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Iron in PDB 3b9j: Structure of Xanthine Oxidase with 2-Hydroxy-6-Methylpurine

Enzymatic activity of Structure of Xanthine Oxidase with 2-Hydroxy-6-Methylpurine

All present enzymatic activity of Structure of Xanthine Oxidase with 2-Hydroxy-6-Methylpurine:
1.17.3.2;

Protein crystallography data

The structure of Structure of Xanthine Oxidase with 2-Hydroxy-6-Methylpurine, PDB code: 3b9j was solved by J.M.Pauff, J.Zhang, C.E.Bell, R.Hille, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 144.34 / 2.30
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 133.187, 73.794, 146.498, 90.00, 98.87, 90.00
R / Rfree (%) 19.4 / 26.3

Other elements in 3b9j:

The structure of Structure of Xanthine Oxidase with 2-Hydroxy-6-Methylpurine also contains other interesting chemical elements:

Molybdenum (Mo) 2 atoms
Calcium (Ca) 1 atom

Iron Binding Sites:

The binding sites of Iron atom in the Structure of Xanthine Oxidase with 2-Hydroxy-6-Methylpurine (pdb code 3b9j). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 8 binding sites of Iron where determined in the Structure of Xanthine Oxidase with 2-Hydroxy-6-Methylpurine, PDB code: 3b9j:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iron binding site 1 out of 8 in 3b9j

Go back to Iron Binding Sites List in 3b9j
Iron binding site 1 out of 8 in the Structure of Xanthine Oxidase with 2-Hydroxy-6-Methylpurine


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Structure of Xanthine Oxidase with 2-Hydroxy-6-Methylpurine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe601

b:18.1
occ:1.00
 FE1 A:FES601 0.0 18.1 1.0
S2 A:FES601 2.2 13.8 1.0
S1 A:FES601 2.2 16.4 1.0
SG A:CYS113 2.5 15.7 1.0
SG A:CYS150 2.5 14.5 1.0
FE2 A:FES601 2.7 18.9 1.0
O C:HOH1422 3.2 27.5 1.0
CB A:CYS150 3.2 17.6 1.0
CB A:CYS113 3.3 14.6 1.0
N A:CYS113 3.7 15.7 1.0
N A:GLY114 3.9 15.0 1.0
CA A:CYS113 3.9 14.7 1.0
N A:CYS150 4.3 16.5 1.0
C A:CYS113 4.3 15.0 1.0
CA A:CYS150 4.4 16.9 1.0
N A:PHE115 4.4 14.0 1.0
SG A:CYS148 4.5 18.2 1.0
N A:ARG149 4.7 17.0 1.0
SG A:CYS116 4.7 17.9 1.0
C A:GLN112 4.9 16.8 1.0
CA A:GLY114 4.9 14.7 1.0
N A:CYS116 5.0 15.1 1.0

Iron binding site 2 out of 8 in 3b9j

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Iron binding site 2 out of 8 in the Structure of Xanthine Oxidase with 2-Hydroxy-6-Methylpurine


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Structure of Xanthine Oxidase with 2-Hydroxy-6-Methylpurine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe601

b:18.9
occ:1.00
 FE2 A:FES601 0.0 18.9 1.0
S2 A:FES601 2.2 13.8 1.0
S1 A:FES601 2.2 16.4 1.0
SG A:CYS116 2.4 17.9 1.0
SG A:CYS148 2.5 18.2 1.0
FE1 A:FES601 2.7 18.1 1.0
CB A:CYS148 3.3 16.7 1.0
CB A:CYS116 3.3 14.5 1.0
CA A:CYS148 3.7 16.8 1.0
N A:ARG149 4.1 17.0 1.0
O A:HOH609 4.2 10.1 1.0
CB A:CYS150 4.2 17.6 1.0
N A:CYS116 4.3 15.1 1.0
C A:CYS148 4.3 16.8 1.0
CA A:CYS116 4.4 15.2 1.0
N A:CYS150 4.5 16.5 1.0
SG A:CYS150 4.6 14.5 1.0
CG2 A:THR151 4.7 17.3 1.0
O A:LEU147 4.8 16.3 1.0
SG A:CYS113 4.9 15.7 1.0
N A:CYS148 4.9 17.2 1.0
C A:CYS116 5.0 14.3 1.0
CA A:CYS150 5.0 16.9 1.0

Iron binding site 3 out of 8 in 3b9j

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Iron binding site 3 out of 8 in the Structure of Xanthine Oxidase with 2-Hydroxy-6-Methylpurine


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Structure of Xanthine Oxidase with 2-Hydroxy-6-Methylpurine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe602

b:14.7
occ:1.00
 FE1 A:FES602 0.0 14.7 1.0
S2 A:FES602 2.2 13.1 1.0
S1 A:FES602 2.2 16.1 1.0
SG A:CYS73 2.3 13.7 1.0
SG A:CYS51 2.3 14.8 1.0
FE2 A:FES602 2.8 18.4 1.0
CB A:CYS73 3.1 16.9 1.0
CB A:CYS51 3.4 16.8 1.0
CB A:ASN71 4.1 16.9 1.0
N A:CYS73 4.2 17.3 1.0
CA A:CYS73 4.3 17.4 1.0
N A:GLY46 4.3 15.6 1.0
CG A:ASN71 4.4 17.0 1.0
OD1 A:ASN71 4.4 19.2 1.0
N A:CYS51 4.4 17.2 1.0
N A:GLY44 4.5 15.7 1.0
CA A:CYS51 4.5 17.4 1.0
SG A:CYS43 4.5 13.1 1.0
SG A:CYS48 4.7 16.1 1.0
CA A:GLY46 4.7 15.3 1.0
CA A:GLY44 4.8 16.4 1.0
N A:GLU45 4.8 16.8 1.0
CA A:ASN71 4.8 16.8 1.0
N A:GLY49 4.9 15.8 1.0

Iron binding site 4 out of 8 in 3b9j

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Iron binding site 4 out of 8 in the Structure of Xanthine Oxidase with 2-Hydroxy-6-Methylpurine


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Structure of Xanthine Oxidase with 2-Hydroxy-6-Methylpurine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe602

b:18.4
occ:1.00
 FE2 A:FES602 0.0 18.4 1.0
S1 A:FES602 2.2 16.1 1.0
S2 A:FES602 2.3 13.1 1.0
SG A:CYS48 2.3 16.1 1.0
SG A:CYS43 2.4 13.1 1.0
FE1 A:FES602 2.8 14.7 1.0
CB A:CYS43 3.5 13.2 1.0
CB A:CYS48 3.5 16.2 1.0
N A:CYS48 3.6 15.5 1.0
N A:CYS43 3.6 13.5 1.0
N A:GLY44 3.8 15.7 1.0
N A:GLY49 3.9 15.8 1.0
CA A:CYS48 3.9 15.8 1.0
CA A:CYS43 4.0 13.9 1.0
C A:GLY42 4.2 13.0 1.0
C A:CYS48 4.3 15.4 1.0
N A:GLY42 4.3 14.2 1.0
C A:CYS43 4.4 15.3 1.0
N A:GLY46 4.4 15.6 1.0
CA A:GLY42 4.4 13.1 1.0
N A:GLY47 4.4 16.1 1.0
SG A:CYS73 4.4 13.7 1.0
N A:GLU45 4.5 16.8 1.0
N A:ALA50 4.5 15.9 1.0
SG A:CYS51 4.7 14.8 1.0
C A:GLY47 4.7 15.5 1.0
C A:GLY46 4.8 16.3 1.0
CA A:GLY44 4.9 16.4 1.0
CA A:GLY49 4.9 15.8 1.0
CA A:GLY46 4.9 15.3 1.0
O A:GLY42 4.9 13.6 1.0

Iron binding site 5 out of 8 in 3b9j

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Iron binding site 5 out of 8 in the Structure of Xanthine Oxidase with 2-Hydroxy-6-Methylpurine


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Structure of Xanthine Oxidase with 2-Hydroxy-6-Methylpurine within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Fe601

b:21.8
occ:1.00
 FE1 I:FES601 0.0 21.8 1.0
S2 I:FES601 2.2 19.9 1.0
S1 I:FES601 2.2 19.5 1.0
SG I:CYS150 2.4 17.8 1.0
SG I:CYS113 2.5 20.6 1.0
FE2 I:FES601 2.8 20.6 1.0
CB I:CYS150 3.1 19.4 1.0
CB I:CYS113 3.5 19.8 1.0
N I:CYS113 3.7 20.3 1.0
O K:HOH1441 3.9 11.5 1.0
N I:GLY114 4.0 17.6 1.0
CA I:CYS113 4.0 19.6 1.0
N I:CYS150 4.0 19.6 1.0
CA I:CYS150 4.2 19.2 1.0
N I:PHE115 4.4 16.4 1.0
SG I:CYS148 4.4 22.6 1.0
C I:CYS113 4.4 18.7 1.0
SG I:CYS116 4.7 21.3 1.0
N I:ARG149 4.7 20.6 1.0
CB I:GLN112 4.7 21.6 1.0
C I:GLN112 4.8 21.1 1.0
CA I:GLY114 4.9 16.5 1.0
N I:GLN112 5.0 21.6 1.0
N I:CYS116 5.0 18.0 1.0

Iron binding site 6 out of 8 in 3b9j

Go back to Iron Binding Sites List in 3b9j
Iron binding site 6 out of 8 in the Structure of Xanthine Oxidase with 2-Hydroxy-6-Methylpurine


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Structure of Xanthine Oxidase with 2-Hydroxy-6-Methylpurine within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Fe601

b:20.6
occ:1.00
 FE2 I:FES601 0.0 20.6 1.0
S1 I:FES601 2.1 19.5 1.0
SG I:CYS116 2.2 21.3 1.0
S2 I:FES601 2.2 19.9 1.0
SG I:CYS148 2.5 22.6 1.0
FE1 I:FES601 2.8 21.8 1.0
CB I:CYS116 3.2 18.6 1.0
CB I:CYS148 3.3 22.2 1.0
CA I:CYS148 3.7 21.7 1.0
N I:CYS116 4.0 18.0 1.0
CA I:CYS116 4.2 19.0 1.0
N I:ARG149 4.2 20.6 1.0
O I:HOH618 4.3 20.3 1.0
C I:CYS148 4.4 21.2 1.0
CB I:CYS150 4.5 19.4 1.0
N I:CYS150 4.5 19.6 1.0
CG2 I:THR151 4.5 20.6 1.0
O I:LEU147 4.7 21.5 1.0
SG I:CYS150 4.8 17.8 1.0
SG I:CYS113 4.8 20.6 1.0
N I:PHE115 4.9 16.4 1.0
C I:CYS116 4.9 19.2 1.0
N I:THR117 5.0 19.6 1.0
N I:CYS148 5.0 21.6 1.0

Iron binding site 7 out of 8 in 3b9j

Go back to Iron Binding Sites List in 3b9j
Iron binding site 7 out of 8 in the Structure of Xanthine Oxidase with 2-Hydroxy-6-Methylpurine


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Structure of Xanthine Oxidase with 2-Hydroxy-6-Methylpurine within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Fe602

b:19.1
occ:1.00
 FE1 I:FES602 0.0 19.1 1.0
S2 I:FES602 2.2 20.6 1.0
S1 I:FES602 2.2 19.1 1.0
SG I:CYS73 2.2 19.7 1.0
SG I:CYS51 2.3 20.9 1.0
FE2 I:FES602 2.9 19.3 1.0
CB I:CYS73 3.1 22.4 1.0
CB I:CYS51 3.4 17.6 1.0
N I:CYS73 4.2 22.1 1.0
CA I:CYS73 4.2 22.2 1.0
CB I:ASN71 4.3 22.7 1.0
N I:GLY46 4.3 21.6 1.0
SG I:CYS43 4.4 18.7 1.0
N I:CYS51 4.4 17.8 1.0
N I:GLY44 4.5 21.0 1.0
CG I:ASN71 4.5 22.5 1.0
CA I:CYS51 4.5 18.2 1.0
CA I:GLY46 4.6 20.9 1.0
OD1 I:ASN71 4.7 23.3 1.0
SG I:CYS48 4.8 18.4 1.0
CA I:GLY44 4.8 21.4 1.0
N I:ALA50 4.9 17.8 1.0
N I:GLU45 4.9 23.1 1.0
N I:GLY49 4.9 17.9 1.0
CA I:ASN71 5.0 23.0 1.0

Iron binding site 8 out of 8 in 3b9j

Go back to Iron Binding Sites List in 3b9j
Iron binding site 8 out of 8 in the Structure of Xanthine Oxidase with 2-Hydroxy-6-Methylpurine


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Structure of Xanthine Oxidase with 2-Hydroxy-6-Methylpurine within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Fe602

b:19.3
occ:1.00
 FE2 I:FES602 0.0 19.3 1.0
S1 I:FES602 2.2 19.1 1.0
SG I:CYS48 2.2 18.4 1.0
S2 I:FES602 2.2 20.6 1.0
SG I:CYS43 2.3 18.7 1.0
FE1 I:FES602 2.9 19.1 1.0
CB I:CYS43 3.4 19.4 1.0
N I:CYS43 3.5 19.0 1.0
CB I:CYS48 3.5 18.7 1.0
N I:CYS48 3.5 19.8 1.0
N I:GLY49 3.8 17.9 1.0
CA I:CYS48 3.9 18.7 1.0
CA I:CYS43 3.9 19.8 1.0
N I:GLY44 4.0 21.0 1.0
C I:GLY42 4.1 19.5 1.0
C I:CYS48 4.1 18.2 1.0
N I:ALA50 4.2 17.8 1.0
N I:GLY47 4.3 20.6 1.0
CA I:GLY42 4.3 19.4 1.0
N I:GLY42 4.4 19.2 1.0
C I:CYS43 4.4 20.0 1.0
N I:GLY46 4.4 21.6 1.0
SG I:CYS73 4.5 19.7 1.0
SG I:CYS51 4.6 20.9 1.0
CA I:GLY49 4.7 17.7 1.0
C I:GLY47 4.7 20.6 1.0
C I:GLY46 4.8 20.5 1.0
N I:GLU45 4.8 23.1 1.0
CA I:GLY46 4.8 20.9 1.0
CB I:ALA50 4.9 17.2 1.0
C I:GLY49 5.0 17.2 1.0
CA I:GLY47 5.0 20.7 1.0

Reference:

J.M.Pauff, J.Zhang, C.E.Bell, R.Hille. Substrate Orientation in Xanthine Oxidase: Crystal Structure of Enzyme in Reaction with 2-Hydroxy-6-Methylpurine. J.Biol.Chem. V. 283 4818 2008.
ISSN: ISSN 0021-9258
PubMed: 18063585
DOI: 10.1074/JBC.M707918200
Page generated: Sun Aug 4 07:51:48 2024

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