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Iron in PDB 3ax9: Bovine Xanthine Oxidase, Protease Cleaved Form

Enzymatic activity of Bovine Xanthine Oxidase, Protease Cleaved Form

All present enzymatic activity of Bovine Xanthine Oxidase, Protease Cleaved Form:
1.17.1.4; 1.17.3.2;

Protein crystallography data

The structure of Bovine Xanthine Oxidase, Protease Cleaved Form, PDB code: 3ax9 was solved by H.Ishikita, B.T.Eger, E.F.Pai, K.Okamoto, T.Nishino, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 38.13 / 2.30
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 133.196, 72.966, 142.261, 90.00, 98.84, 90.00
R / Rfree (%) 21.5 / 27.9

Other elements in 3ax9:

The structure of Bovine Xanthine Oxidase, Protease Cleaved 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 Oxidase, Protease Cleaved Form (pdb code 3ax9). 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 Oxidase, Protease Cleaved Form, PDB code: 3ax9:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iron binding site 1 out of 8 in 3ax9

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Iron binding site 1 out of 8 in the Bovine Xanthine Oxidase, Protease Cleaved 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 Oxidase, Protease Cleaved Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe1333

b:18.9
occ:1.00
 FE1 A:FES1333 0.0 18.9 1.0
S1 A:FES1333 2.2 21.9 1.0
S2 A:FES1333 2.2 22.0 1.0
SG A:CYS150 2.3 19.0 1.0
SG A:CYS113 2.4 14.8 1.0
FE2 A:FES1333 2.7 20.9 1.0
CB A:CYS113 3.3 18.1 1.0
CB A:CYS150 3.3 17.8 1.0
N A:CYS113 3.6 18.0 1.0
O A:HOH1379 3.7 11.2 1.0
CA A:CYS113 3.8 17.6 1.0
N A:GLY114 4.0 17.9 1.0
N A:CYS150 4.1 19.4 1.0
SG A:CYS148 4.3 21.6 1.0
C A:CYS113 4.3 18.2 1.0
CA A:CYS150 4.4 18.5 1.0
N A:PHE115 4.5 17.3 1.0
N A:ARG149 4.7 19.9 1.0
SG A:CYS116 4.7 15.7 1.0
C A:GLN112 4.7 17.8 1.0
CB A:GLN112 4.9 19.0 1.0
N A:CYS116 5.0 17.6 1.0
CA A:GLY114 5.0 17.4 1.0

Iron binding site 2 out of 8 in 3ax9

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Iron binding site 2 out of 8 in the Bovine Xanthine Oxidase, Protease Cleaved 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 Oxidase, Protease Cleaved Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe1333

b:20.9
occ:1.00
 FE2 A:FES1333 0.0 20.9 1.0
S1 A:FES1333 2.1 21.9 1.0
S2 A:FES1333 2.2 22.0 1.0
SG A:CYS116 2.3 15.7 1.0
SG A:CYS148 2.3 21.6 1.0
FE1 A:FES1333 2.7 18.9 1.0
CB A:CYS148 3.2 21.6 1.0
CB A:CYS116 3.3 17.1 1.0
CA A:CYS148 3.6 21.1 1.0
N A:ARG149 4.0 19.9 1.0
N A:CYS116 4.2 17.6 1.0
O A:HOH1456 4.3 27.6 1.0
C A:CYS148 4.3 21.5 1.0
CA A:CYS116 4.4 17.2 1.0
CB A:CYS150 4.4 17.8 1.0
SG A:CYS150 4.4 19.0 1.0
N A:CYS150 4.5 19.4 1.0
CG2 A:THR151 4.6 16.9 1.0
SG A:CYS113 4.7 14.8 1.0
N A:CYS148 4.9 21.1 1.0
O A:LEU147 5.0 21.3 1.0

Iron binding site 3 out of 8 in 3ax9

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Iron binding site 3 out of 8 in the Bovine Xanthine Oxidase, Protease Cleaved 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 Oxidase, Protease Cleaved Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe1334

b:19.0
occ:1.00
 FE1 A:FES1334 0.0 19.0 1.0
S1 A:FES1334 2.2 18.9 1.0
S2 A:FES1334 2.2 18.1 1.0
SG A:CYS51 2.2 19.2 1.0
SG A:CYS73 2.4 20.2 1.0
FE2 A:FES1334 2.9 19.2 1.0
CB A:CYS73 3.1 20.6 1.0
CB A:CYS51 3.4 17.0 1.0
CB A:ASN71 4.1 19.1 1.0
N A:CYS73 4.2 20.8 1.0
CA A:CYS73 4.3 20.9 1.0
SG A:CYS43 4.3 18.8 1.0
N A:GLY44 4.4 20.5 1.0
N A:GLY46 4.4 21.9 1.0
CG A:ASN71 4.5 18.1 1.0
N A:CYS51 4.5 17.4 1.0
OD1 A:ASN71 4.5 20.0 1.0
CA A:CYS51 4.5 17.1 1.0
SG A:CYS48 4.6 13.0 1.0
CA A:GLY44 4.7 21.6 1.0
CA A:GLY46 4.7 21.6 1.0
N A:GLY49 4.8 16.0 1.0
CA A:ASN71 4.8 19.1 1.0
N A:GLU45 4.9 21.1 1.0

Iron binding site 4 out of 8 in 3ax9

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Iron binding site 4 out of 8 in the Bovine Xanthine Oxidase, Protease Cleaved 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 Oxidase, Protease Cleaved Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe1334

b:19.2
occ:1.00
 FE2 A:FES1334 0.0 19.2 1.0
S2 A:FES1334 2.2 18.1 1.0
S1 A:FES1334 2.2 18.9 1.0
SG A:CYS48 2.2 13.0 1.0
SG A:CYS43 2.3 18.8 1.0
FE1 A:FES1334 2.9 19.0 1.0
CB A:CYS48 3.3 15.8 1.0
CB A:CYS43 3.4 20.8 1.0
N A:CYS48 3.5 18.3 1.0
N A:CYS43 3.5 19.5 1.0
N A:GLY49 3.8 16.0 1.0
CA A:CYS48 3.8 17.1 1.0
N A:GLY44 3.9 20.5 1.0
CA A:CYS43 3.9 20.2 1.0
C A:GLY42 4.1 20.7 1.0
C A:CYS48 4.2 16.8 1.0
N A:GLY47 4.3 20.4 1.0
C A:CYS43 4.4 20.9 1.0
N A:GLY42 4.4 19.4 1.0
CA A:GLY42 4.4 19.5 1.0
N A:GLY46 4.5 21.9 1.0
N A:ALA50 4.6 15.3 1.0
SG A:CYS73 4.6 20.2 1.0
SG A:CYS51 4.6 19.2 1.0
C A:GLY47 4.7 19.2 1.0
N A:GLU45 4.7 21.1 1.0
O A:GLY42 4.8 22.5 1.0
C A:GLY46 4.8 21.8 1.0
CA A:GLY49 4.8 16.1 1.0
CA A:GLY46 4.9 21.6 1.0
CA A:GLY44 4.9 21.6 1.0
CA A:GLY47 5.0 19.8 1.0

Iron binding site 5 out of 8 in 3ax9

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Iron binding site 5 out of 8 in the Bovine Xanthine Oxidase, Protease Cleaved 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 Oxidase, Protease Cleaved Form within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe1333

b:20.3
occ:1.00
 FE1 B:FES1333 0.0 20.3 1.0
S2 B:FES1333 2.1 22.2 1.0
S1 B:FES1333 2.2 21.9 1.0
SG B:CYS150 2.3 21.8 1.0
SG B:CYS113 2.3 21.3 1.0
FE2 B:FES1333 2.8 20.5 1.0
CB B:CYS113 3.2 21.5 1.0
CB B:CYS150 3.2 22.7 1.0
N B:CYS113 3.5 20.4 1.0
CA B:CYS113 3.8 20.7 1.0
N B:GLY114 3.9 20.8 1.0
O B:HOH1526 3.9 28.1 1.0
N B:CYS150 4.0 21.7 1.0
SG B:CYS148 4.1 23.1 1.0
C B:CYS113 4.2 20.8 1.0
CA B:CYS150 4.3 22.0 1.0
N B:PHE115 4.4 20.6 1.0
C B:GLN112 4.6 20.5 1.0
N B:ARG149 4.8 20.5 1.0
SG B:CYS116 4.9 19.0 1.0
CB B:GLN112 4.9 20.6 1.0
CA B:GLY114 4.9 19.6 1.0
N B:GLN112 5.0 19.6 1.0

Iron binding site 6 out of 8 in 3ax9

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Iron binding site 6 out of 8 in the Bovine Xanthine Oxidase, Protease Cleaved 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 Oxidase, Protease Cleaved Form within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe1333

b:20.5
occ:1.00
 FE2 B:FES1333 0.0 20.5 1.0
S1 B:FES1333 2.1 21.9 1.0
SG B:CYS148 2.2 23.1 1.0
S2 B:FES1333 2.2 22.2 1.0
SG B:CYS116 2.4 19.0 1.0
FE1 B:FES1333 2.8 20.3 1.0
CB B:CYS148 3.2 20.1 1.0
CB B:CYS116 3.6 20.2 1.0
CA B:CYS148 3.7 20.9 1.0
N B:CYS116 4.2 21.8 1.0
N B:ARG149 4.2 20.5 1.0
C B:CYS148 4.4 21.1 1.0
CA B:CYS116 4.4 21.2 1.0
N B:CYS150 4.5 21.7 1.0
CB B:CYS150 4.6 22.7 1.0
SG B:CYS150 4.6 21.8 1.0
CG2 B:THR151 4.6 22.6 1.0
SG B:CYS113 4.7 21.3 1.0
N B:PHE115 4.9 20.6 1.0
N B:CYS148 5.0 20.5 1.0

Iron binding site 7 out of 8 in 3ax9

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Iron binding site 7 out of 8 in the Bovine Xanthine Oxidase, Protease Cleaved 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 Oxidase, Protease Cleaved Form within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe1334

b:21.6
occ:1.00
 FE1 B:FES1334 0.0 21.6 1.0
S1 B:FES1334 2.1 19.0 1.0
SG B:CYS51 2.2 25.9 1.0
S2 B:FES1334 2.2 21.4 1.0
SG B:CYS73 2.2 18.5 1.0
FE2 B:FES1334 2.9 22.6 1.0
CB B:CYS73 3.2 21.9 1.0
CB B:CYS51 3.5 21.7 1.0
CB B:ASN71 4.0 23.2 1.0
N B:CYS73 4.2 21.8 1.0
CA B:CYS73 4.3 22.0 1.0
N B:GLY44 4.3 20.0 1.0
CG B:ASN71 4.3 25.4 1.0
SG B:CYS43 4.4 18.3 1.0
N B:GLY46 4.5 24.6 1.0
N B:CYS51 4.5 19.8 1.0
OD1 B:ASN71 4.5 27.4 1.0
CA B:GLY44 4.6 21.3 1.0
CA B:CYS51 4.6 20.9 1.0
CA B:GLY46 4.6 24.5 1.0
SG B:CYS48 4.7 21.9 1.0
CA B:ASN71 4.8 22.8 1.0
N B:GLY49 4.8 20.2 1.0
ND2 B:ASN71 4.9 29.5 1.0
C B:ASN71 4.9 22.3 1.0
N B:ALA72 5.0 21.9 1.0

Iron binding site 8 out of 8 in 3ax9

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Iron binding site 8 out of 8 in the Bovine Xanthine Oxidase, Protease Cleaved 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 Oxidase, Protease Cleaved Form within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe1334

b:22.6
occ:1.00
 FE2 B:FES1334 0.0 22.6 1.0
S2 B:FES1334 2.2 21.4 1.0
SG B:CYS48 2.2 21.9 1.0
S1 B:FES1334 2.2 19.0 1.0
SG B:CYS43 2.3 18.3 1.0
FE1 B:FES1334 2.9 21.6 1.0
N B:CYS43 3.2 18.1 1.0
CB B:CYS43 3.3 18.0 1.0
CB B:CYS48 3.5 21.6 1.0
N B:CYS48 3.5 23.1 1.0
CA B:CYS43 3.7 18.8 1.0
N B:GLY44 3.8 20.0 1.0
CA B:CYS48 3.8 21.9 1.0
N B:GLY49 3.9 20.2 1.0
C B:GLY42 3.9 19.9 1.0
C B:CYS43 4.2 19.1 1.0
CA B:GLY42 4.2 19.3 1.0
C B:CYS48 4.2 20.9 1.0
N B:GLY42 4.2 19.1 1.0
N B:GLY47 4.4 24.5 1.0
SG B:CYS73 4.4 18.5 1.0
N B:ALA50 4.4 19.0 1.0
N B:GLY46 4.5 24.6 1.0
SG B:CYS51 4.6 25.9 1.0
C B:GLY47 4.7 24.2 1.0
N B:GLU45 4.7 22.8 1.0
O B:GLY42 4.8 19.9 1.0
CA B:GLY49 4.8 19.7 1.0
CA B:GLY44 4.8 21.3 1.0
C B:GLY46 4.9 24.9 1.0
CA B:GLY46 4.9 24.5 1.0

Reference:

H.Ishikita, B.T.Eger, K.Okamoto, T.Nishino, E.F.Pai. Protein Conformational Gating of Enzymatic Activity in Xanthine Oxidoreductase J.Am.Chem.Soc. V. 134 999 2012.
ISSN: ISSN 0002-7863
PubMed: 22145797
DOI: 10.1021/JA207173P
Page generated: Sun Aug 4 07:25:40 2024

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