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Iron in PDB 1n5x: Xanthine Dehydrogenase From Bovine Milk with Inhibitor Tei-6720 Bound

Enzymatic activity of Xanthine Dehydrogenase From Bovine Milk with Inhibitor Tei-6720 Bound

All present enzymatic activity of Xanthine Dehydrogenase From Bovine Milk with Inhibitor Tei-6720 Bound:
1.1.1.204;

Protein crystallography data

The structure of Xanthine Dehydrogenase From Bovine Milk with Inhibitor Tei-6720 Bound, PDB code: 1n5x was solved by K.Okamoto, B.T.Eger, T.Nishino, S.Kondo, E.F.Pai, T.Nishino, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 2.80
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 168.269, 124.659, 147.325, 90.00, 90.99, 90.00
R / Rfree (%) 24.4 / 27.5

Other elements in 1n5x:

The structure of Xanthine Dehydrogenase From Bovine Milk with Inhibitor Tei-6720 Bound also contains other interesting chemical elements:

Molybdenum (Mo) 2 atoms

Iron Binding Sites:

The binding sites of Iron atom in the Xanthine Dehydrogenase From Bovine Milk with Inhibitor Tei-6720 Bound (pdb code 1n5x). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 8 binding sites of Iron where determined in the Xanthine Dehydrogenase From Bovine Milk with Inhibitor Tei-6720 Bound, PDB code: 1n5x:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iron binding site 1 out of 8 in 1n5x

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Iron binding site 1 out of 8 in the Xanthine Dehydrogenase From Bovine Milk with Inhibitor Tei-6720 Bound


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Xanthine Dehydrogenase From Bovine Milk with Inhibitor Tei-6720 Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe3001

b:6.3
occ:1.00
 FE1 A:FES3001 0.0 6.3 1.0
S2 A:FES3001 2.2 6.3 1.0
S1 A:FES3001 2.2 6.3 1.0
SG A:CYS150 2.4 20.9 1.0
SG A:CYS113 2.4 20.9 1.0
FE2 A:FES3001 2.7 6.3 1.0
CB A:CYS150 3.3 20.9 1.0
CB A:CYS113 3.4 20.9 1.0
N A:CYS113 3.7 20.9 1.0
N A:GLY114 3.9 20.9 1.0
CA A:CYS113 4.0 20.9 1.0
N A:CYS150 4.0 20.9 1.0
C A:CYS113 4.3 20.9 1.0
CA A:CYS150 4.3 20.9 1.0
N A:PHE115 4.4 20.9 1.0
SG A:CYS148 4.5 20.9 1.0
N A:ARG149 4.7 20.9 1.0
SG A:CYS116 4.7 20.9 1.0
CA A:GLY114 4.8 20.9 1.0
C A:GLN112 4.9 20.9 1.0
N A:CYS116 4.9 20.9 1.0
C A:ARG149 4.9 20.9 1.0
CB A:GLN112 4.9 20.9 1.0

Iron binding site 2 out of 8 in 1n5x

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Iron binding site 2 out of 8 in the Xanthine Dehydrogenase From Bovine Milk with Inhibitor Tei-6720 Bound


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Xanthine Dehydrogenase From Bovine Milk with Inhibitor Tei-6720 Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe3001

b:6.3
occ:1.00
 FE2 A:FES3001 0.0 6.3 1.0
S2 A:FES3001 2.1 6.3 1.0
S1 A:FES3001 2.2 6.3 1.0
SG A:CYS116 2.3 20.9 1.0
SG A:CYS148 2.4 20.9 1.0
FE1 A:FES3001 2.7 6.3 1.0
CB A:CYS116 3.3 20.9 1.0
CB A:CYS148 3.4 20.9 1.0
CA A:CYS148 3.8 20.9 1.0
N A:ARG149 4.1 20.9 1.0
N A:CYS116 4.2 20.9 1.0
N A:CYS150 4.3 20.9 1.0
CB A:CYS150 4.3 20.9 1.0
CA A:CYS116 4.3 20.9 1.0
C A:CYS148 4.4 20.9 1.0
SG A:CYS150 4.4 20.9 1.0
SG A:CYS113 4.7 20.9 1.0
CG2 A:THR151 4.9 20.9 1.0
CA A:CYS150 4.9 20.9 1.0
N A:THR117 4.9 20.9 1.0
C A:CYS116 4.9 20.9 1.0
N A:THR151 4.9 20.9 1.0
N A:GLY114 4.9 20.9 1.0

Iron binding site 3 out of 8 in 1n5x

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Iron binding site 3 out of 8 in the Xanthine Dehydrogenase From Bovine Milk with Inhibitor Tei-6720 Bound


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Xanthine Dehydrogenase From Bovine Milk with Inhibitor Tei-6720 Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe3002

b:8.9
occ:1.00
 FE1 A:FES3002 0.0 8.9 1.0
S1 A:FES3002 2.2 8.9 1.0
S2 A:FES3002 2.2 8.9 1.0
SG A:CYS73 2.4 20.9 1.0
SG A:CYS51 2.4 20.9 1.0
FE2 A:FES3002 2.7 8.9 1.0
CB A:CYS73 3.3 20.9 1.0
CB A:CYS51 3.5 20.9 1.0
N A:GLY46 4.2 20.9 1.0
CB A:ASN71 4.2 20.9 1.0
SG A:CYS43 4.3 20.9 1.0
CA A:GLY46 4.3 20.9 1.0
N A:GLY44 4.3 20.9 1.0
N A:CYS73 4.3 20.9 1.0
N A:CYS51 4.3 20.9 1.0
CA A:CYS73 4.4 20.9 1.0
CA A:CYS51 4.5 20.9 1.0
CA A:GLY44 4.5 20.9 1.0
OD1 A:ASN71 4.5 20.9 1.0
SG A:CYS48 4.8 20.9 1.0
N A:GLY49 4.8 20.9 1.0
CG A:ASN71 4.8 20.9 1.0
N A:ALA50 4.9 20.9 1.0
C A:GLY44 4.9 20.9 1.0
N A:GLU45 4.9 20.9 1.0
CA A:ASN71 5.0 20.9 1.0
C A:GLY46 5.0 20.9 1.0

Iron binding site 4 out of 8 in 1n5x

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Iron binding site 4 out of 8 in the Xanthine Dehydrogenase From Bovine Milk with Inhibitor Tei-6720 Bound


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Xanthine Dehydrogenase From Bovine Milk with Inhibitor Tei-6720 Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe3002

b:8.9
occ:1.00
 FE2 A:FES3002 0.0 8.9 1.0
S2 A:FES3002 2.2 8.9 1.0
S1 A:FES3002 2.2 8.9 1.0
SG A:CYS48 2.3 20.9 1.0
SG A:CYS43 2.4 20.9 1.0
FE1 A:FES3002 2.7 8.9 1.0
CB A:CYS48 3.5 20.9 1.0
N A:CYS48 3.5 20.9 1.0
N A:CYS43 3.6 20.9 1.0
CB A:CYS43 3.6 20.9 1.0
N A:GLY49 3.6 20.9 1.0
CA A:CYS48 3.8 20.9 1.0
N A:GLY44 3.9 20.9 1.0
CA A:CYS43 4.0 20.9 1.0
C A:GLY42 4.1 20.9 1.0
C A:CYS48 4.1 20.9 1.0
N A:ALA50 4.2 20.9 1.0
N A:GLY42 4.3 20.9 1.0
N A:GLY47 4.3 20.9 1.0
CA A:GLY42 4.4 20.9 1.0
N A:GLY46 4.4 20.9 1.0
C A:CYS43 4.4 20.9 1.0
CA A:GLY49 4.6 20.9 1.0
C A:GLY47 4.6 20.9 1.0
SG A:CYS73 4.7 20.9 1.0
SG A:CYS51 4.7 20.9 1.0
CA A:GLY46 4.7 20.9 1.0
C A:GLY46 4.7 20.9 1.0
N A:GLU45 4.8 20.9 1.0
CB A:ALA50 4.8 20.9 1.0
CA A:GLY44 4.8 20.9 1.0
C A:GLY49 4.9 20.9 1.0
O A:GLY42 5.0 20.9 1.0
N A:CYS51 5.0 20.9 1.0

Iron binding site 5 out of 8 in 1n5x

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Iron binding site 5 out of 8 in the Xanthine Dehydrogenase From Bovine Milk with Inhibitor Tei-6720 Bound


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Xanthine Dehydrogenase From Bovine Milk with Inhibitor Tei-6720 Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe4001

b:6.3
occ:1.00
 FE1 B:FES4001 0.0 6.3 1.0
S2 B:FES4001 2.2 6.3 1.0
S1 B:FES4001 2.2 6.3 1.0
SG B:CYS150 2.4 20.9 1.0
SG B:CYS113 2.4 20.9 1.0
FE2 B:FES4001 2.7 6.3 1.0
CB B:CYS150 3.3 20.9 1.0
CB B:CYS113 3.4 20.9 1.0
N B:CYS113 3.7 20.9 1.0
N B:GLY114 3.9 20.9 1.0
CA B:CYS113 4.0 20.9 1.0
N B:CYS150 4.0 20.9 1.0
C B:CYS113 4.3 20.9 1.0
CA B:CYS150 4.3 20.9 1.0
N B:PHE115 4.4 20.9 1.0
SG B:CYS148 4.5 20.9 1.0
N B:ARG149 4.7 20.9 1.0
SG B:CYS116 4.7 20.9 1.0
CA B:GLY114 4.8 20.9 1.0
C B:GLN112 4.9 20.9 1.0
N B:CYS116 4.9 20.9 1.0
C B:ARG149 4.9 20.9 1.0
CB B:GLN112 4.9 20.9 1.0

Iron binding site 6 out of 8 in 1n5x

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Iron binding site 6 out of 8 in the Xanthine Dehydrogenase From Bovine Milk with Inhibitor Tei-6720 Bound


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Xanthine Dehydrogenase From Bovine Milk with Inhibitor Tei-6720 Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe4001

b:6.3
occ:1.00
 FE2 B:FES4001 0.0 6.3 1.0
S2 B:FES4001 2.1 6.3 1.0
S1 B:FES4001 2.2 6.3 1.0
SG B:CYS116 2.3 20.9 1.0
SG B:CYS148 2.4 20.9 1.0
FE1 B:FES4001 2.7 6.3 1.0
CB B:CYS116 3.3 20.9 1.0
CB B:CYS148 3.4 20.9 1.0
CA B:CYS148 3.8 20.9 1.0
N B:ARG149 4.1 20.9 1.0
N B:CYS116 4.2 20.9 1.0
N B:CYS150 4.3 20.9 1.0
CB B:CYS150 4.3 20.9 1.0
CA B:CYS116 4.3 20.9 1.0
C B:CYS148 4.4 20.9 1.0
SG B:CYS150 4.4 20.9 1.0
SG B:CYS113 4.7 20.9 1.0
CG2 B:THR151 4.9 20.9 1.0
CA B:CYS150 4.9 20.9 1.0
N B:THR117 4.9 20.9 1.0
C B:CYS116 4.9 20.9 1.0
N B:THR151 4.9 20.9 1.0
N B:GLY114 4.9 20.9 1.0
O B:LEU147 5.0 20.9 1.0

Iron binding site 7 out of 8 in 1n5x

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Iron binding site 7 out of 8 in the Xanthine Dehydrogenase From Bovine Milk with Inhibitor Tei-6720 Bound


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Xanthine Dehydrogenase From Bovine Milk with Inhibitor Tei-6720 Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe4002

b:8.9
occ:1.00
 FE1 B:FES4002 0.0 8.9 1.0
S1 B:FES4002 2.2 8.9 1.0
S2 B:FES4002 2.2 8.9 1.0
SG B:CYS73 2.4 20.9 1.0
SG B:CYS51 2.4 20.9 1.0
FE2 B:FES4002 2.7 8.9 1.0
CB B:CYS73 3.3 20.9 1.0
CB B:CYS51 3.5 20.9 1.0
N B:GLY46 4.2 20.9 1.0
CB B:ASN71 4.2 20.9 1.0
SG B:CYS43 4.3 20.9 1.0
CA B:GLY46 4.3 20.9 1.0
N B:GLY44 4.3 20.9 1.0
N B:CYS73 4.3 20.9 1.0
N B:CYS51 4.3 20.9 1.0
CA B:CYS73 4.4 20.9 1.0
CA B:CYS51 4.5 20.9 1.0
CA B:GLY44 4.5 20.9 1.0
OD1 B:ASN71 4.5 20.9 1.0
SG B:CYS48 4.8 20.9 1.0
N B:GLY49 4.8 20.9 1.0
CG B:ASN71 4.8 20.9 1.0
N B:ALA50 4.9 20.9 1.0
C B:GLY44 4.9 20.9 1.0
N B:GLU45 4.9 20.9 1.0
CA B:ASN71 5.0 20.9 1.0
C B:GLY46 5.0 20.9 1.0

Iron binding site 8 out of 8 in 1n5x

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Iron binding site 8 out of 8 in the Xanthine Dehydrogenase From Bovine Milk with Inhibitor Tei-6720 Bound


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Xanthine Dehydrogenase From Bovine Milk with Inhibitor Tei-6720 Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe4002

b:8.9
occ:1.00
 FE2 B:FES4002 0.0 8.9 1.0
S2 B:FES4002 2.2 8.9 1.0
S1 B:FES4002 2.2 8.9 1.0
SG B:CYS48 2.3 20.9 1.0
SG B:CYS43 2.4 20.9 1.0
FE1 B:FES4002 2.7 8.9 1.0
CB B:CYS48 3.5 20.9 1.0
N B:CYS48 3.5 20.9 1.0
N B:CYS43 3.6 20.9 1.0
CB B:CYS43 3.6 20.9 1.0
N B:GLY49 3.6 20.9 1.0
CA B:CYS48 3.8 20.9 1.0
N B:GLY44 3.9 20.9 1.0
CA B:CYS43 4.0 20.9 1.0
C B:GLY42 4.1 20.9 1.0
C B:CYS48 4.1 20.9 1.0
N B:ALA50 4.2 20.9 1.0
N B:GLY42 4.3 20.9 1.0
N B:GLY47 4.3 20.9 1.0
CA B:GLY42 4.4 20.9 1.0
N B:GLY46 4.4 20.9 1.0
C B:CYS43 4.4 20.9 1.0
CA B:GLY49 4.6 20.9 1.0
C B:GLY47 4.6 20.9 1.0
SG B:CYS73 4.7 20.9 1.0
SG B:CYS51 4.7 20.9 1.0
CA B:GLY46 4.7 20.9 1.0
C B:GLY46 4.7 20.9 1.0
N B:GLU45 4.8 20.9 1.0
CB B:ALA50 4.8 20.9 1.0
CA B:GLY44 4.8 20.9 1.0
C B:GLY49 4.9 20.9 1.0
O B:GLY42 5.0 20.9 1.0
N B:CYS51 5.0 20.9 1.0

Reference:

K.Okamoto, B.T.Eger, T.Nishino, S.Kondo, E.F.Pai, T.Nishino. An Extremely Potent Inhibitor of Xanthine Oxidoreductase: Crystal Structure of the Enzyme-Inhibitor Complex and Mechanism of Inhibition J.Biol.Chem. V. 278 1848 2003.
ISSN: ISSN 0021-9258
PubMed: 12421831
DOI: 10.1074/JBC.M208307200
Page generated: Wed Jul 16 18:28:05 2025

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