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Iron in PDB 3uni: Crystal Structure of Bovine Milk Xanthine Dehydrogenase with Nadh Bound

Enzymatic activity of Crystal Structure of Bovine Milk Xanthine Dehydrogenase with Nadh Bound

All present enzymatic activity of Crystal Structure of Bovine Milk Xanthine Dehydrogenase with Nadh Bound:
1.17.1.4; 1.17.3.2;

Protein crystallography data

The structure of Crystal Structure of Bovine Milk Xanthine Dehydrogenase with Nadh Bound, PDB code: 3uni was solved by B.T.Eger, K.Okamoto, T.Nishino, E.F.Pai, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 2.20
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 100.036, 146.698, 107.016, 90.00, 106.03, 90.00
R / Rfree (%) 19.8 / 24

Other elements in 3uni:

The structure of Crystal Structure of Bovine Milk Xanthine Dehydrogenase with Nadh Bound 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 Crystal Structure of Bovine Milk Xanthine Dehydrogenase with Nadh Bound (pdb code 3uni). 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 Milk Xanthine Dehydrogenase with Nadh Bound, PDB code: 3uni:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iron binding site 1 out of 8 in 3uni

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Iron binding site 1 out of 8 in the Crystal Structure of Bovine Milk Xanthine Dehydrogenase with Nadh Bound


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 Milk Xanthine Dehydrogenase with Nadh Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe1333

b:13.9
occ:1.00
 FE1 A:FES1333 0.0 13.9 1.0
S2 A:FES1333 2.2 13.3 1.0
S1 A:FES1333 2.3 13.2 1.0
SG A:CYS150 2.3 13.7 1.0
SG A:CYS113 2.3 15.1 1.0
FE2 A:FES1333 2.7 12.9 1.0
CB A:CYS113 3.2 12.9 1.0
CB A:CYS150 3.3 10.1 1.0
N A:CYS113 3.5 15.3 1.0
O A:HOH1770 3.5 15.1 1.0
N A:GLY114 3.7 15.1 1.0
CA A:CYS113 3.8 15.1 1.0
N A:CYS150 4.0 12.2 1.0
C A:CYS113 4.2 16.1 1.0
CA A:CYS150 4.3 9.5 1.0
N A:PHE115 4.4 12.7 1.0
SG A:CYS148 4.4 13.5 1.0
SG A:CYS116 4.5 11.3 1.0
C A:GLN112 4.7 15.6 1.0
CA A:GLY114 4.7 13.2 1.0
N A:ARG149 4.7 14.7 1.0
CB A:GLN112 4.8 15.0 1.0
N A:CYS116 4.9 14.6 1.0
C A:GLY114 4.9 13.4 1.0

Iron binding site 2 out of 8 in 3uni

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Iron binding site 2 out of 8 in the Crystal Structure of Bovine Milk Xanthine Dehydrogenase with Nadh Bound


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 Milk Xanthine Dehydrogenase with Nadh Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe1333

b:12.9
occ:1.00
 FE2 A:FES1333 0.0 12.9 1.0
SG A:CYS116 2.1 11.3 1.0
S1 A:FES1333 2.2 13.2 1.0
S2 A:FES1333 2.2 13.3 1.0
SG A:CYS148 2.5 13.5 1.0
FE1 A:FES1333 2.7 13.9 1.0
CB A:CYS148 3.3 14.5 1.0
CB A:CYS116 3.4 13.6 1.0
CA A:CYS148 3.7 15.1 1.0
N A:ARG149 4.2 14.7 1.0
N A:CYS116 4.2 14.6 1.0
O A:HOH1767 4.3 10.2 1.0
C A:CYS148 4.3 15.3 1.0
CA A:CYS116 4.3 14.0 1.0
N A:CYS150 4.4 12.2 1.0
SG A:CYS150 4.5 13.7 1.0
CB A:CYS150 4.5 10.1 1.0
SG A:CYS113 4.7 15.1 1.0
O A:LEU147 4.8 13.9 1.0
CG2 A:THR151 4.9 10.4 1.0
N A:GLY114 4.9 15.1 1.0
C A:CYS116 4.9 13.1 1.0
N A:THR117 5.0 12.6 1.0
N A:CYS148 5.0 13.6 1.0

Iron binding site 3 out of 8 in 3uni

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Iron binding site 3 out of 8 in the Crystal Structure of Bovine Milk Xanthine Dehydrogenase with Nadh Bound


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 Milk Xanthine Dehydrogenase with Nadh Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe1334

b:17.2
occ:1.00
 FE1 A:FES1334 0.0 17.2 1.0
SG A:CYS73 2.2 16.6 1.0
S2 A:FES1334 2.2 15.8 1.0
SG A:CYS51 2.3 17.1 1.0
S1 A:FES1334 2.3 14.7 1.0
FE2 A:FES1334 2.8 16.4 1.0
CB A:CYS73 3.1 17.7 1.0
CB A:CYS51 3.2 14.2 1.0
CB A:ASN71 4.2 15.3 1.0
ND2 A:ASN71 4.2 15.0 1.0
N A:CYS73 4.2 15.8 1.0
N A:CYS51 4.2 14.5 1.0
CA A:CYS73 4.2 17.4 1.0
N A:GLY44 4.3 15.4 1.0
CA A:CYS51 4.3 13.3 1.0
N A:GLY46 4.4 17.6 1.0
CA A:GLY44 4.5 15.4 1.0
SG A:CYS48 4.5 14.4 1.0
SG A:CYS43 4.5 17.3 1.0
CG A:ASN71 4.6 16.6 1.0
CA A:GLY46 4.6 14.2 1.0
C A:GLY44 4.9 17.6 1.0
N A:GLY49 4.9 13.9 1.0
N A:GLU45 4.9 16.8 1.0
CA A:ASN71 4.9 15.6 1.0

Iron binding site 4 out of 8 in 3uni

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Iron binding site 4 out of 8 in the Crystal Structure of Bovine Milk Xanthine Dehydrogenase with Nadh Bound


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 Milk Xanthine Dehydrogenase with Nadh Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe1334

b:16.4
occ:1.00
 FE2 A:FES1334 0.0 16.4 1.0
SG A:CYS48 2.1 14.4 1.0
S1 A:FES1334 2.2 14.7 1.0
S2 A:FES1334 2.4 15.8 1.0
SG A:CYS43 2.4 17.3 1.0
FE1 A:FES1334 2.8 17.2 1.0
N A:CYS43 3.4 13.7 1.0
N A:CYS48 3.4 14.0 1.0
CB A:CYS48 3.4 13.2 1.0
CB A:CYS43 3.5 14.9 1.0
N A:GLY49 3.7 13.9 1.0
N A:GLY44 3.7 15.4 1.0
CA A:CYS48 3.8 12.7 1.0
CA A:CYS43 3.9 14.4 1.0
C A:GLY42 4.1 12.1 1.0
C A:CYS48 4.2 12.2 1.0
C A:CYS43 4.3 15.1 1.0
N A:GLY42 4.3 13.4 1.0
N A:GLY47 4.3 13.4 1.0
N A:ALA50 4.3 14.7 1.0
CA A:GLY42 4.3 12.3 1.0
SG A:CYS73 4.4 16.6 1.0
C A:GLY47 4.5 15.8 1.0
N A:GLY46 4.5 17.6 1.0
N A:GLU45 4.6 16.8 1.0
SG A:CYS51 4.7 17.1 1.0
CA A:GLY49 4.7 14.2 1.0
CA A:GLY44 4.7 15.4 1.0
C A:GLY46 4.8 13.6 1.0
CA A:GLY47 4.9 15.0 1.0
CA A:GLY46 4.9 14.2 1.0
C A:GLY49 4.9 15.5 1.0
N A:CYS51 5.0 14.5 1.0

Iron binding site 5 out of 8 in 3uni

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Iron binding site 5 out of 8 in the Crystal Structure of Bovine Milk Xanthine Dehydrogenase with Nadh Bound


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 Milk Xanthine Dehydrogenase with Nadh Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe1333

b:13.7
occ:1.00
 FE1 B:FES1333 0.0 13.7 1.0
S2 B:FES1333 2.1 11.3 1.0
S1 B:FES1333 2.2 11.6 1.0
SG B:CYS150 2.3 17.7 1.0
SG B:CYS113 2.4 15.7 1.0
FE2 B:FES1333 2.6 12.6 1.0
CB B:CYS113 3.2 14.6 1.0
CB B:CYS150 3.3 15.8 1.0
N B:CYS113 3.5 16.6 1.0
O B:HOH1562 3.6 13.9 1.0
N B:GLY114 3.7 14.7 1.0
CA B:CYS113 3.8 15.6 1.0
N B:CYS150 4.1 16.6 1.0
C B:CYS113 4.2 16.4 1.0
CA B:CYS150 4.3 15.2 1.0
N B:PHE115 4.4 12.7 1.0
SG B:CYS148 4.4 13.2 1.0
SG B:CYS116 4.5 11.8 1.0
C B:GLN112 4.6 17.8 1.0
CA B:GLY114 4.6 12.5 1.0
N B:ARG149 4.7 17.8 1.0
CB B:GLN112 4.8 17.4 1.0
N B:CYS116 4.9 13.9 1.0
C B:GLY114 4.9 12.1 1.0
N B:GLN112 5.0 16.1 1.0

Iron binding site 6 out of 8 in 3uni

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Iron binding site 6 out of 8 in the Crystal Structure of Bovine Milk Xanthine Dehydrogenase with Nadh Bound


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 Milk Xanthine Dehydrogenase with Nadh Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe1333

b:12.6
occ:1.00
 FE2 B:FES1333 0.0 12.6 1.0
S1 B:FES1333 2.1 11.6 1.0
S2 B:FES1333 2.1 11.3 1.0
SG B:CYS116 2.2 11.8 1.0
SG B:CYS148 2.5 13.2 1.0
FE1 B:FES1333 2.6 13.7 1.0
CB B:CYS116 3.3 13.6 1.0
CB B:CYS148 3.4 14.0 1.0
CA B:CYS148 3.7 16.3 1.0
N B:ARG149 4.1 17.8 1.0
N B:CYS116 4.2 13.9 1.0
O B:HOH1565 4.3 9.4 1.0
CA B:CYS116 4.3 14.0 1.0
C B:CYS148 4.3 17.9 1.0
N B:CYS150 4.4 16.6 1.0
SG B:CYS150 4.4 17.7 1.0
CB B:CYS150 4.4 15.8 1.0
SG B:CYS113 4.6 15.7 1.0
N B:GLY114 4.8 14.7 1.0
CG2 B:THR151 4.9 16.7 1.0
O B:LEU147 4.9 16.4 1.0
C B:CYS116 5.0 13.5 1.0
CA B:CYS150 5.0 15.2 1.0
N B:THR117 5.0 13.7 1.0

Iron binding site 7 out of 8 in 3uni

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Iron binding site 7 out of 8 in the Crystal Structure of Bovine Milk Xanthine Dehydrogenase with Nadh Bound


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 Milk Xanthine Dehydrogenase with Nadh Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe1334

b:16.3
occ:1.00
 FE1 B:FES1334 0.0 16.3 1.0
SG B:CYS73 2.2 16.5 1.0
S2 B:FES1334 2.3 17.2 1.0
S1 B:FES1334 2.3 14.7 1.0
SG B:CYS51 2.4 17.2 1.0
FE2 B:FES1334 2.8 14.8 1.0
CB B:CYS73 3.1 17.9 1.0
CB B:CYS51 3.4 14.6 1.0
ND2 B:ASN71 4.2 15.2 1.0
CB B:ASN71 4.2 16.8 1.0
N B:GLY46 4.3 18.9 1.0
N B:CYS73 4.3 17.5 1.0
N B:CYS51 4.3 14.0 1.0
CA B:CYS73 4.3 17.6 1.0
N B:GLY44 4.3 16.8 1.0
CA B:CYS51 4.4 14.8 1.0
SG B:CYS43 4.5 16.0 1.0
CA B:GLY46 4.5 18.2 1.0
SG B:CYS48 4.5 11.4 1.0
CA B:GLY44 4.5 16.1 1.0
CG B:ASN71 4.6 17.6 1.0
N B:GLU45 4.8 17.9 1.0
N B:GLY49 4.9 14.7 1.0
C B:GLY44 4.9 18.0 1.0
CA B:ASN71 5.0 16.4 1.0

Iron binding site 8 out of 8 in 3uni

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Iron binding site 8 out of 8 in the Crystal Structure of Bovine Milk Xanthine Dehydrogenase with Nadh Bound


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 Milk Xanthine Dehydrogenase with Nadh Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe1334

b:14.8
occ:1.00
 FE2 B:FES1334 0.0 14.8 1.0
SG B:CYS48 2.1 11.4 1.0
S1 B:FES1334 2.1 14.7 1.0
S2 B:FES1334 2.4 17.2 1.0
SG B:CYS43 2.5 16.0 1.0
FE1 B:FES1334 2.8 16.3 1.0
CB B:CYS48 3.4 16.3 1.0
N B:CYS48 3.4 16.7 1.0
N B:CYS43 3.4 13.8 1.0
N B:GLY49 3.7 14.7 1.0
CB B:CYS43 3.7 15.3 1.0
CA B:CYS48 3.8 14.8 1.0
N B:GLY44 3.8 16.8 1.0
CA B:CYS43 4.0 16.1 1.0
C B:CYS48 4.1 14.2 1.0
C B:GLY42 4.1 12.9 1.0
N B:GLY42 4.2 15.6 1.0
N B:ALA50 4.3 14.3 1.0
CA B:GLY42 4.3 14.3 1.0
N B:GLY47 4.3 17.9 1.0
C B:CYS43 4.4 15.9 1.0
N B:GLY46 4.5 18.9 1.0
SG B:CYS73 4.5 16.5 1.0
C B:GLY47 4.6 19.0 1.0
N B:GLU45 4.6 17.9 1.0
CA B:GLY49 4.6 14.0 1.0
SG B:CYS51 4.7 17.2 1.0
C B:GLY46 4.7 17.9 1.0
CA B:GLY46 4.8 18.2 1.0
CA B:GLY44 4.8 16.1 1.0
C B:GLY49 4.9 15.2 1.0
CB B:ALA50 5.0 15.6 1.0
CA B:GLY47 5.0 16.9 1.0
N B:CYS51 5.0 14.0 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 21:16:17 2024

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