3 1.0
N A:CYS51 4.3 20.2 1.0
CA A:CYS73 4.3 27.6 1.0
N A:GLY46 4.3 33.0 1.0
SG A:CYS43 4.4 28.0 1.0
CG A:ASN71 4.4 27.4 1.0
CA A:CYS51 4.5 21.4 1.0
CA A:GLY44 4.5 31.6 1.0
CA A:GLY46 4.6 30.7 1.0
SG A:CYS48 4.7 27.8 1.0
CA A:ASN71 4.8 26.0 1.0
N A:GLY49 4.8 26.3 1.0
N A:GLU45 4.9 32.3 1.0
C A:GLY44 4.9 32.3 1.0

Iron binding site 4 out of 8 in 4ytz

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Iron binding site 4 out of 8 in the Rat Xanthine Oxidoreductase, C-Terminal Deletion Protein Variant, Crystal Grown Without Dithiothreitol


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, C-Terminal Deletion Protein Variant, Crystal Grown Without Dithiothreitol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe1402

b:25.7
occ:1.00
 FE2 A:FES1402 0.0 25.7 1.0
S1 A:FES1402 2.2 26.2 1.0
SG A:CYS48 2.2 27.8 1.0
S2 A:FES1402 2.2 27.3 1.0
SG A:CYS43 2.3 28.0 1.0
FE1 A:FES1402 2.9 26.8 1.0
CB A:CYS48 3.3 28.3 1.0
N A:CYS43 3.4 25.2 1.0
CB A:CYS43 3.4 27.5 1.0
N A:CYS48 3.4 28.9 1.0
N A:GLY44 3.7 30.1 1.0
CA A:CYS48 3.7 28.5 1.0
N A:GLY49 3.8 26.3 1.0
CA A:CYS43 3.8 28.4 1.0
C A:CYS48 4.1 27.7 1.0
C A:CYS43 4.2 29.4 1.0
C A:GLY42 4.2 25.6 1.0
N A:GLY47 4.3 30.8 1.0
N A:ALA50 4.4 22.0 1.0
N A:GLY42 4.4 22.8 1.0
CA A:GLY42 4.5 23.9 1.0
N A:GLY46 4.5 33.0 1.0
SG A:CYS73 4.6 30.4 1.0
SG A:CYS51 4.6 25.6 1.0
C A:GLY47 4.6 31.6 1.0
N A:GLU45 4.7 32.3 1.0
CA A:GLY44 4.8 31.6 1.0
CA A:GLY49 4.8 25.1 1.0
C A:GLY46 4.8 30.9 1.0
CA A:GLY46 4.9 30.7 1.0

Iron binding site 5 out of 8 in 4ytz

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Iron binding site 5 out of 8 in the Rat Xanthine Oxidoreductase, C-Terminal Deletion Protein Variant, Crystal Grown Without Dithiothreitol


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, C-Terminal Deletion Protein Variant, Crystal Grown Without Dithiothreitol within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe1401

b:33.1
occ:1.00
 FE1 B:FES1401 0.0 33.1 1.0
S2 B:FES1401 2.2 30.7 1.0
S1 B:FES1401 2.2 32.3 1.0
SG B:CYS112 2.3 29.8 1.0
SG B:CYS149 2.8 33.6 1.0
FE2 B:FES1401 2.8 32.0 1.0
CB B:CYS112 3.3 25.8 1.0
O B:HOH1548 3.6 25.2 1.0
CB B:CYS149 3.7 27.9 1.0
N B:CYS112 3.7 24.7 1.0
N B:GLY113 3.8 21.9 1.0
CA B:CYS112 3.9 24.9 1.0
C B:CYS112 4.3 23.9 1.0
N B:CYS149 4.3 26.5 1.0
N B:PHE114 4.4 22.2 1.0
SG B:CYS147 4.5 32.2 1.0
CA B:CYS149 4.6 28.1 1.0
SG B:CYS115 4.6 28.8 1.0
N B:ARG148 4.8 26.9 1.0
CA B:GLY113 4.8 22.5 1.0
N B:CYS115 4.9 23.1 1.0
C B:GLN111 4.9 26.1 1.0

Iron binding site 6 out of 8 in 4ytz

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Iron binding site 6 out of 8 in the Rat Xanthine Oxidoreductase, C-Terminal Deletion Protein Variant, Crystal Grown Without Dithiothreitol


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, C-Terminal Deletion Protein Variant, Crystal Grown Without Dithiothreitol within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe1401

b:32.0
occ:1.00
 FE2 B:FES1401 0.0 32.0 1.0
S1 B:FES1401 2.2 32.3 1.0
S2 B:FES1401 2.2 30.7 1.0
SG B:CYS115 2.2 28.8 1.0
SG B:CYS147 2.4 32.2 1.0
FE1 B:FES1401 2.8 33.1 1.0
CB B:CYS147 3.2 27.2 1.0
CB B:CYS115 3.3 24.5 1.0
CA B:CYS147 3.6 26.9 1.0
N B:ARG148 4.2 26.9 1.0
C B:CYS147 4.3 26.6 1.0
N B:CYS115 4.3 23.1 1.0
CA B:CYS115 4.4 23.5 1.0
N B:CYS149 4.5 26.5 1.0
CG2 B:THR150 4.5 25.3 1.0
SG B:CYS112 4.8 29.8 1.0
CB B:CYS149 4.8 27.9 1.0
C B:CYS115 4.9 23.1 1.0
N B:GLY113 4.9 21.9 1.0
N B:CYS147 4.9 26.3 1.0
SG B:CYS149 4.9 33.6 1.0
O B:LEU146 5.0 25.9 1.0

Iron binding site 7 out of 8 in 4ytz

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Iron binding site 7 out of 8 in the Rat Xanthine Oxidoreductase, C-Terminal Deletion Protein Variant, Crystal Grown Without Dithiothreitol


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, C-Terminal Deletion Protein Variant, Crystal Grown Without Dithiothreitol within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe1402

b:24.1
occ:1.00
 FE1 B:FES1402 0.0 24.1 1.0
S1 B:FES1402 2.2 25.6 1.0
S2 B:FES1402 2.2 25.9 1.0
SG B:CYS51 2.3 23.6 1.0
SG B:CYS73 2.4 23.2 1.0
FE2 B:FES1402 2.8 24.0 1.0
CB B:CYS73 3.2 23.9 1.0
CB B:CYS51 3.5 21.0 1.0
ND2 B:ASN71 4.2 26.6 1.0
N B:CYS73 4.2 22.2 1.0
CB B:ASN71 4.3 22.8 1.0
CA B:CYS73 4.3 23.3 1.0
N B:GLY44 4.4 25.1 1.0
N B:CYS51 4.4 24.1 1.0
SG B:CYS43 4.4 24.0 1.0
N B:GLY46 4.4 25.2 1.0
CG B:ASN71 4.4 24.0 1.0
CA B:GLY44 4.5 24.1 1.0
CA B:CYS51 4.6 21.8 1.0
N B:GLU45 4.6 25.3 1.0
SG B:CYS48 4.8 23.1 1.0
CA B:GLY46 4.8 25.3 1.0
C B:GLY44 4.8 24.7 1.0
N B:GLY49 4.8 23.1 1.0
CA B:ASN71 4.9 22.4 1.0

Iron binding site 8 out of 8 in 4ytz

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Iron binding site 8 out of 8 in the Rat Xanthine Oxidoreductase, C-Terminal Deletion Protein Variant, Crystal Grown Without Dithiothreitol


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, C-Terminal Deletion Protein Variant, Crystal Grown Without Dithiothreitol within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe1402

b:24.0
occ:1.00
 FE2 B:FES1402 0.0 24.0 1.0
S2 B:FES1402 2.2 25.9 1.0
S1 B:FES1402 2.2 25.6 1.0
SG B:CYS48 2.3 23.1 1.0
SG B:CYS43 2.3 24.0 1.0
FE1 B:FES1402 2.8 24.1 1.0
CB B:CYS48 3.3 23.7 1.0
CB B:CYS43 3.3 23.8 1.0
N B:CYS43 3.4 22.7 1.0
N B:CYS48 3.6 24.4 1.0
CA B:CYS43 3.8 23.1 1.0
CA B:CYS48 3.8 23.9 1.0
N B:GLY49 3.8 23.1 1.0
N B:GLY44 3.8 25.1 1.0
C B:GLY42 4.1 23.1 1.0
C B:CYS48 4.1 23.7 1.0
N B:GLY42 4.3 23.7 1.0
C B:CYS43 4.3 24.2 1.0
CA B:GLY42 4.3 21.8 1.0
N B:ALA50 4.4 23.4 1.0
N B:GLU45 4.5 25.3 1.0
N B:GLY47 4.6 23.8 1.0
N B:GLY46 4.6 25.2 1.0
SG B:CYS51 4.6 23.6 1.0
SG B:CYS73 4.7 23.2 1.0
CA B:GLY44 4.8 24.1 1.0
CA B:GLY49 4.8 23.4 1.0
C B:GLY47 4.8 25.2 1.0
O B:GLY42 4.9 23.3 1.0
C B:GLY46 4.9 25.5 1.0

Reference:

T.Nishino, K.Okamoto, Y.Kawaguchi, T.Matsumura, B.T.Eger, E.F.Pai, T.Nishino. The C-Terminal Peptide Plays A Role in the Formation of An Intermediate Form During the Transition Between Xanthine Dehydrogenase and Xanthine Oxidase Febs J. 2015.
ISSN: ISSN 1742-464X
PubMed: 25817260
DOI: 10.1111/FEBS.13277
Page generated: Mon Aug 5 16:51:14 2024

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