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Iron in PDB 4yty: Structure of Rat Xanthine Oxidoreductase, C535A/C992R/C1324S, Nadh Bound Form

Enzymatic activity of Structure of Rat Xanthine Oxidoreductase, C535A/C992R/C1324S, Nadh Bound Form

All present enzymatic activity of Structure of Rat Xanthine Oxidoreductase, C535A/C992R/C1324S, Nadh Bound Form:
1.17.1.4; 1.17.3.2;

Protein crystallography data

The structure of Structure of Rat Xanthine Oxidoreductase, C535A/C992R/C1324S, Nadh Bound Form, PDB code: 4yty 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) 49.50 / 2.20
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 98.988, 137.404, 222.705, 90.00, 90.00, 90.00
R / Rfree (%) 17.8 / 22.1

Other elements in 4yty:

The structure of Structure of Rat Xanthine Oxidoreductase, C535A/C992R/C1324S, 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, C535A/C992R/C1324S, Nadh Bound Form (pdb code 4yty). 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, C535A/C992R/C1324S, Nadh Bound Form, PDB code: 4yty:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iron binding site 1 out of 8 in 4yty

Go back to Iron Binding Sites List in 4yty
Iron binding site 1 out of 8 in the Structure of Rat Xanthine Oxidoreductase, C535A/C992R/C1324S, 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, C535A/C992R/C1324S, Nadh Bound Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe3001

b:21.9
occ:1.00
 FE1 A:FES3001 0.0 21.9 1.0
S2 A:FES3001 2.2 20.3 1.0
S1 A:FES3001 2.2 23.3 1.0
SG A:CYS112 2.3 14.9 1.0
SG A:CYS149 2.6 23.1 1.0
FE2 A:FES3001 2.8 20.6 1.0
CB A:CYS112 3.2 14.8 1.0
CB A:CYS149 3.4 18.7 1.0
O A:HOH3533 3.5 13.5 1.0
N A:CYS112 3.7 14.9 1.0
CA A:CYS112 3.8 14.6 1.0
N A:GLY113 4.0 13.3 1.0
N A:CYS149 4.2 17.0 1.0
C A:CYS112 4.2 13.9 1.0
N A:PHE114 4.4 11.4 1.0
CA A:CYS149 4.4 18.1 1.0
SG A:CYS147 4.4 16.4 1.0
SG A:CYS115 4.6 16.0 1.0
N A:ARG148 4.8 15.2 1.0
C A:GLN111 4.9 15.5 1.0
N A:CYS115 4.9 11.3 1.0
CA A:GLY113 5.0 12.5 1.0

Iron binding site 2 out of 8 in 4yty

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Iron binding site 2 out of 8 in the Structure of Rat Xanthine Oxidoreductase, C535A/C992R/C1324S, 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, C535A/C992R/C1324S, Nadh Bound Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe3001

b:20.6
occ:1.00
 FE2 A:FES3001 0.0 20.6 1.0
SG A:CYS115 2.2 16.0 1.0
S2 A:FES3001 2.2 20.3 1.0
S1 A:FES3001 2.2 23.3 1.0
SG A:CYS147 2.3 16.4 1.0
FE1 A:FES3001 2.8 21.9 1.0
CB A:CYS147 3.3 15.2 1.0
CB A:CYS115 3.4 11.9 1.0
CA A:CYS147 3.7 14.8 1.0
N A:ARG148 4.1 15.2 1.0
N A:CYS115 4.3 11.3 1.0
O A:HOH3233 4.4 15.4 1.0
N A:CYS149 4.4 17.0 1.0
C A:CYS147 4.4 15.0 1.0
CA A:CYS115 4.4 11.6 1.0
CB A:CYS149 4.5 18.7 1.0
CG2 A:THR150 4.7 17.3 1.0
SG A:CYS149 4.7 23.1 1.0
SG A:CYS112 4.7 14.9 1.0
O A:LEU146 4.9 13.4 1.0
C A:CYS115 5.0 10.9 1.0
CA A:CYS149 5.0 18.1 1.0

Iron binding site 3 out of 8 in 4yty

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Iron binding site 3 out of 8 in the Structure of Rat Xanthine Oxidoreductase, C535A/C992R/C1324S, 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, C535A/C992R/C1324S, Nadh Bound Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe3002

b:11.1
occ:1.00
 FE1 A:FES3002 0.0 11.1 1.0
S1 A:FES3002 2.2 11.0 1.0
S2 A:FES3002 2.2 10.3 1.0
SG A:CYS51 2.3 10.1 1.0
SG A:CYS73 2.4 11.2 1.0
FE2 A:FES3002 2.8 10.8 1.0
CB A:CYS73 3.2 11.3 1.0
CB A:CYS51 3.4 9.9 1.0
N A:CYS51 4.3 10.0 1.0
N A:GLY46 4.3 16.1 1.0
CB A:ASN71 4.3 11.7 1.0
N A:CYS73 4.3 11.3 1.0
CA A:CYS73 4.3 11.7 1.0
OD1 A:ASN71 4.3 13.7 1.0
N A:GLY44 4.4 13.7 1.0
SG A:CYS43 4.4 13.2 1.0
CA A:CYS51 4.5 10.3 1.0
CG A:ASN71 4.6 13.1 1.0
CA A:GLY46 4.6 15.7 1.0
SG A:CYS48 4.6 11.1 1.0
CA A:GLY44 4.6 14.6 1.0
N A:GLU45 4.7 15.7 1.0
C A:GLY44 4.9 15.3 1.0
N A:GLY49 4.9 10.7 1.0
N A:ALA50 5.0 9.8 1.0
CA A:ASN71 5.0 11.9 1.0

Iron binding site 4 out of 8 in 4yty

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Iron binding site 4 out of 8 in the Structure of Rat Xanthine Oxidoreductase, C535A/C992R/C1324S, 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, C535A/C992R/C1324S, Nadh Bound Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe3002

b:10.8
occ:1.00
 FE2 A:FES3002 0.0 10.8 1.0
S1 A:FES3002 2.2 11.0 1.0
SG A:CYS48 2.2 11.1 1.0
S2 A:FES3002 2.2 10.3 1.0
SG A:CYS43 2.4 13.2 1.0
FE1 A:FES3002 2.8 11.1 1.0
CB A:CYS48 3.4 11.1 1.0
N A:CYS43 3.5 13.6 1.0
CB A:CYS43 3.5 12.8 1.0
N A:CYS48 3.5 12.9 1.0
N A:GLY44 3.9 13.7 1.0
N A:GLY49 3.9 10.7 1.0
CA A:CYS48 3.9 11.6 1.0
CA A:CYS43 3.9 13.5 1.0
C A:GLY42 4.2 13.4 1.0
C A:CYS48 4.2 11.3 1.0
N A:ALA50 4.3 9.8 1.0
N A:GLY42 4.3 12.6 1.0
C A:CYS43 4.3 13.5 1.0
N A:GLY47 4.4 15.1 1.0
CA A:GLY42 4.4 12.9 1.0
N A:GLY46 4.5 16.1 1.0
SG A:CYS73 4.6 11.2 1.0
SG A:CYS51 4.6 10.1 1.0
N A:GLU45 4.6 15.7 1.0
C A:GLY47 4.7 14.4 1.0
CB A:ALA50 4.8 10.1 1.0
CA A:GLY49 4.8 10.4 1.0
CA A:GLY44 4.9 14.6 1.0
C A:GLY46 4.9 15.2 1.0
CA A:GLY46 5.0 15.7 1.0
N A:CYS51 5.0 10.0 1.0
C A:GLY49 5.0 10.0 1.0

Iron binding site 5 out of 8 in 4yty

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Iron binding site 5 out of 8 in the Structure of Rat Xanthine Oxidoreductase, C535A/C992R/C1324S, 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, C535A/C992R/C1324S, Nadh Bound Form within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe4001

b:22.7
occ:1.00
 FE1 B:FES4001 0.0 22.7 1.0
S2 B:FES4001 2.2 20.3 1.0
S1 B:FES4001 2.2 23.6 1.0
SG B:CYS112 2.2 15.2 1.0
SG B:CYS149 2.7 23.6 1.0
FE2 B:FES4001 2.8 20.8 1.0
CB B:CYS112 3.1 15.1 1.0
CB B:CYS149 3.4 17.9 1.0
N B:CYS112 3.6 15.6 1.0
O B:HOH4384 3.7 11.5 1.0
CA B:CYS112 3.8 15.0 1.0
N B:GLY113 3.9 13.6 1.0
N B:CYS149 4.2 15.9 1.0
C B:CYS112 4.2 14.3 1.0
CA B:CYS149 4.4 17.4 1.0
SG B:CYS147 4.5 15.2 1.0
N B:PHE114 4.5 11.6 1.0
SG B:CYS115 4.5 15.8 1.0
C B:GLN111 4.7 16.3 1.0
N B:ARG148 4.8 14.3 1.0
N B:CYS115 4.9 11.2 1.0
CB B:GLN111 4.9 16.8 1.0
CA B:GLY113 5.0 12.6 1.0

Iron binding site 6 out of 8 in 4yty

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Iron binding site 6 out of 8 in the Structure of Rat Xanthine Oxidoreductase, C535A/C992R/C1324S, 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, C535A/C992R/C1324S, Nadh Bound Form within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe4001

b:20.8
occ:1.00
 FE2 B:FES4001 0.0 20.8 1.0
SG B:CYS115 2.1 15.8 1.0
S1 B:FES4001 2.2 23.6 1.0
S2 B:FES4001 2.2 20.3 1.0
SG B:CYS147 2.3 15.2 1.0
FE1 B:FES4001 2.8 22.7 1.0
CB B:CYS115 3.3 11.8 1.0
CB B:CYS147 3.3 13.9 1.0
CA B:CYS147 3.7 13.9 1.0
N B:ARG148 4.1 14.3 1.0
O B:HOH4361 4.2 10.8 1.0
N B:CYS115 4.3 11.2 1.0
CA B:CYS115 4.3 11.6 1.0
C B:CYS147 4.4 14.4 1.0
N B:CYS149 4.4 15.9 1.0
CB B:CYS149 4.5 17.9 1.0
SG B:CYS112 4.7 15.2 1.0
CG2 B:THR150 4.8 14.9 1.0
SG B:CYS149 4.8 23.6 1.0
O B:LEU146 4.9 13.2 1.0
C B:CYS115 4.9 10.7 1.0

Iron binding site 7 out of 8 in 4yty

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Iron binding site 7 out of 8 in the Structure of Rat Xanthine Oxidoreductase, C535A/C992R/C1324S, 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, C535A/C992R/C1324S, Nadh Bound Form within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe4002

b:10.6
occ:1.00
 FE1 B:FES4002 0.0 10.6 1.0
S1 B:FES4002 2.2 9.8 1.0
S2 B:FES4002 2.2 10.7 1.0
SG B:CYS51 2.3 9.1 1.0
SG B:CYS73 2.3 11.0 1.0
FE2 B:FES4002 2.9 10.4 1.0
CB B:CYS73 3.1 10.0 1.0
CB B:CYS51 3.5 7.8 1.0
CB B:ASN71 4.2 9.0 1.0
N B:CYS73 4.3 8.7 1.0
CA B:CYS73 4.3 9.9 1.0
N B:GLY46 4.3 11.5 1.0
N B:CYS51 4.3 8.3 1.0
N B:GLY44 4.4 11.1 1.0
OD1 B:ASN71 4.4 12.8 1.0
SG B:CYS43 4.4 9.6 1.0
CA B:CYS51 4.5 8.5 1.0
CA B:GLY44 4.5 11.8 1.0
CA B:GLY46 4.6 11.1 1.0
CG B:ASN71 4.6 10.6 1.0
N B:GLU45 4.7 12.3 1.0
SG B:CYS48 4.7 8.9 1.0
C B:GLY44 4.9 12.4 1.0
N B:GLY49 4.9 9.2 1.0
CA B:ASN71 4.9 9.4 1.0

Iron binding site 8 out of 8 in 4yty

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Iron binding site 8 out of 8 in the Structure of Rat Xanthine Oxidoreductase, C535A/C992R/C1324S, 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, C535A/C992R/C1324S, Nadh Bound Form within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe4002

b:10.4
occ:1.00
 FE2 B:FES4002 0.0 10.4 1.0
S2 B:FES4002 2.2 10.7 1.0
S1 B:FES4002 2.2 9.8 1.0
SG B:CYS48 2.3 8.9 1.0
SG B:CYS43 2.3 9.6 1.0
FE1 B:FES4002 2.9 10.6 1.0
CB B:CYS48 3.3 10.0 1.0
CB B:CYS43 3.5 10.4 1.0
N B:CYS43 3.5 10.8 1.0
N B:CYS48 3.5 11.0 1.0
N B:GLY49 3.8 9.2 1.0
CA B:CYS48 3.8 9.5 1.0
N B:GLY44 3.9 11.1 1.0
CA B:CYS43 3.9 10.7 1.0
C B:GLY42 4.1 11.2 1.0
C B:CYS48 4.1 9.2 1.0
N B:GLY42 4.3 10.4 1.0
N B:ALA50 4.3 8.8 1.0
C B:CYS43 4.3 11.2 1.0
CA B:GLY42 4.4 11.0 1.0
N B:GLY47 4.4 11.1 1.0
N B:GLY46 4.5 11.5 1.0
SG B:CYS73 4.6 11.0 1.0
N B:GLU45 4.6 12.3 1.0
C B:GLY47 4.7 11.8 1.0
SG B:CYS51 4.7 9.1 1.0
CA B:GLY49 4.8 8.9 1.0
C B:GLY46 4.8 11.4 1.0
CA B:GLY44 4.8 11.8 1.0
CA B:GLY46 4.9 11.1 1.0
O B:GLY42 4.9 11.1 1.0
CB B:ALA50 5.0 8.5 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 16:51:07 2024

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