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Iron in PDB 2ckj: Human Milk Xanthine Oxidoreductase

Enzymatic activity of Human Milk Xanthine Oxidoreductase

All present enzymatic activity of Human Milk Xanthine Oxidoreductase:
1.1.1.204; 1.17.3.2; 1.2.3.2;

Protein crystallography data

The structure of Human Milk Xanthine Oxidoreductase, PDB code: 2ckj was solved by A.R.Pearson, B.L.J.Godber, R.Eisenthal, G.L.Taylor, R.Harrison, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.76 / 3.59
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 197.734, 197.734, 285.538, 90.00, 90.00, 120.00
R / Rfree (%) 17.8 / 25.8

Iron Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 16;

Binding sites:

The binding sites of Iron atom in the Human Milk Xanthine Oxidoreductase (pdb code 2ckj). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 16 binding sites of Iron where determined in the Human Milk Xanthine Oxidoreductase, PDB code: 2ckj:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 16 in 2ckj

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Iron binding site 1 out of 16 in the Human Milk Xanthine Oxidoreductase


Mono view


Stereo pair view

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

b:7.1
occ:1.00
 FE1 A:FES3001 0.0 7.1 1.0
S1 A:FES3001 2.2 8.5 1.0
S2 A:FES3001 2.2 9.4 1.0
SG A:CYS148 2.3 7.3 1.0
SG A:CYS116 2.4 9.6 1.0
FE2 A:FES3001 2.7 7.2 1.0
CB A:CYS148 3.3 9.9 1.0
CB A:CYS116 3.4 9.9 1.0
CA A:CYS148 3.9 9.9 1.0
N A:ARG149 4.0 11.0 1.0
N A:CYS116 4.1 9.8 1.0
N A:CYS150 4.2 11.4 1.0
CG2 A:THR151 4.3 13.2 1.0
SG A:CYS113 4.3 15.1 1.0
C A:CYS148 4.4 10.6 1.0
CA A:CYS116 4.4 9.9 1.0
CB A:CYS150 4.6 11.5 1.0
SG A:CYS150 4.6 4.9 1.0
N A:PHE115 4.8 11.6 1.0
N A:GLY114 4.9 12.8 1.0

Iron binding site 2 out of 16 in 2ckj

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Iron binding site 2 out of 16 in the Human Milk Xanthine Oxidoreductase


Mono view


Stereo pair view

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

b:7.2
occ:1.00
 FE2 A:FES3001 0.0 7.2 1.0
SG A:CYS113 2.1 15.1 1.0
S2 A:FES3001 2.2 9.4 1.0
S1 A:FES3001 2.2 8.5 1.0
SG A:CYS150 2.5 4.9 1.0
FE1 A:FES3001 2.7 7.1 1.0
CB A:CYS113 2.9 14.9 1.0
CB A:CYS150 3.3 11.5 1.0
N A:CYS113 3.7 14.4 1.0
CA A:CYS113 3.7 14.2 1.0
N A:GLY114 3.8 12.8 1.0
N A:CYS150 4.0 11.4 1.0
C A:CYS113 4.2 13.5 1.0
CA A:CYS150 4.3 11.2 1.0
SG A:CYS148 4.3 7.3 1.0
N A:PHE115 4.5 11.6 1.0
SG A:CYS116 4.8 9.6 1.0
O A:GLY796 4.9 14.2 1.0
C A:GLN112 4.9 14.9 1.0
N A:ARG149 4.9 11.0 1.0
CA A:GLY114 5.0 12.8 1.0
C A:ARG149 5.0 12.0 1.0

Iron binding site 3 out of 16 in 2ckj

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Iron binding site 3 out of 16 in the Human Milk Xanthine Oxidoreductase


Mono view


Stereo pair view

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

b:5.5
occ:1.00
 FE1 A:FES3002 0.0 5.5 1.0
S1 A:FES3002 2.2 4.0 1.0
S2 A:FES3002 2.2 3.0 1.0
SG A:CYS43 2.3 13.9 1.0
SG A:CYS48 2.4 6.5 1.0
FE2 A:FES3002 2.7 3.5 1.0
CB A:CYS48 3.1 10.7 1.0
N A:CYS48 3.1 13.4 1.0
N A:CYS43 3.3 10.8 1.0
CA A:CYS48 3.4 12.1 1.0
N A:GLY49 3.5 12.0 1.0
CB A:CYS43 3.6 11.6 1.0
C A:CYS48 3.8 12.5 1.0
CA A:CYS43 4.0 11.7 1.0
N A:GLY44 4.1 12.4 1.0
C A:GLY42 4.2 10.9 1.0
C A:GLY47 4.3 15.2 1.0
N A:GLY47 4.4 16.4 1.0
SG A:CYS51 4.4 5.0 1.0
N A:ALA50 4.4 10.5 1.0
CA A:GLY49 4.4 11.4 1.0
C A:GLY46 4.4 16.3 1.0
CA A:GLY42 4.5 10.7 1.0
N A:GLY46 4.5 15.9 1.0
N A:GLY42 4.6 10.0 1.0
C A:CYS43 4.6 11.9 1.0
O A:GLY46 4.7 17.1 1.0
SG A:CYS73 4.7 10.1 1.0
CA A:GLY47 4.8 15.6 1.0
O A:CYS48 4.8 13.5 1.0
CA A:GLY46 4.8 16.1 1.0
C A:GLY49 4.9 10.9 1.0

Iron binding site 4 out of 16 in 2ckj

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Iron binding site 4 out of 16 in the Human Milk Xanthine Oxidoreductase


Mono view


Stereo pair view

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

b:3.5
occ:1.00
 FE2 A:FES3002 0.0 3.5 1.0
S2 A:FES3002 2.2 3.0 1.0
S1 A:FES3002 2.2 4.0 1.0
SG A:CYS51 2.3 5.0 1.0
SG A:CYS73 2.4 10.1 1.0
FE1 A:FES3002 2.7 5.5 1.0
CB A:CYS51 3.1 6.7 1.0
CB A:CYS73 3.1 8.5 1.0
N A:GLY44 3.9 12.4 1.0
SG A:CYS43 4.1 13.9 1.0
CA A:GLY44 4.3 14.3 1.0
SG A:CYS48 4.4 6.5 1.0
CA A:CYS51 4.5 6.7 1.0
N A:CYS43 4.5 10.8 1.0
N A:CYS51 4.5 8.1 1.0
CA A:CYS73 4.6 8.1 1.0
N A:GLY42 4.7 10.0 1.0
N A:GLY46 4.7 15.9 1.0
CB A:ASN71 4.9 8.7 1.0
N A:CYS73 4.9 7.0 1.0
N A:ALA50 4.9 10.5 1.0
N A:GLY49 5.0 12.0 1.0

Iron binding site 5 out of 16 in 2ckj

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Iron binding site 5 out of 16 in the Human Milk Xanthine Oxidoreductase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Human Milk Xanthine Oxidoreductase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe3001

b:6.8
occ:1.00
 FE1 B:FES3001 0.0 6.8 1.0
S1 B:FES3001 2.2 7.2 1.0
S2 B:FES3001 2.2 10.2 1.0
SG B:CYS116 2.3 9.4 1.0
SG B:CYS148 2.4 7.9 1.0
FE2 B:FES3001 2.7 8.0 1.0
CB B:CYS148 3.4 9.8 1.0
CB B:CYS116 3.5 9.5 1.0
N B:CYS116 4.0 10.3 1.0
CA B:CYS148 4.1 9.4 1.0
CG2 B:THR151 4.2 13.2 1.0
N B:ARG149 4.3 10.5 1.0
CA B:CYS116 4.3 10.3 1.0
N B:CYS150 4.3 11.6 1.0
SG B:CYS113 4.5 14.7 1.0
C B:CYS148 4.6 10.1 1.0
CB B:CYS150 4.7 11.5 1.0
N B:PHE115 4.7 11.6 1.0
SG B:CYS150 4.7 5.1 1.0
N B:GLY114 4.9 12.3 1.0

Iron binding site 6 out of 16 in 2ckj

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Iron binding site 6 out of 16 in the Human Milk Xanthine Oxidoreductase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Human Milk Xanthine Oxidoreductase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe3001

b:8.0
occ:1.00
 FE2 B:FES3001 0.0 8.0 1.0
S2 B:FES3001 2.2 10.2 1.0
S1 B:FES3001 2.2 7.2 1.0
SG B:CYS113 2.3 14.7 1.0
SG B:CYS150 2.6 5.1 1.0
FE1 B:FES3001 2.7 6.8 1.0
CB B:CYS113 3.0 14.8 1.0
CB B:CYS150 3.3 11.5 1.0
CA B:CYS113 3.8 14.2 1.0
N B:CYS150 3.9 11.6 1.0
N B:CYS113 3.9 14.1 1.0
N B:GLY114 4.0 12.3 1.0
CA B:CYS150 4.2 11.3 1.0
SG B:CYS148 4.2 7.9 1.0
C B:CYS113 4.3 12.9 1.0
N B:PHE115 4.5 11.6 1.0
SG B:CYS116 4.8 9.4 1.0
N B:ARG149 4.9 10.5 1.0
C B:ARG149 4.9 12.2 1.0

Iron binding site 7 out of 16 in 2ckj

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Iron binding site 7 out of 16 in the Human Milk Xanthine Oxidoreductase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Human Milk Xanthine Oxidoreductase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe3002

b:4.7
occ:1.00
 FE1 B:FES3002 0.0 4.7 1.0
SG B:CYS43 2.1 13.1 1.0
S1 B:FES3002 2.2 2.0 1.0
S2 B:FES3002 2.2 2.1 1.0
SG B:CYS48 2.4 5.7 1.0
FE2 B:FES3002 2.6 2.8 1.0
N B:CYS43 3.2 10.9 1.0
CB B:CYS48 3.3 10.2 1.0
N B:CYS48 3.3 13.1 1.0
CB B:CYS43 3.5 11.3 1.0
N B:GLY49 3.6 12.1 1.0
CA B:CYS48 3.7 11.5 1.0
C B:CYS48 3.8 12.6 1.0
N B:GLY44 3.8 11.8 1.0
CA B:CYS43 3.9 11.3 1.0
N B:GLY47 4.1 16.8 1.0
C B:GLY42 4.2 11.2 1.0
C B:GLY46 4.3 17.4 1.0
C B:GLY47 4.4 14.7 1.0
C B:CYS43 4.4 11.3 1.0
N B:ALA50 4.4 10.4 1.0
SG B:CYS51 4.5 7.1 1.0
SG B:CYS73 4.5 11.9 1.0
CA B:GLY49 4.5 11.4 1.0
N B:GLY42 4.5 9.8 1.0
CA B:GLY42 4.6 10.6 1.0
N B:GLY46 4.6 15.7 1.0
CA B:GLY46 4.6 16.7 1.0
O B:CYS48 4.7 14.1 1.0
CA B:GLY47 4.7 15.8 1.0
O B:GLY46 4.7 18.0 1.0
CA B:GLY44 4.9 13.6 1.0
C B:GLY49 5.0 11.0 1.0
N B:GLU45 5.0 15.7 1.0

Iron binding site 8 out of 16 in 2ckj

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Iron binding site 8 out of 16 in the Human Milk Xanthine Oxidoreductase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Human Milk Xanthine Oxidoreductase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe3002

b:2.8
occ:1.00
 FE2 B:FES3002 0.0 2.8 1.0
S2 B:FES3002 2.1 2.1 1.0
S1 B:FES3002 2.1 2.0 1.0
SG B:CYS51 2.3 7.1 1.0
SG B:CYS73 2.5 11.9 1.0
FE1 B:FES3002 2.6 4.7 1.0
CB B:CYS51 3.1 6.6 1.0
CB B:CYS73 3.2 8.2 1.0
N B:GLY44 3.9 11.8 1.0
SG B:CYS43 4.1 13.1 1.0
CA B:CYS51 4.3 6.9 1.0
N B:CYS51 4.3 8.2 1.0
CA B:GLY44 4.3 13.6 1.0
SG B:CYS48 4.4 5.7 1.0
N B:CYS43 4.5 10.9 1.0
N B:GLY42 4.6 9.8 1.0
CA B:CYS73 4.6 7.7 1.0
N B:ALA50 4.8 10.4 1.0
CB B:ASN71 4.9 8.6 1.0
N B:GLY46 4.9 15.7 1.0
C B:CYS43 4.9 11.3 1.0
N B:CYS73 4.9 7.0 1.0
C B:GLY44 5.0 14.9 1.0

Iron binding site 9 out of 16 in 2ckj

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Iron binding site 9 out of 16 in the Human Milk Xanthine Oxidoreductase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of Human Milk Xanthine Oxidoreductase within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe3001

b:6.2
occ:1.00
 FE1 C:FES3001 0.0 6.2 1.0
S1 C:FES3001 2.2 8.7 1.0
S2 C:FES3001 2.2 8.9 1.0
SG C:CYS116 2.2 10.5 1.0
SG C:CYS148 2.4 6.7 1.0
FE2 C:FES3001 2.6 6.8 1.0
CB C:CYS148 3.0 9.7 1.0
CB C:CYS116 3.6 10.5 1.0
CA C:CYS148 3.9 9.4 1.0
N C:CYS116 4.1 10.1 1.0
N C:ARG149 4.1 10.8 1.0
N C:CYS150 4.3 11.8 1.0
C C:CYS148 4.4 10.3 1.0
CG2 C:THR151 4.5 13.3 1.0
CA C:CYS116 4.5 10.6 1.0
CB C:CYS150 4.6 12.3 1.0
SG C:CYS113 4.7 12.6 1.0
SG C:CYS150 4.8 7.7 1.0
N C:PHE115 4.9 11.4 1.0
CA C:CYS150 5.0 11.8 1.0

Iron binding site 10 out of 16 in 2ckj

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Iron binding site 10 out of 16 in the Human Milk Xanthine Oxidoreductase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of Human Milk Xanthine Oxidoreductase within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe3001

b:6.8
occ:1.00
 FE2 C:FES3001 0.0 6.8 1.0
S2 C:FES3001 2.2 8.9 1.0
S1 C:FES3001 2.2 8.7 1.0
SG C:CYS113 2.4 12.6 1.0
FE1 C:FES3001 2.6 6.2 1.0
SG C:CYS150 2.7 7.7 1.0
CB C:CYS113 3.0 14.5 1.0
CB C:CYS150 3.4 12.3 1.0
N C:GLY114 3.8 12.8 1.0
CA C:CYS113 3.9 13.8 1.0
N C:CYS150 3.9 11.8 1.0
N C:CYS113 4.0 14.3 1.0
C C:CYS113 4.3 13.4 1.0
CA C:CYS150 4.3 11.8 1.0
SG C:CYS148 4.4 6.7 1.0
N C:PHE115 4.5 11.4 1.0
SG C:CYS116 4.5 10.5 1.0
N C:ARG149 4.9 10.8 1.0
CA C:GLY114 4.9 12.5 1.0
N C:CYS116 4.9 10.1 1.0
C C:ARG149 5.0 12.4 1.0

Reference:

A.R.Pearson, B.L.J.Godber, R.Eisenthal, G.L.Taylor, R.Harrison. Human Milk Xanthine Dehydrogenase Is Incompletely Converted to the Oxidase Form in the Absence of Proteolysis. A Structural Explanation. To Be Published.
Page generated: Sat Aug 3 20:29:22 2024

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