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Iron in PDB 1fo4: Crystal Structure of Xanthine Dehydrogenase Isolated From Bovine Milk

Enzymatic activity of Crystal Structure of Xanthine Dehydrogenase Isolated From Bovine Milk

All present enzymatic activity of Crystal Structure of Xanthine Dehydrogenase Isolated From Bovine Milk:
1.1.1.204;

Protein crystallography data

The structure of Crystal Structure of Xanthine Dehydrogenase Isolated From Bovine Milk, PDB code: 1fo4 was solved by C.Enroth, B.T.Eger, K.Okamoto, T.Nishino, T.Nishino, E.F.Pai, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 25.00 / 2.10
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 169.451, 124.493, 148.327, 90.00, 90.94, 90.00
R / Rfree (%) 19.8 / 23.8

Other elements in 1fo4:

The structure of Crystal Structure of Xanthine Dehydrogenase Isolated From Bovine Milk 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 Xanthine Dehydrogenase Isolated From Bovine Milk (pdb code 1fo4). 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 Xanthine Dehydrogenase Isolated From Bovine Milk, PDB code: 1fo4:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iron binding site 1 out of 8 in 1fo4

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Iron binding site 1 out of 8 in the Crystal Structure of Xanthine Dehydrogenase Isolated From Bovine Milk


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 Xanthine Dehydrogenase Isolated From Bovine Milk within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe3001

b:22.4
occ:1.00
 FE1 A:FES3001 0.0 22.4 1.0
S2 A:FES3001 2.2 20.9 1.0
S1 A:FES3001 2.2 21.7 1.0
SG A:CYS113 2.3 19.6 1.0
SG A:CYS150 2.5 23.1 1.0
FE2 A:FES3001 2.7 22.2 1.0
CB A:CYS113 3.3 20.2 1.0
CB A:CYS150 3.4 22.3 1.0
O A:HOH4012 3.5 13.6 1.0
N A:CYS113 3.6 19.4 1.0
N A:GLY114 3.9 19.2 1.0
CA A:CYS113 3.9 19.7 1.0
N A:CYS150 4.0 21.4 1.0
C A:CYS113 4.3 19.7 1.0
CA A:CYS150 4.3 21.9 1.0
N A:PHE115 4.4 19.1 1.0
SG A:CYS148 4.5 21.1 1.0
N A:ARG149 4.7 20.4 1.0
SG A:CYS116 4.7 20.5 1.0
C A:GLN112 4.7 19.2 1.0
CB A:GLN112 4.8 18.9 1.0
CA A:GLY114 4.8 19.4 1.0
N A:CYS116 4.9 19.3 1.0
C A:ARG149 5.0 21.1 1.0

Iron binding site 2 out of 8 in 1fo4

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Iron binding site 2 out of 8 in the Crystal Structure of Xanthine Dehydrogenase Isolated From Bovine Milk


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 Xanthine Dehydrogenase Isolated From Bovine Milk within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe3001

b:22.2
occ:1.00
 FE2 A:FES3001 0.0 22.2 1.0
S2 A:FES3001 2.2 20.9 1.0
S1 A:FES3001 2.2 21.7 1.0
SG A:CYS116 2.3 20.5 1.0
SG A:CYS148 2.5 21.1 1.0
FE1 A:FES3001 2.7 22.4 1.0
CB A:CYS116 3.4 20.3 1.0
CB A:CYS148 3.4 20.6 1.0
CA A:CYS148 3.7 20.2 1.0
N A:ARG149 4.0 20.4 1.0
N A:CYS116 4.2 19.3 1.0
N A:CYS150 4.3 21.4 1.0
C A:CYS148 4.3 19.8 1.0
O A:HOH4029 4.3 21.6 1.0
CA A:CYS116 4.4 19.6 1.0
CB A:CYS150 4.5 22.3 1.0
SG A:CYS150 4.6 23.1 1.0
SG A:CYS113 4.7 19.6 1.0
CG2 A:THR151 4.8 20.6 1.0
O A:LEU147 4.9 20.6 1.0
CA A:CYS150 5.0 21.9 1.0
C A:CYS116 5.0 19.9 1.0
N A:CYS148 5.0 20.6 1.0
N A:THR117 5.0 20.3 1.0
N A:THR151 5.0 21.6 1.0

Iron binding site 3 out of 8 in 1fo4

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Iron binding site 3 out of 8 in the Crystal Structure of Xanthine Dehydrogenase Isolated From Bovine Milk


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 Xanthine Dehydrogenase Isolated From Bovine Milk within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe3002

b:21.2
occ:1.00
 FE1 A:FES3002 0.0 21.2 1.0
S1 A:FES3002 2.2 21.6 1.0
S2 A:FES3002 2.2 23.1 1.0
SG A:CYS51 2.3 19.8 1.0
SG A:CYS73 2.5 21.8 1.0
FE2 A:FES3002 2.7 22.4 1.0
CB A:CYS73 3.2 21.4 1.0
CB A:CYS51 3.4 19.1 1.0
CB A:ASN71 4.2 19.1 1.0
N A:CYS51 4.2 18.5 1.0
N A:GLY46 4.2 23.7 1.0
N A:GLY44 4.3 21.7 1.0
N A:CYS73 4.3 21.1 1.0
CA A:CYS73 4.4 22.4 1.0
OD1 A:ASN71 4.4 19.4 1.0
CA A:CYS51 4.4 19.0 1.0
CA A:GLY46 4.5 24.0 1.0
CA A:GLY44 4.5 22.4 1.0
SG A:CYS43 4.5 23.2 1.0
CG A:ASN71 4.6 18.9 1.0
N A:GLU45 4.7 23.3 1.0
SG A:CYS48 4.7 20.7 1.0
N A:GLY49 4.8 20.8 1.0
CA A:ASN71 4.9 20.2 1.0
N A:ALA50 5.0 18.4 1.0

Iron binding site 4 out of 8 in 1fo4

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Iron binding site 4 out of 8 in the Crystal Structure of Xanthine Dehydrogenase Isolated From Bovine Milk


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 Xanthine Dehydrogenase Isolated From Bovine Milk within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe3002

b:22.4
occ:1.00
 FE2 A:FES3002 0.0 22.4 1.0
S2 A:FES3002 2.2 23.1 1.0
S1 A:FES3002 2.2 21.6 1.0
SG A:CYS48 2.4 20.7 1.0
SG A:CYS43 2.4 23.2 1.0
FE1 A:FES3002 2.7 21.2 1.0
N A:CYS43 3.3 20.0 1.0
N A:CYS48 3.5 22.8 1.0
CB A:CYS48 3.5 21.7 1.0
CB A:CYS43 3.5 21.4 1.0
N A:GLY44 3.7 21.7 1.0
N A:GLY49 3.8 20.8 1.0
CA A:CYS43 3.9 21.1 1.0
CA A:CYS48 3.9 21.7 1.0
C A:GLY42 4.0 20.0 1.0
N A:GLY42 4.2 20.3 1.0
C A:CYS43 4.2 21.6 1.0
C A:CYS48 4.2 21.2 1.0
CA A:GLY42 4.2 19.6 1.0
N A:GLY46 4.3 23.7 1.0
N A:GLY47 4.4 24.4 1.0
N A:ALA50 4.4 18.4 1.0
N A:GLU45 4.5 23.3 1.0
SG A:CYS73 4.6 21.8 1.0
C A:GLY47 4.7 24.1 1.0
SG A:CYS51 4.7 19.8 1.0
CA A:GLY44 4.7 22.4 1.0
C A:GLY46 4.7 24.4 1.0
CA A:GLY46 4.8 24.0 1.0
CA A:GLY49 4.8 19.4 1.0
O A:GLY42 4.9 18.0 1.0

Iron binding site 5 out of 8 in 1fo4

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Iron binding site 5 out of 8 in the Crystal Structure of Xanthine Dehydrogenase Isolated From Bovine Milk


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 Xanthine Dehydrogenase Isolated From Bovine Milk within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe4001

b:19.9
occ:1.00
 FE1 B:FES4001 0.0 19.9 1.0
S2 B:FES4001 2.2 21.3 1.0
S1 B:FES4001 2.2 20.8 1.0
SG B:CYS113 2.4 18.7 1.0
SG B:CYS150 2.5 21.9 1.0
FE2 B:FES4001 2.7 20.4 1.0
CB B:CYS150 3.2 19.0 1.0
CB B:CYS113 3.2 19.2 1.0
N B:CYS113 3.5 19.4 1.0
O B:HOH4042 3.5 17.2 1.0
N B:GLY114 3.8 17.9 1.0
CA B:CYS113 3.8 19.1 1.0
N B:CYS150 4.0 19.0 1.0
C B:CYS113 4.2 18.8 1.0
CA B:CYS150 4.3 19.6 1.0
N B:PHE115 4.4 18.5 1.0
SG B:CYS148 4.5 18.6 1.0
C B:GLN112 4.7 19.1 1.0
SG B:CYS116 4.7 19.4 1.0
CB B:GLN112 4.7 18.7 1.0
CA B:GLY114 4.7 18.0 1.0
N B:ARG149 4.8 18.0 1.0
N B:CYS116 5.0 17.6 1.0

Iron binding site 6 out of 8 in 1fo4

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Iron binding site 6 out of 8 in the Crystal Structure of Xanthine Dehydrogenase Isolated From Bovine Milk


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 Xanthine Dehydrogenase Isolated From Bovine Milk within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe4001

b:20.4
occ:1.00
 FE2 B:FES4001 0.0 20.4 1.0
S2 B:FES4001 2.2 21.3 1.0
S1 B:FES4001 2.2 20.8 1.0
SG B:CYS116 2.3 19.4 1.0
SG B:CYS148 2.4 18.6 1.0
FE1 B:FES4001 2.7 19.9 1.0
CB B:CYS116 3.3 18.7 1.0
CB B:CYS148 3.4 18.4 1.0
CA B:CYS148 3.6 18.2 1.0
N B:ARG149 4.0 18.0 1.0
N B:CYS116 4.2 17.6 1.0
C B:CYS148 4.3 18.1 1.0
N B:CYS150 4.3 19.0 1.0
CA B:CYS116 4.4 17.7 1.0
O B:HOH4058 4.4 16.6 1.0
CB B:CYS150 4.4 19.0 1.0
SG B:CYS150 4.7 21.9 1.0
SG B:CYS113 4.7 18.7 1.0
O B:LEU147 4.8 19.1 1.0
CG2 B:THR151 4.9 20.4 1.0
CA B:CYS150 4.9 19.6 1.0
N B:CYS148 4.9 19.4 1.0
N B:GLY114 4.9 17.9 1.0
C B:CYS116 4.9 17.8 1.0
N B:THR117 5.0 18.0 1.0

Iron binding site 7 out of 8 in 1fo4

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Iron binding site 7 out of 8 in the Crystal Structure of Xanthine Dehydrogenase Isolated From Bovine Milk


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 Xanthine Dehydrogenase Isolated From Bovine Milk within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe4002

b:21.7
occ:1.00
 FE1 B:FES4002 0.0 21.7 1.0
S1 B:FES4002 2.2 20.7 1.0
S2 B:FES4002 2.2 20.4 1.0
SG B:CYS51 2.4 19.9 1.0
SG B:CYS73 2.4 22.4 1.0
FE2 B:FES4002 2.7 21.1 1.0
CB B:CYS73 3.2 21.7 1.0
CB B:CYS51 3.5 18.5 1.0
N B:GLY46 4.1 21.8 1.0
N B:GLY44 4.2 21.6 1.0
OD1 B:ASN71 4.3 22.7 1.0
CB B:ASN71 4.3 20.5 1.0
CA B:GLY46 4.3 21.7 1.0
N B:CYS73 4.3 20.7 1.0
CA B:CYS73 4.4 21.5 1.0
CA B:GLY44 4.4 21.6 1.0
N B:CYS51 4.4 17.8 1.0
SG B:CYS43 4.4 22.0 1.0
CG B:ASN71 4.5 22.2 1.0
CA B:CYS51 4.6 18.6 1.0
N B:GLU45 4.7 21.7 1.0
SG B:CYS48 4.7 20.5 1.0
N B:GLY49 4.8 20.8 1.0
C B:GLY44 4.9 22.0 1.0
CA B:ASN71 5.0 19.9 1.0
C B:GLY46 5.0 21.9 1.0

Iron binding site 8 out of 8 in 1fo4

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Iron binding site 8 out of 8 in the Crystal Structure of Xanthine Dehydrogenase Isolated From Bovine Milk


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 Xanthine Dehydrogenase Isolated From Bovine Milk within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe4002

b:21.1
occ:1.00
 FE2 B:FES4002 0.0 21.1 1.0
S2 B:FES4002 2.2 20.4 1.0
S1 B:FES4002 2.2 20.7 1.0
SG B:CYS48 2.4 20.5 1.0
SG B:CYS43 2.4 22.0 1.0
FE1 B:FES4002 2.7 21.7 1.0
N B:CYS43 3.4 19.9 1.0
N B:CYS48 3.5 21.7 1.0
CB B:CYS48 3.5 20.5 1.0
CB B:CYS43 3.6 20.5 1.0
N B:GLY44 3.7 21.6 1.0
N B:GLY49 3.8 20.8 1.0
CA B:CYS48 3.9 21.3 1.0
CA B:CYS43 3.9 21.3 1.0
C B:GLY42 4.1 19.9 1.0
C B:CYS48 4.2 20.8 1.0
C B:CYS43 4.3 21.3 1.0
N B:GLY42 4.3 18.4 1.0
N B:GLY46 4.3 21.8 1.0
N B:GLY47 4.3 21.9 1.0
CA B:GLY42 4.4 19.1 1.0
N B:ALA50 4.4 19.0 1.0
N B:GLU45 4.5 21.7 1.0
SG B:CYS73 4.6 22.4 1.0
SG B:CYS51 4.6 19.9 1.0
C B:GLY47 4.7 22.0 1.0
CA B:GLY44 4.7 21.6 1.0
C B:GLY46 4.7 21.9 1.0
CA B:GLY46 4.7 21.7 1.0
CA B:GLY49 4.8 20.4 1.0
O B:GLY42 5.0 19.0 1.0
CA B:GLY47 5.0 21.8 1.0

Reference:

C.Enroth, B.T.Eger, K.Okamoto, T.Nishino, T.Nishino, E.F.Pai. Crystal Structures of Bovine Milk Xanthine Dehydrogenase and Xanthine Oxidase: Structure-Based Mechanism of Conversion. Proc.Natl.Acad.Sci.Usa V. 97 10723 2000.
ISSN: ISSN 0027-8424
PubMed: 11005854
DOI: 10.1073/PNAS.97.20.10723
Page generated: Sun Dec 13 14:14:07 2020

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