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Iron in PDB 1wyg: Crystal Structure of A Rat Xanthine Dehydrogenase Triple Mutant (C535A, C992R and C1324S)

Enzymatic activity of Crystal Structure of A Rat Xanthine Dehydrogenase Triple Mutant (C535A, C992R and C1324S)

All present enzymatic activity of Crystal Structure of A Rat Xanthine Dehydrogenase Triple Mutant (C535A, C992R and C1324S):
1.1.1.204; 1.1.3.22;

Protein crystallography data

The structure of Crystal Structure of A Rat Xanthine Dehydrogenase Triple Mutant (C535A, C992R and C1324S), PDB code: 1wyg was solved by T.Nishino, K.Okamoto, Y.Kawaguchi, H.Hori, T.Matsumura, B.T.Eger, E.F.Pai, T.Nishino, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 25.00 / 2.60
Space group I 41 2 2
Cell size a, b, c (Å), α, β, γ (°) 134.253, 134.253, 523.315, 90.00, 90.00, 90.00
R / Rfree (%) 20.3 / 24.8

Other elements in 1wyg:

The structure of Crystal Structure of A Rat Xanthine Dehydrogenase Triple Mutant (C535A, C992R and C1324S) also contains other interesting chemical elements:

Calcium (Ca) 1 atom

Iron Binding Sites:

The binding sites of Iron atom in the Crystal Structure of A Rat Xanthine Dehydrogenase Triple Mutant (C535A, C992R and C1324S) (pdb code 1wyg). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Crystal Structure of A Rat Xanthine Dehydrogenase Triple Mutant (C535A, C992R and C1324S), PDB code: 1wyg:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 1wyg

Go back to Iron Binding Sites List in 1wyg
Iron binding site 1 out of 4 in the Crystal Structure of A Rat Xanthine Dehydrogenase Triple Mutant (C535A, C992R and C1324S)


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 A Rat Xanthine Dehydrogenase Triple Mutant (C535A, C992R and C1324S) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe4002

b:32.0
occ:1.00
 FE1 A:FES4002 0.0 32.0 1.0
S1 A:FES4002 2.2 34.0 1.0
S2 A:FES4002 2.3 31.8 1.0
SG A:CYS115 2.4 30.2 1.0
SG A:CYS147 2.5 30.6 1.0
FE2 A:FES4002 2.6 36.6 1.0
CB A:CYS115 3.5 27.5 1.0
CB A:CYS147 3.6 26.8 1.0
O A:HOH4159 4.0 27.5 1.0
CA A:CYS147 4.0 26.3 1.0
SG A:CYS112 4.1 35.5 1.0
N A:CYS115 4.1 24.8 1.0
N A:ARG148 4.3 25.6 1.0
CA A:CYS115 4.4 23.2 1.0
N A:CYS149 4.5 26.5 1.0
C A:CYS147 4.6 26.7 1.0
CB A:CYS149 4.7 32.1 1.0
SG A:CYS149 4.8 38.6 1.0
N A:GLY113 4.8 26.9 1.0
N A:THR116 4.9 20.6 1.0
CD1 A:LEU744 4.9 27.4 1.0
OG1 A:THR150 4.9 31.3 1.0
N A:PHE114 4.9 22.3 1.0
C A:CYS115 5.0 21.7 1.0

Iron binding site 2 out of 4 in 1wyg

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Iron binding site 2 out of 4 in the Crystal Structure of A Rat Xanthine Dehydrogenase Triple Mutant (C535A, C992R and C1324S)


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 A Rat Xanthine Dehydrogenase Triple Mutant (C535A, C992R and C1324S) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe4002

b:36.6
occ:1.00
 FE2 A:FES4002 0.0 36.6 1.0
S1 A:FES4002 2.3 34.0 1.0
S2 A:FES4002 2.3 31.8 1.0
SG A:CYS112 2.4 35.5 1.0
SG A:CYS149 2.4 38.6 1.0
FE1 A:FES4002 2.6 32.0 1.0
CB A:CYS149 3.1 32.1 1.0
CB A:CYS112 3.3 31.4 1.0
O A:HOH4049 3.6 19.4 1.0
N A:CYS112 3.6 33.9 1.0
N A:CYS149 3.8 26.5 1.0
CA A:CYS112 4.0 31.5 1.0
SG A:CYS147 4.0 30.6 1.0
CA A:CYS149 4.1 28.7 1.0
N A:GLY113 4.2 26.9 1.0
N A:ARG148 4.5 25.6 1.0
CB A:GLN111 4.6 36.4 1.0
C A:CYS112 4.6 29.8 1.0
C A:ARG148 4.6 24.9 1.0
C A:GLN111 4.8 34.7 1.0
SG A:CYS115 4.8 30.2 1.0
N A:PHE114 4.9 22.3 1.0

Iron binding site 3 out of 4 in 1wyg

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Iron binding site 3 out of 4 in the Crystal Structure of A Rat Xanthine Dehydrogenase Triple Mutant (C535A, C992R and C1324S)


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 A Rat Xanthine Dehydrogenase Triple Mutant (C535A, C992R and C1324S) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe4003

b:23.2
occ:1.00
 FE1 A:FES4003 0.0 23.2 1.0
S2 A:FES4003 1.9 26.2 1.0
SG A:CYS73 2.3 22.9 1.0
SG A:CYS51 2.4 23.4 1.0
S1 A:FES4003 2.4 23.6 1.0
CB A:CYS73 2.9 28.0 1.0
FE2 A:FES4003 3.0 22.6 1.0
CB A:CYS51 3.4 21.5 1.0
N A:GLY44 4.0 23.0 1.0
CA A:CYS73 4.2 26.7 1.0
N A:CYS73 4.2 27.0 1.0
CA A:GLY44 4.2 25.1 1.0
SG A:CYS43 4.3 25.2 1.0
N A:GLY46 4.3 29.7 1.0
OD1 A:ASN71 4.4 30.7 1.0
N A:CYS51 4.5 18.2 1.0
CB A:ASN71 4.5 32.4 1.0
CA A:GLY46 4.5 27.8 1.0
CA A:CYS51 4.6 18.3 1.0
N A:GLU45 4.7 29.8 1.0
C A:GLY44 4.7 26.9 1.0
CG A:ASN71 4.8 32.6 1.0
C A:CYS73 5.0 27.4 1.0

Iron binding site 4 out of 4 in 1wyg

Go back to Iron Binding Sites List in 1wyg
Iron binding site 4 out of 4 in the Crystal Structure of A Rat Xanthine Dehydrogenase Triple Mutant (C535A, C992R and C1324S)


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 A Rat Xanthine Dehydrogenase Triple Mutant (C535A, C992R and C1324S) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe4003

b:22.6
occ:1.00
 FE2 A:FES4003 0.0 22.6 1.0
S1 A:FES4003 2.2 23.6 1.0
S2 A:FES4003 2.2 26.2 1.0
SG A:CYS48 2.3 19.4 1.0
SG A:CYS43 2.4 25.2 1.0
FE1 A:FES4003 3.0 23.2 1.0
N A:CYS48 3.4 24.9 1.0
CB A:CYS48 3.4 23.6 1.0
N A:GLY49 3.4 18.4 1.0
N A:CYS43 3.5 21.9 1.0
CB A:CYS43 3.6 22.8 1.0
CA A:CYS48 3.7 21.8 1.0
C A:CYS48 4.0 19.4 1.0
N A:GLY44 4.0 23.0 1.0
CA A:CYS43 4.0 22.1 1.0
N A:ALA50 4.1 17.5 1.0
C A:GLY42 4.2 22.6 1.0
N A:GLY42 4.3 24.3 1.0
N A:GLY47 4.3 26.6 1.0
N A:GLY46 4.4 29.7 1.0
CA A:GLY49 4.4 19.0 1.0
CA A:GLY42 4.4 23.9 1.0
C A:CYS43 4.5 21.4 1.0
C A:GLY47 4.5 26.3 1.0
SG A:CYS51 4.7 23.4 1.0
C A:GLY46 4.7 27.9 1.0
C A:GLY49 4.7 18.9 1.0
CA A:GLY46 4.8 27.8 1.0
N A:GLU45 4.8 29.8 1.0
CB A:ALA50 4.8 15.7 1.0
N A:CYS51 4.9 18.2 1.0
CA A:GLY47 4.9 26.5 1.0
SG A:CYS73 5.0 22.9 1.0

Reference:

T.Nishino, K.Okamoto, Y.Kawaguchi, H.Hori, T.Matsumura, B.T.Eger, E.F.Pai, T.Nishino. Mechanism of the Conversion of Xanthine Dehydrogenase to Xanthine Oxidase: Identification of the Two Cysteine Disulfide Bonds and Crystal Structure of A Non-Convertible Rat Liver Xanthine Dehydrogenase Mutant J.Biol.Chem. V. 280 24888 2005.
ISSN: ISSN 0021-9258
PubMed: 15878860
DOI: 10.1074/JBC.M501830200
Page generated: Sat Aug 3 16:40:38 2024

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