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Iron in PDB 3am9: Complex of Bovine Xanthine Dehydrogenase and Trihydroxy Fyx-051

Enzymatic activity of Complex of Bovine Xanthine Dehydrogenase and Trihydroxy Fyx-051

All present enzymatic activity of Complex of Bovine Xanthine Dehydrogenase and Trihydroxy Fyx-051:
1.17.1.4; 1.17.3.2;

Protein crystallography data

The structure of Complex of Bovine Xanthine Dehydrogenase and Trihydroxy Fyx-051, PDB code: 3am9 was solved by K.Matsumoto, K.Okamoto, N.Ashizawa, T.Matsumura, T.Kusano, T.Nishino, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 33.44 / 2.17
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 168.916, 124.722, 146.195, 90.00, 91.04, 90.00
R / Rfree (%) 17.4 / 24.3

Other elements in 3am9:

The structure of Complex of Bovine Xanthine Dehydrogenase and Trihydroxy Fyx-051 also contains other interesting chemical elements:

Molybdenum (Mo) 2 atoms
Calcium (Ca) 4 atoms

Iron Binding Sites:

The binding sites of Iron atom in the Complex of Bovine Xanthine Dehydrogenase and Trihydroxy Fyx-051 (pdb code 3am9). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 8 binding sites of Iron where determined in the Complex of Bovine Xanthine Dehydrogenase and Trihydroxy Fyx-051, PDB code: 3am9:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iron binding site 1 out of 8 in 3am9

Go back to Iron Binding Sites List in 3am9
Iron binding site 1 out of 8 in the Complex of Bovine Xanthine Dehydrogenase and Trihydroxy Fyx-051


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Complex of Bovine Xanthine Dehydrogenase and Trihydroxy Fyx-051 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe3001

b:17.9
occ:1.00
 FE1 A:FES3001 0.0 17.9 1.0
SG A:CYS113 2.2 17.2 1.0
S2 A:FES3001 2.2 19.2 1.0
S1 A:FES3001 2.2 18.1 1.0
SG A:CYS150 2.3 17.3 1.0
FE2 A:FES3001 2.7 16.8 1.0
CB A:CYS150 3.1 15.7 1.0
CB A:CYS113 3.4 15.0 1.0
N A:CYS113 3.6 15.5 1.0
O A:HOH1485 3.6 14.8 1.0
N A:GLY114 3.9 13.8 1.0
CA A:CYS113 3.9 13.8 1.0
N A:CYS150 4.1 17.2 1.0
CA A:CYS150 4.2 15.8 1.0
SG A:CYS148 4.3 16.2 1.0
C A:CYS113 4.3 13.6 1.0
N A:PHE115 4.4 15.9 1.0
SG A:CYS116 4.6 16.0 1.0
C A:GLN112 4.7 15.4 1.0
CB A:GLN112 4.7 15.3 1.0
N A:ARG149 4.8 14.2 1.0
CA A:GLY114 4.8 13.4 1.0
N A:CYS116 4.9 15.6 1.0
N A:GLN112 5.0 15.3 1.0

Iron binding site 2 out of 8 in 3am9

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Iron binding site 2 out of 8 in the Complex of Bovine Xanthine Dehydrogenase and Trihydroxy Fyx-051


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Complex of Bovine Xanthine Dehydrogenase and Trihydroxy Fyx-051 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe3001

b:16.8
occ:1.00
 FE2 A:FES3001 0.0 16.8 1.0
S1 A:FES3001 2.2 18.1 1.0
S2 A:FES3001 2.2 19.2 1.0
SG A:CYS116 2.3 16.0 1.0
SG A:CYS148 2.3 16.2 1.0
FE1 A:FES3001 2.7 17.9 1.0
CB A:CYS148 3.3 14.9 1.0
CB A:CYS116 3.3 15.2 1.0
CA A:CYS148 3.7 15.1 1.0
N A:ARG149 4.1 14.2 1.0
N A:CYS116 4.2 15.6 1.0
N A:CYS150 4.2 17.2 1.0
O A:HOH1490 4.3 10.7 1.0
CB A:CYS150 4.3 15.7 1.0
C A:CYS148 4.3 14.9 1.0
CA A:CYS116 4.3 15.5 1.0
SG A:CYS150 4.5 17.3 1.0
SG A:CYS113 4.6 17.2 1.0
CG2 A:THR151 4.7 18.4 1.0
O A:LEU147 4.8 16.5 1.0
CA A:CYS150 4.9 15.8 1.0
N A:CYS148 5.0 16.5 1.0
C A:CYS116 5.0 16.7 1.0

Iron binding site 3 out of 8 in 3am9

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Iron binding site 3 out of 8 in the Complex of Bovine Xanthine Dehydrogenase and Trihydroxy Fyx-051


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Complex of Bovine Xanthine Dehydrogenase and Trihydroxy Fyx-051 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe3002

b:17.7
occ:1.00
 FE1 A:FES3002 0.0 17.7 1.0
S1 A:FES3002 2.1 18.6 1.0
S2 A:FES3002 2.1 17.1 1.0
SG A:CYS73 2.3 18.3 1.0
SG A:CYS51 2.3 18.0 1.0
FE2 A:FES3002 2.7 16.3 1.0
CB A:CYS73 3.2 13.2 1.0
CB A:CYS51 3.5 15.7 1.0
OD1 A:ASN71 4.2 21.1 1.0
N A:GLY46 4.2 18.5 1.0
CB A:ASN71 4.3 16.6 1.0
SG A:CYS43 4.3 18.9 1.0
N A:CYS73 4.3 15.6 1.0
N A:GLY44 4.3 19.6 1.0
N A:CYS51 4.4 14.8 1.0
CA A:CYS73 4.4 16.8 1.0
CA A:GLY46 4.4 19.6 1.0
CA A:CYS51 4.5 16.0 1.0
CG A:ASN71 4.6 18.9 1.0
CA A:GLY44 4.7 20.4 1.0
SG A:CYS48 4.7 19.2 1.0
N A:GLY49 4.8 16.2 1.0
N A:GLU45 4.9 19.8 1.0

Iron binding site 4 out of 8 in 3am9

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Iron binding site 4 out of 8 in the Complex of Bovine Xanthine Dehydrogenase and Trihydroxy Fyx-051


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Complex of Bovine Xanthine Dehydrogenase and Trihydroxy Fyx-051 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe3002

b:16.3
occ:1.00
 FE2 A:FES3002 0.0 16.3 1.0
S1 A:FES3002 2.2 18.6 1.0
S2 A:FES3002 2.2 17.1 1.0
SG A:CYS43 2.3 18.9 1.0
SG A:CYS48 2.3 19.2 1.0
FE1 A:FES3002 2.7 17.7 1.0
N A:CYS43 3.4 17.6 1.0
CB A:CYS48 3.5 16.1 1.0
N A:CYS48 3.5 19.0 1.0
CB A:CYS43 3.5 17.0 1.0
N A:GLY44 3.8 19.6 1.0
N A:GLY49 3.8 16.2 1.0
CA A:CYS43 3.9 18.2 1.0
CA A:CYS48 3.9 17.6 1.0
C A:GLY42 4.1 16.8 1.0
C A:CYS48 4.3 17.3 1.0
C A:CYS43 4.3 19.5 1.0
N A:GLY42 4.3 14.5 1.0
N A:GLY47 4.4 20.0 1.0
CA A:GLY42 4.4 14.9 1.0
N A:ALA50 4.4 15.4 1.0
N A:GLY46 4.4 18.5 1.0
SG A:CYS73 4.5 18.3 1.0
SG A:CYS51 4.6 18.0 1.0
C A:GLY47 4.7 20.5 1.0
N A:GLU45 4.7 19.8 1.0
C A:GLY46 4.8 19.7 1.0
CA A:GLY49 4.8 15.7 1.0
CA A:GLY46 4.9 19.6 1.0
CA A:GLY44 4.9 20.4 1.0
O A:GLY42 4.9 17.8 1.0

Iron binding site 5 out of 8 in 3am9

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Iron binding site 5 out of 8 in the Complex of Bovine Xanthine Dehydrogenase and Trihydroxy Fyx-051


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Complex of Bovine Xanthine Dehydrogenase and Trihydroxy Fyx-051 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe4001

b:17.8
occ:1.00
 FE1 B:FES4001 0.0 17.8 1.0
S2 B:FES4001 2.2 18.9 1.0
S1 B:FES4001 2.2 18.1 1.0
SG B:CYS113 2.3 17.0 1.0
SG B:CYS150 2.4 16.7 1.0
FE2 B:FES4001 2.7 15.5 1.0
CB B:CYS113 3.3 15.7 1.0
CB B:CYS150 3.4 16.1 1.0
N B:CYS113 3.4 14.4 1.0
O B:HOH1436 3.6 13.3 1.0
CA B:CYS113 3.8 13.7 1.0
N B:GLY114 3.9 14.3 1.0
N B:CYS150 4.1 14.9 1.0
C B:CYS113 4.2 13.3 1.0
CA B:CYS150 4.3 15.8 1.0
N B:PHE115 4.4 16.5 1.0
SG B:CYS148 4.4 17.6 1.0
C B:GLN112 4.6 15.0 1.0
SG B:CYS116 4.6 16.1 1.0
CB B:GLN112 4.8 14.4 1.0
N B:ARG149 4.8 16.3 1.0
CA B:GLY114 4.9 14.1 1.0
N B:CYS116 4.9 16.3 1.0

Iron binding site 6 out of 8 in 3am9

Go back to Iron Binding Sites List in 3am9
Iron binding site 6 out of 8 in the Complex of Bovine Xanthine Dehydrogenase and Trihydroxy Fyx-051


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Complex of Bovine Xanthine Dehydrogenase and Trihydroxy Fyx-051 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe4001

b:15.5
occ:1.00
 FE2 B:FES4001 0.0 15.5 1.0
S1 B:FES4001 2.2 18.1 1.0
S2 B:FES4001 2.2 18.9 1.0
SG B:CYS116 2.3 16.1 1.0
SG B:CYS148 2.4 17.6 1.0
FE1 B:FES4001 2.7 17.8 1.0
CB B:CYS116 3.3 14.9 1.0
CB B:CYS148 3.3 15.8 1.0
CA B:CYS148 3.7 15.3 1.0
N B:ARG149 4.2 16.3 1.0
N B:CYS116 4.2 16.3 1.0
O B:HOH1429 4.3 13.0 1.0
N B:CYS150 4.3 14.9 1.0
C B:CYS148 4.3 16.9 1.0
CA B:CYS116 4.3 15.8 1.0
SG B:CYS150 4.5 16.7 1.0
CB B:CYS150 4.5 16.1 1.0
SG B:CYS113 4.6 17.0 1.0
CG2 B:THR151 4.8 16.5 1.0
O B:LEU147 5.0 17.4 1.0
C B:CYS116 5.0 15.6 1.0
N B:CYS148 5.0 17.4 1.0

Iron binding site 7 out of 8 in 3am9

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Iron binding site 7 out of 8 in the Complex of Bovine Xanthine Dehydrogenase and Trihydroxy Fyx-051


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Complex of Bovine Xanthine Dehydrogenase and Trihydroxy Fyx-051 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe4002

b:15.9
occ:1.00
 FE1 B:FES4002 0.0 15.9 1.0
S1 B:FES4002 2.1 16.1 1.0
S2 B:FES4002 2.2 14.8 1.0
SG B:CYS51 2.3 17.3 1.0
SG B:CYS73 2.3 20.7 1.0
FE2 B:FES4002 2.8 17.5 1.0
CB B:CYS73 3.2 15.9 1.0
CB B:CYS51 3.5 15.2 1.0
N B:CYS73 4.2 17.9 1.0
N B:CYS51 4.2 15.5 1.0
CA B:CYS73 4.3 20.6 1.0
CB B:ASN71 4.3 20.4 1.0
N B:GLY46 4.3 21.2 1.0
OD1 B:ASN71 4.3 24.6 1.0
SG B:CYS43 4.4 17.5 1.0
N B:GLY44 4.4 18.6 1.0
CA B:CYS51 4.5 16.5 1.0
CA B:GLY46 4.5 19.8 1.0
SG B:CYS48 4.6 18.2 1.0
CG B:ASN71 4.6 20.5 1.0
CA B:GLY44 4.7 19.8 1.0
N B:GLY49 4.8 13.9 1.0
N B:GLU45 4.8 20.4 1.0
CA B:ASN71 4.9 18.8 1.0
N B:ALA50 4.9 13.8 1.0

Iron binding site 8 out of 8 in 3am9

Go back to Iron Binding Sites List in 3am9
Iron binding site 8 out of 8 in the Complex of Bovine Xanthine Dehydrogenase and Trihydroxy Fyx-051


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Complex of Bovine Xanthine Dehydrogenase and Trihydroxy Fyx-051 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe4002

b:17.5
occ:1.00
 FE2 B:FES4002 0.0 17.5 1.0
S2 B:FES4002 2.2 14.8 1.0
SG B:CYS48 2.2 18.2 1.0
S1 B:FES4002 2.2 16.1 1.0
SG B:CYS43 2.3 17.5 1.0
FE1 B:FES4002 2.8 15.9 1.0
N B:CYS43 3.3 14.7 1.0
CB B:CYS43 3.5 16.4 1.0
CB B:CYS48 3.5 16.1 1.0
N B:CYS48 3.5 18.6 1.0
N B:GLY44 3.8 18.6 1.0
N B:GLY49 3.8 13.9 1.0
CA B:CYS43 3.8 16.6 1.0
CA B:CYS48 3.9 16.9 1.0
C B:GLY42 4.1 15.9 1.0
C B:CYS48 4.2 15.6 1.0
C B:CYS43 4.2 18.0 1.0
N B:GLY42 4.3 15.2 1.0
CA B:GLY42 4.4 15.6 1.0
N B:ALA50 4.4 13.8 1.0
N B:GLY47 4.4 20.0 1.0
SG B:CYS73 4.5 20.7 1.0
N B:GLY46 4.5 21.2 1.0
N B:GLU45 4.6 20.4 1.0
SG B:CYS51 4.6 17.3 1.0
C B:GLY47 4.7 19.7 1.0
CA B:GLY44 4.8 19.8 1.0
C B:GLY46 4.8 20.3 1.0
CA B:GLY49 4.8 14.2 1.0
CA B:GLY46 4.9 19.8 1.0

Reference:

K.Matsumoto, K.Okamoto, N.Ashizawa, T.Nishino. Fyx-051: A Novel and Potent Hybrid-Type Inhibitor of Xanthine Oxidoreductase J.Pharmacol.Exp.Ther. V. 336 95 2011.
ISSN: ISSN 0022-3565
PubMed: 20952484
DOI: 10.1124/JPET.110.174540
Page generated: Sun Aug 4 07:16:45 2024

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