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Iron in PDB 3nrz: Crystal Structure of Bovine Xanthine Oxidase in Complex with Hypoxanthine

Enzymatic activity of Crystal Structure of Bovine Xanthine Oxidase in Complex with Hypoxanthine

All present enzymatic activity of Crystal Structure of Bovine Xanthine Oxidase in Complex with Hypoxanthine:
1.17.1.4; 1.17.3.2;

Protein crystallography data

The structure of Crystal Structure of Bovine Xanthine Oxidase in Complex with Hypoxanthine, PDB code: 3nrz was solved by H.Cao, J.M.Pauff, R.Hille, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 23.50 / 1.80
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 133.016, 73.645, 138.696, 90.00, 97.05, 90.00
R / Rfree (%) 19.7 / 23.4

Other elements in 3nrz:

The structure of Crystal Structure of Bovine Xanthine Oxidase in Complex with Hypoxanthine also contains other interesting chemical elements:

Molybdenum (Mo) 2 atoms

Iron Binding Sites:

The binding sites of Iron atom in the Crystal Structure of Bovine Xanthine Oxidase in Complex with Hypoxanthine (pdb code 3nrz). 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 Xanthine Oxidase in Complex with Hypoxanthine, PDB code: 3nrz:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iron binding site 1 out of 8 in 3nrz

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Iron binding site 1 out of 8 in the Crystal Structure of Bovine Xanthine Oxidase in Complex with Hypoxanthine


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 Xanthine Oxidase in Complex with Hypoxanthine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe601

b:10.6
occ:1.00
 FE1 A:FES601 0.0 10.6 1.0
S2 A:FES601 2.2 11.9 1.0
S1 A:FES601 2.2 11.5 1.0
SG A:CYS113 2.3 10.1 1.0
SG A:CYS150 2.4 12.6 1.0
FE2 A:FES601 2.7 10.7 1.0
CB A:CYS113 3.3 10.1 1.0
CB A:CYS150 3.3 11.5 1.0
N A:CYS113 3.6 10.1 1.0
O C:HOH100 3.6 12.4 1.0
CA A:CYS113 3.8 9.7 1.0
N A:GLY114 3.9 8.5 1.0
N A:CYS150 4.1 9.8 1.0
C A:CYS113 4.2 8.7 1.0
CA A:CYS150 4.4 10.3 1.0
N A:PHE115 4.4 6.5 1.0
SG A:CYS148 4.4 9.5 1.0
SG A:CYS116 4.6 10.1 1.0
C A:GLN112 4.7 10.6 1.0
N A:ARG149 4.8 8.2 1.0
CB A:GLN112 4.9 11.6 1.0
N A:CYS116 4.9 7.5 1.0
CA A:GLY114 4.9 7.8 1.0

Iron binding site 2 out of 8 in 3nrz

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Iron binding site 2 out of 8 in the Crystal Structure of Bovine Xanthine Oxidase in Complex with Hypoxanthine


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 Xanthine Oxidase in Complex with Hypoxanthine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe601

b:10.7
occ:1.00
 FE2 A:FES601 0.0 10.7 1.0
S2 A:FES601 2.2 11.9 1.0
S1 A:FES601 2.2 11.5 1.0
SG A:CYS116 2.3 10.1 1.0
SG A:CYS148 2.4 9.5 1.0
FE1 A:FES601 2.7 10.6 1.0
CB A:CYS148 3.3 9.5 1.0
CB A:CYS116 3.4 7.7 1.0
CA A:CYS148 3.6 9.7 1.0
N A:ARG149 4.1 8.2 1.0
N A:CYS116 4.2 7.5 1.0
C A:CYS148 4.3 9.2 1.0
O A:HOH171 4.3 14.4 1.0
N A:CYS150 4.4 9.8 1.0
CA A:CYS116 4.4 8.3 1.0
CB A:CYS150 4.4 11.5 1.0
SG A:CYS150 4.5 12.6 1.0
SG A:CYS113 4.7 10.1 1.0
CG2 A:THR151 4.8 10.4 1.0
O A:LEU147 4.9 10.6 1.0
N A:CYS148 5.0 9.8 1.0

Iron binding site 3 out of 8 in 3nrz

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Iron binding site 3 out of 8 in the Crystal Structure of Bovine Xanthine Oxidase in Complex with Hypoxanthine


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 Xanthine Oxidase in Complex with Hypoxanthine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe602

b:11.9
occ:1.00
 FE1 A:FES602 0.0 11.9 1.0
S1 A:FES602 2.2 12.8 1.0
S2 A:FES602 2.2 13.6 1.0
SG A:CYS73 2.3 13.1 1.0
SG A:CYS51 2.3 12.0 1.0
FE2 A:FES602 2.8 12.9 1.0
CB A:CYS73 3.1 13.2 1.0
CB A:CYS51 3.4 10.5 1.0
N A:CYS73 4.2 12.2 1.0
CA A:CYS73 4.2 13.8 1.0
CB A:ASN71 4.2 14.3 1.0
OD1 A:ASN71 4.3 18.1 1.0
N A:CYS51 4.4 10.8 1.0
N A:GLY46 4.4 14.8 1.0
N A:GLY44 4.4 15.6 1.0
SG A:CYS43 4.5 12.9 1.0
CG A:ASN71 4.5 16.5 1.0
CA A:CYS51 4.5 11.0 1.0
CA A:GLY46 4.6 15.1 1.0
CA A:GLY44 4.7 16.0 1.0
SG A:CYS48 4.7 11.6 1.0
N A:GLU45 4.9 15.5 1.0
N A:GLY49 4.9 10.6 1.0
CA A:ASN71 4.9 13.9 1.0

Iron binding site 4 out of 8 in 3nrz

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Iron binding site 4 out of 8 in the Crystal Structure of Bovine Xanthine Oxidase in Complex with Hypoxanthine


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 Xanthine Oxidase in Complex with Hypoxanthine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe602

b:12.9
occ:1.00
 FE2 A:FES602 0.0 12.9 1.0
S2 A:FES602 2.2 13.6 1.0
S1 A:FES602 2.3 12.8 1.0
SG A:CYS48 2.3 11.6 1.0
SG A:CYS43 2.4 12.9 1.0
FE1 A:FES602 2.8 11.9 1.0
CB A:CYS48 3.4 11.8 1.0
N A:CYS43 3.4 14.3 1.0
CB A:CYS43 3.5 15.1 1.0
N A:CYS48 3.5 13.8 1.0
CA A:CYS43 3.8 15.2 1.0
N A:GLY49 3.8 10.6 1.0
N A:GLY44 3.9 15.6 1.0
CA A:CYS48 3.9 12.7 1.0
C A:GLY42 4.1 14.8 1.0
C A:CYS48 4.2 11.5 1.0
N A:GLY42 4.2 13.3 1.0
C A:CYS43 4.3 16.2 1.0
CA A:GLY42 4.3 13.8 1.0
N A:ALA50 4.4 11.2 1.0
N A:GLY47 4.4 14.9 1.0
SG A:CYS73 4.5 13.1 1.0
N A:GLY46 4.5 14.8 1.0
SG A:CYS51 4.7 12.0 1.0
N A:GLU45 4.7 15.5 1.0
C A:GLY47 4.7 15.4 1.0
CA A:GLY49 4.8 9.8 1.0
CA A:GLY44 4.9 16.0 1.0
C A:GLY46 4.9 15.7 1.0
CB A:ALA50 4.9 11.0 1.0
O A:GLY42 5.0 14.3 1.0
CA A:GLY46 5.0 15.1 1.0

Iron binding site 5 out of 8 in 3nrz

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Iron binding site 5 out of 8 in the Crystal Structure of Bovine Xanthine Oxidase in Complex with Hypoxanthine


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 Xanthine Oxidase in Complex with Hypoxanthine within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Fe601

b:11.3
occ:1.00
 FE1 J:FES601 0.0 11.3 1.0
S2 J:FES601 2.2 13.6 1.0
S1 J:FES601 2.2 12.3 1.0
SG J:CYS113 2.3 10.3 1.0
SG J:CYS150 2.4 12.8 1.0
FE2 J:FES601 2.7 11.8 1.0
CB J:CYS150 3.3 11.1 1.0
CB J:CYS113 3.3 11.9 1.0
N J:CYS113 3.6 11.6 1.0
O L:HOH75 3.7 11.5 1.0
CA J:CYS113 3.9 10.5 1.0
N J:GLY114 3.9 10.5 1.0
N J:CYS150 4.1 11.9 1.0
C J:CYS113 4.3 11.1 1.0
CA J:CYS150 4.3 11.1 1.0
SG J:CYS148 4.4 11.9 1.0
N J:PHE115 4.4 10.1 1.0
SG J:CYS116 4.6 15.0 1.0
C J:GLN112 4.7 10.7 1.0
N J:ARG149 4.7 11.2 1.0
CB J:GLN112 4.9 11.9 1.0
CA J:GLY114 5.0 11.1 1.0
N J:CYS116 5.0 11.2 1.0

Iron binding site 6 out of 8 in 3nrz

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Iron binding site 6 out of 8 in the Crystal Structure of Bovine Xanthine Oxidase in Complex with Hypoxanthine


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 Xanthine Oxidase in Complex with Hypoxanthine within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Fe601

b:11.8
occ:1.00
 FE2 J:FES601 0.0 11.8 1.0
S2 J:FES601 2.2 13.6 1.0
S1 J:FES601 2.2 12.3 1.0
SG J:CYS116 2.3 15.0 1.0
SG J:CYS148 2.4 11.9 1.0
FE1 J:FES601 2.7 11.3 1.0
CB J:CYS148 3.4 12.6 1.0
CB J:CYS116 3.5 12.1 1.0
CA J:CYS148 3.7 12.1 1.0
N J:ARG149 4.1 11.2 1.0
N J:CYS116 4.2 11.2 1.0
C J:CYS148 4.3 11.8 1.0
N J:CYS150 4.3 11.9 1.0
O J:HOH237 4.4 16.4 1.0
CB J:CYS150 4.4 11.1 1.0
CA J:CYS116 4.5 12.4 1.0
SG J:CYS150 4.5 12.8 1.0
SG J:CYS113 4.6 10.3 1.0
CG2 J:THR151 4.8 11.8 1.0
O J:LEU147 4.9 12.3 1.0
CA J:CYS150 5.0 11.1 1.0
N J:CYS148 5.0 12.1 1.0

Iron binding site 7 out of 8 in 3nrz

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Iron binding site 7 out of 8 in the Crystal Structure of Bovine Xanthine Oxidase in Complex with Hypoxanthine


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 Xanthine Oxidase in Complex with Hypoxanthine within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Fe602

b:13.7
occ:1.00
 FE1 J:FES602 0.0 13.7 1.0
S1 J:FES602 2.2 13.9 1.0
S2 J:FES602 2.2 14.7 1.0
SG J:CYS51 2.3 12.9 1.0
SG J:CYS73 2.3 14.2 1.0
FE2 J:FES602 2.8 14.3 1.0
CB J:CYS73 3.1 15.3 1.0
CB J:CYS51 3.4 12.8 1.0
CB J:ASN71 4.2 15.8 1.0
N J:CYS73 4.2 13.7 1.0
CA J:CYS73 4.3 15.1 1.0
N J:CYS51 4.3 11.8 1.0
OD1 J:ASN71 4.3 17.6 1.0
N J:GLY46 4.3 16.3 1.0
N J:GLY44 4.4 16.5 1.0
SG J:CYS43 4.5 13.8 1.0
CG J:ASN71 4.5 16.4 1.0
CA J:CYS51 4.5 12.1 1.0
CA J:GLY46 4.6 16.5 1.0
CA J:GLY44 4.7 16.7 1.0
SG J:CYS48 4.7 14.4 1.0
N J:GLY49 4.8 12.3 1.0
N J:GLU45 4.9 16.8 1.0
CA J:ASN71 4.9 14.7 1.0

Iron binding site 8 out of 8 in 3nrz

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Iron binding site 8 out of 8 in the Crystal Structure of Bovine Xanthine Oxidase in Complex with Hypoxanthine


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 Xanthine Oxidase in Complex with Hypoxanthine within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Fe602

b:14.3
occ:1.00
 FE2 J:FES602 0.0 14.3 1.0
S2 J:FES602 2.2 14.7 1.0
S1 J:FES602 2.3 13.9 1.0
SG J:CYS48 2.3 14.4 1.0
SG J:CYS43 2.3 13.8 1.0
FE1 J:FES602 2.8 13.7 1.0
N J:CYS43 3.4 15.5 1.0
CB J:CYS48 3.4 14.3 1.0
CB J:CYS43 3.5 14.7 1.0
N J:CYS48 3.5 15.7 1.0
N J:GLY44 3.8 16.5 1.0
N J:GLY49 3.8 12.3 1.0
CA J:CYS48 3.8 14.2 1.0
CA J:CYS43 3.8 16.1 1.0
C J:GLY42 4.1 15.5 1.0
C J:CYS48 4.2 13.5 1.0
N J:GLY42 4.3 12.9 1.0
C J:CYS43 4.3 16.9 1.0
N J:GLY47 4.4 16.6 1.0
CA J:GLY42 4.4 13.8 1.0
N J:ALA50 4.4 11.6 1.0
N J:GLY46 4.5 16.3 1.0
SG J:CYS73 4.5 14.2 1.0
SG J:CYS51 4.6 12.9 1.0
N J:GLU45 4.7 16.8 1.0
C J:GLY47 4.7 17.5 1.0
CA J:GLY49 4.8 12.1 1.0
CA J:GLY44 4.8 16.7 1.0
C J:GLY46 4.8 16.5 1.0
O J:GLY42 4.9 15.9 1.0
CA J:GLY46 4.9 16.5 1.0
CB J:ALA50 5.0 10.9 1.0

Reference:

H.Cao, J.M.Pauff, R.Hille. Substrate Orientation and Catalytic Specificity in the Action of Xanthine Oxidase: the Sequential Hydroxylation of Hypoxanthine to Uric Acid. J.Biol.Chem. V. 285 28044 2010.
ISSN: ISSN 0021-9258
PubMed: 20615869
DOI: 10.1074/JBC.M110.128561
Page generated: Sun Aug 4 16:40:54 2024

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