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Iron in PDB 3bdj: Crystal Structure of Bovine Milk Xanthine Dehydrogenase with A Covalently Bound Oxipurinol Inhibitor

Enzymatic activity of Crystal Structure of Bovine Milk Xanthine Dehydrogenase with A Covalently Bound Oxipurinol Inhibitor

All present enzymatic activity of Crystal Structure of Bovine Milk Xanthine Dehydrogenase with A Covalently Bound Oxipurinol Inhibitor:
1.17.1.4; 1.17.3.2;

Protein crystallography data

The structure of Crystal Structure of Bovine Milk Xanthine Dehydrogenase with A Covalently Bound Oxipurinol Inhibitor, PDB code: 3bdj was solved by B.T.Eger, K.Okamoto, T.Nishino, E.F.Pai, T.Nishino, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.96 / 2.00
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 166.517, 124.074, 148.797, 90.00, 91.01, 90.00
R / Rfree (%) 19.1 / 22.4

Other elements in 3bdj:

The structure of Crystal Structure of Bovine Milk Xanthine Dehydrogenase with A Covalently Bound Oxipurinol Inhibitor also contains other interesting chemical elements:

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

Iron Binding Sites:

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

Iron binding site 1 out of 8 in 3bdj

Go back to Iron Binding Sites List in 3bdj
Iron binding site 1 out of 8 in the Crystal Structure of Bovine Milk Xanthine Dehydrogenase with A Covalently Bound Oxipurinol Inhibitor


Mono view


Stereo pair view

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

b:13.9
occ:1.00
 FE1 A:FES3001 0.0 13.9 1.0
S2 A:FES3001 2.2 11.2 1.0
S1 A:FES3001 2.2 13.9 1.0
SG A:CYS113 2.3 10.4 1.0
SG A:CYS150 2.4 12.6 1.0
FE2 A:FES3001 2.7 11.9 1.0
CB A:CYS113 3.2 11.1 1.0
CB A:CYS150 3.3 15.7 1.0
O A:HOH5728 3.5 8.6 1.0
N A:CYS113 3.6 8.8 1.0
CA A:CYS113 3.8 10.1 1.0
N A:GLY114 3.9 10.7 1.0
N A:CYS150 4.0 13.1 1.0
C A:CYS113 4.2 9.7 1.0
CA A:CYS150 4.3 14.8 1.0
SG A:CYS148 4.4 11.8 1.0
N A:PHE115 4.5 13.2 1.0
SG A:CYS116 4.6 14.4 1.0
C A:GLN112 4.7 10.2 1.0
N A:ARG149 4.8 14.2 1.0
CB A:GLN112 4.9 11.2 1.0
CA A:GLY114 4.9 10.7 1.0

Iron binding site 2 out of 8 in 3bdj

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Iron binding site 2 out of 8 in the Crystal Structure of Bovine Milk Xanthine Dehydrogenase with A Covalently Bound Oxipurinol Inhibitor


Mono view


Stereo pair view

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

b:11.9
occ:1.00
 FE2 A:FES3001 0.0 11.9 1.0
S2 A:FES3001 2.2 11.2 1.0
S1 A:FES3001 2.2 13.9 1.0
SG A:CYS116 2.3 14.4 1.0
SG A:CYS148 2.3 11.8 1.0
FE1 A:FES3001 2.7 13.9 1.0
CB A:CYS148 3.4 14.0 1.0
CB A:CYS116 3.4 13.1 1.0
CA A:CYS148 3.7 13.6 1.0
N A:ARG149 4.1 14.2 1.0
O A:HOH5740 4.3 10.4 1.0
N A:CYS116 4.3 12.0 1.0
N A:CYS150 4.4 13.1 1.0
C A:CYS148 4.4 14.1 1.0
CA A:CYS116 4.4 11.1 1.0
CB A:CYS150 4.5 15.7 1.0
SG A:CYS150 4.6 12.6 1.0
SG A:CYS113 4.6 10.4 1.0
CG2 A:THR151 4.8 11.7 1.0
O A:LEU147 4.9 13.0 1.0
CA A:CYS150 5.0 14.8 1.0
C A:CYS116 5.0 10.9 1.0

Iron binding site 3 out of 8 in 3bdj

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Iron binding site 3 out of 8 in the Crystal Structure of Bovine Milk Xanthine Dehydrogenase with A Covalently Bound Oxipurinol Inhibitor


Mono view


Stereo pair view

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

b:12.1
occ:1.00
 FE1 A:FES3002 0.0 12.1 1.0
S1 A:FES3002 2.2 11.7 1.0
S2 A:FES3002 2.2 11.5 1.0
SG A:CYS51 2.3 12.6 1.0
SG A:CYS73 2.3 13.9 1.0
FE2 A:FES3002 2.8 11.8 1.0
CB A:CYS73 3.2 14.3 1.0
CB A:CYS51 3.4 11.0 1.0
CB A:ASN71 4.2 13.1 1.0
ND2 A:ASN71 4.2 16.8 1.0
N A:GLY46 4.2 13.5 1.0
N A:CYS73 4.2 11.5 1.0
N A:CYS51 4.2 11.0 1.0
CA A:CYS73 4.3 14.2 1.0
CA A:GLY46 4.4 14.8 1.0
SG A:CYS43 4.4 13.5 1.0
N A:GLY44 4.4 14.7 1.0
CA A:CYS51 4.4 11.7 1.0
CG A:ASN71 4.5 13.6 1.0
SG A:CYS48 4.6 9.5 1.0
CA A:GLY44 4.7 13.9 1.0
N A:GLY49 4.9 13.3 1.0
CA A:ASN71 4.9 11.7 1.0
N A:GLU45 4.9 14.0 1.0

Iron binding site 4 out of 8 in 3bdj

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Iron binding site 4 out of 8 in the Crystal Structure of Bovine Milk Xanthine Dehydrogenase with A Covalently Bound Oxipurinol Inhibitor


Mono view


Stereo pair view

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

b:11.8
occ:1.00
 FE2 A:FES3002 0.0 11.8 1.0
SG A:CYS48 2.2 9.5 1.0
S2 A:FES3002 2.3 11.5 1.0
SG A:CYS43 2.3 13.5 1.0
S1 A:FES3002 2.3 11.7 1.0
FE1 A:FES3002 2.8 12.1 1.0
N A:CYS43 3.3 10.9 1.0
CB A:CYS48 3.4 12.8 1.0
CB A:CYS43 3.4 11.4 1.0
N A:CYS48 3.5 15.1 1.0
N A:GLY44 3.8 14.7 1.0
CA A:CYS43 3.8 11.4 1.0
CA A:CYS48 3.9 14.2 1.0
N A:GLY49 3.9 13.3 1.0
C A:GLY42 3.9 12.4 1.0
N A:GLY42 4.1 14.7 1.0
CA A:GLY42 4.2 11.7 1.0
C A:CYS43 4.2 13.3 1.0
C A:CYS48 4.3 14.0 1.0
N A:GLY47 4.4 14.2 1.0
N A:ALA50 4.4 12.5 1.0
N A:GLY46 4.5 13.5 1.0
SG A:CYS73 4.5 13.9 1.0
C A:GLY47 4.7 17.7 1.0
N A:GLU45 4.7 14.0 1.0
SG A:CYS51 4.7 12.6 1.0
O A:GLY42 4.8 12.5 1.0
CA A:GLY46 4.8 14.8 1.0
CA A:GLY44 4.8 13.9 1.0
C A:GLY46 4.8 14.7 1.0
CA A:GLY49 4.9 13.4 1.0
CB A:ALA50 5.0 13.1 1.0

Iron binding site 5 out of 8 in 3bdj

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Iron binding site 5 out of 8 in the Crystal Structure of Bovine Milk Xanthine Dehydrogenase with A Covalently Bound Oxipurinol Inhibitor


Mono view


Stereo pair view

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

b:12.9
occ:1.00
 FE1 B:FES4001 0.0 12.9 1.0
S2 B:FES4001 2.3 12.7 1.0
SG B:CYS113 2.3 10.7 1.0
S1 B:FES4001 2.3 14.1 1.0
SG B:CYS150 2.3 12.4 1.0
FE2 B:FES4001 2.7 11.5 1.0
CB B:CYS113 3.3 10.8 1.0
CB B:CYS150 3.3 11.9 1.0
N B:CYS113 3.5 10.5 1.0
O B:HOH5700 3.6 8.2 1.0
N B:GLY114 3.8 10.1 1.0
CA B:CYS113 3.8 10.3 1.0
N B:CYS150 4.1 12.5 1.0
C B:CYS113 4.2 11.4 1.0
CA B:CYS150 4.3 12.6 1.0
SG B:CYS148 4.4 12.6 1.0
N B:PHE115 4.5 11.4 1.0
SG B:CYS116 4.6 11.6 1.0
C B:GLN112 4.6 11.4 1.0
CB B:GLN112 4.7 11.6 1.0
CA B:GLY114 4.8 10.3 1.0
N B:ARG149 4.8 11.8 1.0
N B:CYS116 4.9 12.1 1.0
N B:GLN112 5.0 11.2 1.0

Iron binding site 6 out of 8 in 3bdj

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Iron binding site 6 out of 8 in the Crystal Structure of Bovine Milk Xanthine Dehydrogenase with A Covalently Bound Oxipurinol Inhibitor


Mono view


Stereo pair view

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

b:11.5
occ:1.00
 FE2 B:FES4001 0.0 11.5 1.0
SG B:CYS116 2.2 11.6 1.0
S1 B:FES4001 2.2 14.1 1.0
S2 B:FES4001 2.3 12.7 1.0
SG B:CYS148 2.3 12.6 1.0
FE1 B:FES4001 2.7 12.9 1.0
CB B:CYS148 3.3 12.2 1.0
CB B:CYS116 3.3 12.6 1.0
CA B:CYS148 3.7 13.7 1.0
N B:ARG149 4.1 11.8 1.0
N B:CYS116 4.3 12.1 1.0
O B:HOH5703 4.3 10.0 1.0
N B:CYS150 4.3 12.5 1.0
C B:CYS148 4.4 13.1 1.0
CA B:CYS116 4.4 10.5 1.0
CB B:CYS150 4.4 11.9 1.0
SG B:CYS150 4.5 12.4 1.0
SG B:CYS113 4.6 10.7 1.0
CG2 B:THR151 4.8 8.8 1.0
O B:LEU147 4.9 15.6 1.0
CA B:CYS150 4.9 12.6 1.0
C B:CYS116 5.0 12.0 1.0
N B:GLY114 5.0 10.1 1.0
N B:THR151 5.0 11.6 1.0
N B:CYS148 5.0 14.1 1.0
N B:THR117 5.0 12.0 1.0

Iron binding site 7 out of 8 in 3bdj

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Iron binding site 7 out of 8 in the Crystal Structure of Bovine Milk Xanthine Dehydrogenase with A Covalently Bound Oxipurinol Inhibitor


Mono view


Stereo pair view

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

b:12.2
occ:1.00
 FE1 B:FES4002 0.0 12.2 1.0
S1 B:FES4002 2.1 11.9 1.0
S2 B:FES4002 2.2 12.6 1.0
SG B:CYS51 2.3 9.8 1.0
SG B:CYS73 2.3 12.5 1.0
FE2 B:FES4002 2.8 12.3 1.0
CB B:CYS73 3.2 12.7 1.0
CB B:CYS51 3.4 8.3 1.0
N B:GLY46 4.2 13.5 1.0
CB B:ASN71 4.2 10.8 1.0
N B:CYS73 4.2 9.2 1.0
N B:CYS51 4.3 8.1 1.0
CA B:CYS73 4.3 12.2 1.0
CA B:GLY46 4.4 12.7 1.0
SG B:CYS43 4.4 13.5 1.0
ND2 B:ASN71 4.4 11.8 1.0
N B:GLY44 4.5 11.0 1.0
CA B:CYS51 4.5 10.0 1.0
SG B:CYS48 4.6 11.7 1.0
CG B:ASN71 4.6 13.8 1.0
CA B:GLY44 4.8 11.9 1.0
N B:GLY49 4.8 12.8 1.0
CA B:ASN71 4.9 10.7 1.0

Iron binding site 8 out of 8 in 3bdj

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Iron binding site 8 out of 8 in the Crystal Structure of Bovine Milk Xanthine Dehydrogenase with A Covalently Bound Oxipurinol Inhibitor


Mono view


Stereo pair view

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

b:12.3
occ:1.00
 FE2 B:FES4002 0.0 12.3 1.0
S2 B:FES4002 2.2 12.6 1.0
SG B:CYS48 2.3 11.7 1.0
S1 B:FES4002 2.3 11.9 1.0
SG B:CYS43 2.3 13.5 1.0
FE1 B:FES4002 2.8 12.2 1.0
N B:CYS43 3.3 10.9 1.0
CB B:CYS48 3.4 11.6 1.0
CB B:CYS43 3.5 10.9 1.0
N B:CYS48 3.5 14.3 1.0
N B:GLY44 3.8 11.0 1.0
N B:GLY49 3.8 12.8 1.0
CA B:CYS43 3.8 11.7 1.0
CA B:CYS48 3.9 12.7 1.0
C B:GLY42 4.1 12.3 1.0
N B:GLY42 4.2 11.3 1.0
C B:CYS48 4.2 12.8 1.0
C B:CYS43 4.3 12.0 1.0
N B:GLY47 4.3 13.3 1.0
CA B:GLY42 4.3 12.6 1.0
N B:GLY46 4.4 13.5 1.0
N B:ALA50 4.5 9.8 1.0
SG B:CYS73 4.5 12.5 1.0
SG B:CYS51 4.6 9.8 1.0
C B:GLY47 4.7 16.7 1.0
N B:GLU45 4.7 12.3 1.0
CA B:GLY46 4.7 12.7 1.0
C B:GLY46 4.7 14.0 1.0
CA B:GLY49 4.8 10.7 1.0
CA B:GLY44 4.8 11.9 1.0
O B:GLY42 5.0 11.9 1.0

Reference:

K.Okamoto, B.T.Eger, T.Nishino, E.F.Pai, T.Nishino. Mechanism of Inhibition of Xanthine Oxidoreductase By Allopurinol: Crystal Structure of Reduced Bovine Milk Xanthine Oxidoreductase Bound with Oxipurinol. Nucleosides Nucleotides V. 27 888 2008NUCLEIC Acids.
ISSN: ISSN 1525-7770
PubMed: 18600558
DOI: 10.1080/15257770802146577
Page generated: Sun Aug 4 07:51:48 2024

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