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Iron in PDB 3amz: Bovine Xanthine Oxidoreductase Urate Bound Form

Enzymatic activity of Bovine Xanthine Oxidoreductase Urate Bound Form

All present enzymatic activity of Bovine Xanthine Oxidoreductase Urate Bound Form:
1.17.1.4; 1.17.3.2;

Protein crystallography data

The structure of Bovine Xanthine Oxidoreductase Urate Bound Form, PDB code: 3amz was solved by K.Okamoto, 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) 34.83 / 2.10
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 168.211, 124.530, 148.025, 90.00, 91.07, 90.00
R / Rfree (%) 15.1 / 20.2

Other elements in 3amz:

The structure of Bovine Xanthine Oxidoreductase Urate Bound Form 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 Bovine Xanthine Oxidoreductase Urate Bound Form (pdb code 3amz). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 8 binding sites of Iron where determined in the Bovine Xanthine Oxidoreductase Urate Bound Form, PDB code: 3amz:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iron binding site 1 out of 8 in 3amz

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Iron binding site 1 out of 8 in the Bovine Xanthine Oxidoreductase Urate Bound Form


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Bovine Xanthine Oxidoreductase Urate Bound Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe3001

b:15.4
occ:1.00
 FE1 A:FES3001 0.0 15.4 1.0
S2 A:FES3001 2.2 17.4 1.0
S1 A:FES3001 2.2 17.0 1.0
SG A:CYS113 2.3 12.8 1.0
SG A:CYS150 2.3 17.5 1.0
FE2 A:FES3001 2.8 15.4 1.0
CB A:CYS150 3.3 14.3 1.0
CB A:CYS113 3.3 12.0 1.0
O A:HOH1693 3.5 14.4 1.0
N A:CYS113 3.6 12.3 1.0
N A:GLY114 3.8 11.5 1.0
CA A:CYS113 3.8 12.4 1.0
N A:CYS150 4.1 15.0 1.0
C A:CYS113 4.2 12.2 1.0
N A:PHE115 4.3 14.6 1.0
CA A:CYS150 4.3 14.9 1.0
SG A:CYS148 4.4 14.5 1.0
SG A:CYS116 4.6 16.6 1.0
C A:GLN112 4.7 12.7 1.0
N A:ARG149 4.8 14.2 1.0
CB A:GLN112 4.8 11.6 1.0
CA A:GLY114 4.8 12.5 1.0
N A:CYS116 4.9 13.7 1.0
N A:GLN112 5.0 13.1 1.0

Iron binding site 2 out of 8 in 3amz

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Iron binding site 2 out of 8 in the Bovine Xanthine Oxidoreductase Urate Bound Form


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Bovine Xanthine Oxidoreductase Urate Bound Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe3001

b:15.4
occ:1.00
 FE2 A:FES3001 0.0 15.4 1.0
S1 A:FES3001 2.2 17.0 1.0
SG A:CYS116 2.2 16.6 1.0
S2 A:FES3001 2.2 17.4 1.0
SG A:CYS148 2.3 14.5 1.0
FE1 A:FES3001 2.8 15.4 1.0
CB A:CYS148 3.2 14.3 1.0
CB A:CYS116 3.5 12.3 1.0
CA A:CYS148 3.6 15.3 1.0
N A:ARG149 4.1 14.2 1.0
O A:HOH1468 4.2 13.4 1.0
N A:CYS116 4.2 13.7 1.0
N A:CYS150 4.3 15.0 1.0
C A:CYS148 4.3 15.1 1.0
CA A:CYS116 4.4 13.7 1.0
CB A:CYS150 4.4 14.3 1.0
SG A:CYS150 4.5 17.5 1.0
CG2 A:THR151 4.6 15.8 1.0
SG A:CYS113 4.7 12.8 1.0
O A:LEU147 4.9 15.6 1.0
N A:CYS148 5.0 14.7 1.0
CA A:CYS150 5.0 14.9 1.0

Iron binding site 3 out of 8 in 3amz

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Iron binding site 3 out of 8 in the Bovine Xanthine Oxidoreductase Urate Bound Form


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Bovine Xanthine Oxidoreductase Urate Bound Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe3002

b:15.6
occ:1.00
 FE1 A:FES3002 0.0 15.6 1.0
S1 A:FES3002 2.2 17.1 1.0
S2 A:FES3002 2.2 18.1 1.0
SG A:CYS51 2.3 14.5 1.0
SG A:CYS73 2.3 15.3 1.0
FE2 A:FES3002 2.8 15.7 1.0
CB A:CYS73 3.2 13.8 1.0
CB A:CYS51 3.4 11.7 1.0
OD1 A:ASN71 4.2 20.7 1.0
N A:CYS73 4.3 14.5 1.0
N A:GLY46 4.3 14.4 1.0
CB A:ASN71 4.3 12.0 1.0
N A:CYS51 4.3 11.4 1.0
CA A:CYS73 4.3 15.2 1.0
SG A:CYS43 4.4 16.2 1.0
N A:GLY44 4.4 16.9 1.0
CA A:CYS51 4.4 12.7 1.0
CG A:ASN71 4.6 14.5 1.0
CA A:GLY44 4.6 17.1 1.0
CA A:GLY46 4.7 15.1 1.0
SG A:CYS48 4.7 17.3 1.0
N A:GLU45 4.8 14.3 1.0
N A:GLY49 4.9 16.0 1.0
CA A:ASN71 4.9 12.8 1.0
C A:GLY44 4.9 16.8 1.0

Iron binding site 4 out of 8 in 3amz

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Iron binding site 4 out of 8 in the Bovine Xanthine Oxidoreductase Urate Bound Form


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Bovine Xanthine Oxidoreductase Urate Bound Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe3002

b:15.7
occ:1.00
 FE2 A:FES3002 0.0 15.7 1.0
S1 A:FES3002 2.2 17.1 1.0
S2 A:FES3002 2.2 18.1 1.0
SG A:CYS48 2.3 17.3 1.0
SG A:CYS43 2.3 16.2 1.0
FE1 A:FES3002 2.8 15.6 1.0
N A:CYS43 3.4 15.8 1.0
CB A:CYS43 3.5 14.2 1.0
CB A:CYS48 3.5 15.5 1.0
N A:CYS48 3.5 16.1 1.0
N A:GLY49 3.8 16.0 1.0
N A:GLY44 3.8 16.9 1.0
CA A:CYS43 3.9 17.4 1.0
CA A:CYS48 3.9 16.9 1.0
C A:GLY42 4.1 17.2 1.0
N A:GLY42 4.2 15.4 1.0
CA A:GLY42 4.3 15.7 1.0
C A:CYS48 4.3 16.9 1.0
C A:CYS43 4.3 17.0 1.0
N A:GLY47 4.4 15.5 1.0
N A:GLY46 4.5 14.4 1.0
N A:ALA50 4.5 15.6 1.0
SG A:CYS73 4.5 15.3 1.0
SG A:CYS51 4.6 14.5 1.0
N A:GLU45 4.6 14.3 1.0
C A:GLY47 4.7 18.0 1.0
CA A:GLY49 4.8 15.6 1.0
CA A:GLY44 4.8 17.1 1.0
C A:GLY46 4.9 16.7 1.0
O A:GLY42 5.0 16.6 1.0
N A:CYS51 5.0 11.4 1.0
CA A:GLY46 5.0 15.1 1.0

Iron binding site 5 out of 8 in 3amz

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Iron binding site 5 out of 8 in the Bovine Xanthine Oxidoreductase Urate Bound Form


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Bovine Xanthine Oxidoreductase Urate Bound Form within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe4001

b:16.9
occ:1.00
 FE1 B:FES4001 0.0 16.9 1.0
S2 B:FES4001 2.2 16.4 1.0
S1 B:FES4001 2.2 14.9 1.0
SG B:CYS113 2.3 13.9 1.0
SG B:CYS150 2.4 19.0 1.0
FE2 B:FES4001 2.7 15.4 1.0
CB B:CYS150 3.3 14.3 1.0
CB B:CYS113 3.4 13.7 1.0
O B:HOH1377 3.4 14.1 1.0
N B:CYS113 3.6 12.9 1.0
CA B:CYS113 3.8 14.1 1.0
N B:GLY114 3.9 13.7 1.0
N B:CYS150 4.1 14.9 1.0
C B:CYS113 4.2 14.6 1.0
CA B:CYS150 4.3 15.1 1.0
N B:PHE115 4.4 14.6 1.0
SG B:CYS148 4.4 15.4 1.0
SG B:CYS116 4.6 17.5 1.0
C B:GLN112 4.7 14.4 1.0
N B:ARG149 4.8 14.8 1.0
CB B:GLN112 4.9 14.3 1.0
N B:CYS116 4.9 12.8 1.0
CA B:GLY114 4.9 14.9 1.0

Iron binding site 6 out of 8 in 3amz

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Iron binding site 6 out of 8 in the Bovine Xanthine Oxidoreductase Urate Bound Form


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Bovine Xanthine Oxidoreductase Urate Bound Form within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe4001

b:15.4
occ:1.00
 FE2 B:FES4001 0.0 15.4 1.0
S1 B:FES4001 2.2 14.9 1.0
S2 B:FES4001 2.2 16.4 1.0
SG B:CYS116 2.2 17.5 1.0
SG B:CYS148 2.4 15.4 1.0
FE1 B:FES4001 2.7 16.9 1.0
CB B:CYS148 3.4 12.1 1.0
CB B:CYS116 3.4 14.1 1.0
CA B:CYS148 3.7 13.6 1.0
N B:ARG149 4.1 14.8 1.0
N B:CYS116 4.2 12.8 1.0
C B:CYS148 4.3 13.5 1.0
O B:HOH1557 4.3 14.3 1.0
N B:CYS150 4.3 14.9 1.0
CB B:CYS150 4.4 14.3 1.0
CA B:CYS116 4.4 13.7 1.0
SG B:CYS150 4.5 19.0 1.0
CG2 B:THR151 4.7 11.5 1.0
SG B:CYS113 4.7 13.9 1.0
O B:LEU147 4.9 14.3 1.0
N B:CYS148 5.0 14.5 1.0
CA B:CYS150 5.0 15.1 1.0

Iron binding site 7 out of 8 in 3amz

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Iron binding site 7 out of 8 in the Bovine Xanthine Oxidoreductase Urate Bound Form


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Bovine Xanthine Oxidoreductase Urate Bound Form within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe4002

b:15.8
occ:1.00
 FE1 B:FES4002 0.0 15.8 1.0
S1 B:FES4002 2.2 16.6 1.0
S2 B:FES4002 2.2 14.9 1.0
SG B:CYS73 2.3 17.4 1.0
SG B:CYS51 2.3 15.5 1.0
FE2 B:FES4002 2.8 16.5 1.0
CB B:CYS73 3.2 15.9 1.0
CB B:CYS51 3.5 13.9 1.0
CB B:ASN71 4.2 15.1 1.0
N B:CYS73 4.2 17.3 1.0
N B:GLY46 4.3 17.4 1.0
OD1 B:ASN71 4.3 20.3 1.0
N B:GLY44 4.3 16.9 1.0
CA B:CYS73 4.3 18.0 1.0
N B:CYS51 4.3 15.4 1.0
SG B:CYS43 4.4 16.0 1.0
CA B:CYS51 4.5 15.1 1.0
CG B:ASN71 4.6 15.1 1.0
CA B:GLY44 4.6 16.0 1.0
CA B:GLY46 4.6 16.9 1.0
SG B:CYS48 4.7 13.3 1.0
N B:GLU45 4.7 17.4 1.0
N B:GLY49 4.9 14.2 1.0
CA B:ASN71 4.9 15.8 1.0
C B:GLY44 4.9 18.3 1.0

Iron binding site 8 out of 8 in 3amz

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Iron binding site 8 out of 8 in the Bovine Xanthine Oxidoreductase Urate Bound Form


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Bovine Xanthine Oxidoreductase Urate Bound Form within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe4002

b:16.5
occ:1.00
 FE2 B:FES4002 0.0 16.5 1.0
S2 B:FES4002 2.2 14.9 1.0
S1 B:FES4002 2.2 16.6 1.0
SG B:CYS48 2.3 13.3 1.0
SG B:CYS43 2.3 16.0 1.0
FE1 B:FES4002 2.8 15.8 1.0
N B:CYS43 3.4 14.0 1.0
CB B:CYS48 3.4 14.3 1.0
N B:CYS48 3.5 16.6 1.0
CB B:CYS43 3.5 15.6 1.0
N B:GLY49 3.8 14.2 1.0
N B:GLY44 3.8 16.9 1.0
CA B:CYS48 3.9 15.4 1.0
CA B:CYS43 3.9 15.0 1.0
C B:GLY42 4.1 14.8 1.0
C B:CYS48 4.2 15.3 1.0
N B:GLY42 4.2 15.0 1.0
C B:CYS43 4.3 16.7 1.0
CA B:GLY42 4.3 14.6 1.0
N B:ALA50 4.4 14.4 1.0
N B:GLY47 4.4 17.9 1.0
N B:GLY46 4.5 17.4 1.0
SG B:CYS73 4.6 17.4 1.0
N B:GLU45 4.6 17.4 1.0
C B:GLY47 4.6 18.8 1.0
SG B:CYS51 4.7 15.5 1.0
CA B:GLY49 4.8 14.0 1.0
C B:GLY46 4.9 18.2 1.0
CA B:GLY44 4.9 16.0 1.0
CA B:GLY46 4.9 16.9 1.0
O B:GLY42 5.0 14.0 1.0

Reference:

K.Okamoto, Y.Kawaguchi, B.T.Eger, E.F.Pai, T.Nishino. Crystal Structures of Urate Bound Form of Xanthine Oxidoreductase: Substrate Orientation and Structure of the Key Reaction Intermediate J.Am.Chem.Soc. V. 132 17080 2010.
ISSN: ISSN 0002-7863
PubMed: 21077683
DOI: 10.1021/JA1077574
Page generated: Sun Aug 4 07:16:55 2024

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