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Iron in PDB 4ysw: Structure of Rat Xanthine Oxidoreductase, C-Terminal Deletion Protein Variant, Nadh Bound Form

Enzymatic activity of Structure of Rat Xanthine Oxidoreductase, C-Terminal Deletion Protein Variant, Nadh Bound Form

All present enzymatic activity of Structure of Rat Xanthine Oxidoreductase, C-Terminal Deletion Protein Variant, Nadh Bound Form:
1.17.1.4; 1.17.3.2;

Protein crystallography data

The structure of Structure of Rat Xanthine Oxidoreductase, C-Terminal Deletion Protein Variant, Nadh Bound Form, PDB code: 4ysw was solved by T.Nishino, K.Okamoto, Y.Kawaguchi, T.Matsumura, B.T.Eger, E.F.Pai, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 42.41 / 1.99
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 98.460, 137.643, 222.067, 90.00, 90.00, 90.00
R / Rfree (%) 18.1 / 21.9

Other elements in 4ysw:

The structure of Structure of Rat Xanthine Oxidoreductase, C-Terminal Deletion Protein Variant, Nadh Bound Form also contains other interesting chemical elements:

Calcium (Ca) 2 atoms

Iron Binding Sites:

The binding sites of Iron atom in the Structure of Rat Xanthine Oxidoreductase, C-Terminal Deletion Protein Variant, Nadh Bound Form (pdb code 4ysw). 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 Rat Xanthine Oxidoreductase, C-Terminal Deletion Protein Variant, Nadh Bound Form, PDB code: 4ysw:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iron binding site 1 out of 8 in 4ysw

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Iron binding site 1 out of 8 in the Structure of Rat Xanthine Oxidoreductase, C-Terminal Deletion Protein Variant, Nadh Bound Form


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Structure of Rat Xanthine Oxidoreductase, C-Terminal Deletion Protein Variant, Nadh Bound Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe3001

b:26.7
occ:1.00
 FE1 A:FES3001 0.0 26.7 1.0
S2 A:FES3001 2.2 26.9 1.0
S1 A:FES3001 2.2 28.6 1.0
SG A:CYS112 2.2 19.9 1.0
SG A:CYS149 2.7 28.7 1.0
FE2 A:FES3001 2.9 26.8 1.0
CB A:CYS112 3.2 19.3 1.0
CB A:CYS149 3.4 23.1 1.0
O A:HOH3596 3.6 20.9 1.0
N A:CYS112 3.7 19.9 1.0
CA A:CYS112 3.8 19.2 1.0
N A:GLY113 3.9 17.7 1.0
N A:CYS149 4.2 22.1 1.0
C A:CYS112 4.2 18.7 1.0
N A:PHE114 4.4 15.6 1.0
CA A:CYS149 4.4 23.2 1.0
SG A:CYS147 4.5 23.1 1.0
SG A:CYS115 4.5 20.6 1.0
C A:GLN111 4.8 20.3 1.0
N A:ARG148 4.8 21.6 1.0
N A:CYS115 4.9 15.5 1.0
CA A:GLY113 5.0 16.4 1.0

Iron binding site 2 out of 8 in 4ysw

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Iron binding site 2 out of 8 in the Structure of Rat Xanthine Oxidoreductase, C-Terminal Deletion Protein Variant, Nadh Bound Form


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Structure of Rat Xanthine Oxidoreductase, C-Terminal Deletion Protein Variant, Nadh Bound Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe3001

b:26.8
occ:1.00
 FE2 A:FES3001 0.0 26.8 1.0
SG A:CYS115 2.1 20.6 1.0
S2 A:FES3001 2.2 26.9 1.0
S1 A:FES3001 2.2 28.6 1.0
SG A:CYS147 2.3 23.1 1.0
FE1 A:FES3001 2.9 26.7 1.0
CB A:CYS147 3.3 21.6 1.0
CB A:CYS115 3.3 16.2 1.0
CA A:CYS147 3.6 21.5 1.0
N A:ARG148 4.1 21.6 1.0
N A:CYS115 4.2 15.5 1.0
C A:CYS147 4.3 21.5 1.0
O A:HOH3196 4.3 15.5 1.0
CA A:CYS115 4.4 15.8 1.0
N A:CYS149 4.4 22.1 1.0
CB A:CYS149 4.5 23.1 1.0
CG2 A:THR150 4.7 22.8 1.0
SG A:CYS112 4.8 19.9 1.0
SG A:CYS149 4.8 28.7 1.0
O A:LEU146 4.8 20.1 1.0
N A:CYS147 4.9 21.2 1.0
CA A:CYS149 5.0 23.2 1.0
C A:CYS115 5.0 15.4 1.0

Iron binding site 3 out of 8 in 4ysw

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Iron binding site 3 out of 8 in the Structure of Rat Xanthine Oxidoreductase, C-Terminal Deletion Protein Variant, Nadh Bound Form


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Structure of Rat Xanthine Oxidoreductase, C-Terminal Deletion Protein Variant, Nadh Bound Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe3002

b:17.6
occ:1.00
 FE1 A:FES3002 0.0 17.6 1.0
S2 A:FES3002 2.2 19.0 1.0
S1 A:FES3002 2.2 19.6 1.0
SG A:CYS51 2.3 15.8 1.0
SG A:CYS73 2.3 18.2 1.0
FE2 A:FES3002 2.9 18.1 1.0
CB A:CYS73 3.1 18.8 1.0
CB A:CYS51 3.4 15.0 1.0
OD1 A:ASN71 4.2 19.9 1.0
N A:CYS73 4.2 17.9 1.0
CB A:ASN71 4.2 18.2 1.0
CA A:CYS73 4.3 18.8 1.0
N A:CYS51 4.3 14.8 1.0
N A:GLY46 4.3 20.1 1.0
N A:GLY44 4.4 18.8 1.0
CA A:CYS51 4.4 15.3 1.0
SG A:CYS43 4.5 18.6 1.0
CG A:ASN71 4.6 18.8 1.0
CA A:GLY44 4.6 19.0 1.0
CA A:GLY46 4.6 19.9 1.0
SG A:CYS48 4.7 16.1 1.0
N A:GLU45 4.7 19.5 1.0
C A:GLY44 4.9 19.5 1.0
N A:GLY49 4.9 15.7 1.0
CA A:ASN71 4.9 18.2 1.0
N A:ALA50 5.0 14.7 1.0

Iron binding site 4 out of 8 in 4ysw

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Iron binding site 4 out of 8 in the Structure of Rat Xanthine Oxidoreductase, C-Terminal Deletion Protein Variant, Nadh Bound Form


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Structure of Rat Xanthine Oxidoreductase, C-Terminal Deletion Protein Variant, Nadh Bound Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe3002

b:18.1
occ:1.00
 FE2 A:FES3002 0.0 18.1 1.0
SG A:CYS48 2.2 16.1 1.0
S2 A:FES3002 2.2 19.0 1.0
S1 A:FES3002 2.2 19.6 1.0
SG A:CYS43 2.4 18.6 1.0
FE1 A:FES3002 2.9 17.6 1.0
CB A:CYS48 3.4 16.8 1.0
N A:CYS43 3.4 18.2 1.0
N A:CYS48 3.5 17.8 1.0
CB A:CYS43 3.5 18.6 1.0
N A:GLY49 3.8 15.7 1.0
N A:GLY44 3.8 18.8 1.0
CA A:CYS48 3.9 16.7 1.0
CA A:CYS43 3.9 18.6 1.0
C A:GLY42 4.1 17.9 1.0
C A:CYS48 4.2 16.2 1.0
N A:ALA50 4.3 14.7 1.0
N A:GLY42 4.3 17.3 1.0
C A:CYS43 4.3 18.9 1.0
CA A:GLY42 4.3 17.4 1.0
N A:GLY47 4.3 19.3 1.0
N A:GLY46 4.5 20.1 1.0
SG A:CYS73 4.6 18.2 1.0
N A:GLU45 4.6 19.5 1.0
SG A:CYS51 4.7 15.8 1.0
C A:GLY47 4.7 19.0 1.0
CA A:GLY49 4.7 15.2 1.0
CA A:GLY44 4.8 19.0 1.0
C A:GLY46 4.9 19.7 1.0
CB A:ALA50 4.9 14.5 1.0
O A:GLY42 4.9 18.0 1.0
C A:GLY49 5.0 14.8 1.0
CA A:GLY47 5.0 19.5 1.0
CA A:GLY46 5.0 19.9 1.0

Iron binding site 5 out of 8 in 4ysw

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Iron binding site 5 out of 8 in the Structure of Rat Xanthine Oxidoreductase, C-Terminal Deletion Protein Variant, Nadh Bound Form


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Structure of Rat Xanthine Oxidoreductase, C-Terminal Deletion Protein Variant, Nadh Bound Form within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe4001

b:24.4
occ:1.00
 FE1 B:FES4001 0.0 24.4 1.0
S2 B:FES4001 2.2 24.1 1.0
S1 B:FES4001 2.2 25.3 1.0
SG B:CYS112 2.2 17.7 1.0
SG B:CYS149 2.8 26.3 1.0
FE2 B:FES4001 2.8 24.0 1.0
CB B:CYS112 3.2 17.8 1.0
CB B:CYS149 3.3 20.8 1.0
N B:CYS112 3.6 18.2 1.0
O B:HOH4717 3.6 17.2 1.0
CA B:CYS112 3.8 17.9 1.0
N B:GLY113 3.9 16.6 1.0
N B:CYS149 4.2 18.8 1.0
C B:CYS112 4.3 17.4 1.0
CA B:CYS149 4.4 20.5 1.0
N B:PHE114 4.5 14.4 1.0
SG B:CYS147 4.5 19.1 1.0
SG B:CYS115 4.6 19.2 1.0
C B:GLN111 4.7 18.8 1.0
N B:ARG148 4.8 17.3 1.0
CB B:GLN111 4.8 19.4 1.0
CA B:GLY113 4.9 15.3 1.0
N B:CYS115 5.0 13.7 1.0

Iron binding site 6 out of 8 in 4ysw

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Iron binding site 6 out of 8 in the Structure of Rat Xanthine Oxidoreductase, C-Terminal Deletion Protein Variant, Nadh Bound Form


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Structure of Rat Xanthine Oxidoreductase, C-Terminal Deletion Protein Variant, Nadh Bound Form within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe4001

b:24.0
occ:1.00
 FE2 B:FES4001 0.0 24.0 1.0
SG B:CYS115 2.2 19.2 1.0
S1 B:FES4001 2.2 25.3 1.0
S2 B:FES4001 2.2 24.1 1.0
SG B:CYS147 2.4 19.1 1.0
FE1 B:FES4001 2.8 24.4 1.0
CB B:CYS147 3.3 17.0 1.0
CB B:CYS115 3.4 14.8 1.0
CA B:CYS147 3.7 16.8 1.0
N B:ARG148 4.1 17.3 1.0
O B:HOH4244 4.3 16.3 1.0
N B:CYS115 4.3 13.7 1.0
C B:CYS147 4.4 16.9 1.0
CA B:CYS115 4.4 14.5 1.0
N B:CYS149 4.4 18.8 1.0
CB B:CYS149 4.4 20.8 1.0
CG2 B:THR150 4.6 20.0 1.0
SG B:CYS112 4.7 17.7 1.0
O B:LEU146 4.9 15.1 1.0
SG B:CYS149 4.9 26.3 1.0
N B:CYS147 5.0 16.6 1.0

Iron binding site 7 out of 8 in 4ysw

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Iron binding site 7 out of 8 in the Structure of Rat Xanthine Oxidoreductase, C-Terminal Deletion Protein Variant, Nadh Bound Form


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Structure of Rat Xanthine Oxidoreductase, C-Terminal Deletion Protein Variant, Nadh Bound Form within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe4002

b:13.5
occ:1.00
 FE1 B:FES4002 0.0 13.5 1.0
S1 B:FES4002 2.2 14.6 1.0
S2 B:FES4002 2.2 13.3 1.0
SG B:CYS51 2.3 12.8 1.0
SG B:CYS73 2.3 12.4 1.0
FE2 B:FES4002 2.8 12.9 1.0
CB B:CYS73 3.1 13.2 1.0
CB B:CYS51 3.4 12.0 1.0
CB B:ASN71 4.2 11.4 1.0
N B:GLY46 4.3 14.3 1.0
OD1 B:ASN71 4.3 13.0 1.0
N B:CYS73 4.3 13.0 1.0
CA B:CYS73 4.3 13.6 1.0
N B:CYS51 4.3 11.6 1.0
SG B:CYS43 4.4 13.7 1.0
N B:GLY44 4.4 14.4 1.0
CA B:CYS51 4.5 12.0 1.0
CA B:GLY46 4.6 14.2 1.0
CG B:ASN71 4.6 12.5 1.0
CA B:GLY44 4.6 14.1 1.0
N B:GLU45 4.7 14.1 1.0
SG B:CYS48 4.7 11.7 1.0
C B:GLY44 4.9 14.8 1.0
N B:GLY49 4.9 12.2 1.0
CA B:ASN71 4.9 12.0 1.0

Iron binding site 8 out of 8 in 4ysw

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Iron binding site 8 out of 8 in the Structure of Rat Xanthine Oxidoreductase, C-Terminal Deletion Protein Variant, Nadh Bound Form


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Structure of Rat Xanthine Oxidoreductase, C-Terminal Deletion Protein Variant, Nadh Bound Form within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe4002

b:12.9
occ:1.00
 FE2 B:FES4002 0.0 12.9 1.0
S1 B:FES4002 2.2 14.6 1.0
S2 B:FES4002 2.2 13.3 1.0
SG B:CYS48 2.3 11.7 1.0
SG B:CYS43 2.3 13.7 1.0
FE1 B:FES4002 2.8 13.5 1.0
N B:CYS43 3.4 13.0 1.0
CB B:CYS48 3.5 12.8 1.0
CB B:CYS43 3.5 13.4 1.0
N B:CYS48 3.5 13.9 1.0
N B:GLY44 3.8 14.4 1.0
CA B:CYS43 3.8 13.7 1.0
N B:GLY49 3.9 12.2 1.0
CA B:CYS48 3.9 12.8 1.0
C B:GLY42 4.1 13.4 1.0
C B:CYS48 4.2 12.7 1.0
N B:GLY42 4.3 13.2 1.0
C B:CYS43 4.3 14.0 1.0
CA B:GLY42 4.4 13.2 1.0
N B:ALA50 4.4 11.8 1.0
N B:GLY47 4.4 14.4 1.0
N B:GLY46 4.4 14.3 1.0
SG B:CYS73 4.6 12.4 1.0
N B:GLU45 4.6 14.1 1.0
SG B:CYS51 4.6 12.8 1.0
C B:GLY47 4.7 15.1 1.0
CA B:GLY49 4.8 12.0 1.0
CA B:GLY44 4.8 14.1 1.0
C B:GLY46 4.8 14.4 1.0
CA B:GLY46 4.9 14.2 1.0
CB B:ALA50 5.0 11.2 1.0
O B:GLY42 5.0 13.1 1.0

Reference:

T.Nishino, K.Okamoto, Y.Kawaguchi, T.Matsumura, B.T.Eger, E.F.Pai, T.Nishino. The C-Terminal Peptide Plays A Role in the Formation of An Intermediate Form During the Transition Between Xanthine Dehydrogenase and Xanthine Oxidase. Febs J. 2015.
ISSN: ISSN 1742-464X
PubMed: 25817260
DOI: 10.1111/FEBS.13277
Page generated: Mon Aug 5 16:40:02 2024

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