Atomistry » Iron » PDB 4yph-4z6p » 4yty
Atomistry »
  Iron »
    PDB 4yph-4z6p »
      4yty »

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

Go back to Iron Binding Sites List in 4yty
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

Go back to Iron Binding Sites List in 4yty
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

Go back to Iron Binding Sites List in 4yty
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

Go back to Iron Binding Sites List in 4yty
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

Go back to Iron Binding Sites List in 4yty
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

Go back to Iron Binding Sites List in 4yty
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

Go back to Iron Binding Sites List in 4yty
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

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy