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

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

Go back to Iron Binding Sites List in 4ysw
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

Go back to Iron Binding Sites List in 4ysw
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

Go back to Iron Binding Sites List in 4ysw
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

Go back to Iron Binding Sites List in 4ysw
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

Go back to Iron Binding Sites List in 4ysw
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

Go back to Iron Binding Sites List in 4ysw
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

Go back to Iron Binding Sites List in 4ysw
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

Go back to Iron Binding Sites List in 4ysw
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

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy