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Iron in PDB 3eub: Crystal Structure of Desulfo-Xanthine Oxidase with Xanthine

Enzymatic activity of Crystal Structure of Desulfo-Xanthine Oxidase with Xanthine

All present enzymatic activity of Crystal Structure of Desulfo-Xanthine Oxidase with Xanthine:
1.17.1.4; 1.17.3.2;

Protein crystallography data

The structure of Crystal Structure of Desulfo-Xanthine Oxidase with Xanthine, PDB code: 3eub was solved by J.M.Pauff, H.Cao, R.Hille, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 33.08 / 2.60
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 73.298, 133.176, 142.633, 96.88, 93.11, 90.02
R / Rfree (%) 21.4 / 26.8

Other elements in 3eub:

The structure of Crystal Structure of Desulfo-Xanthine Oxidase with Xanthine also contains other interesting chemical elements:

Molybdenum (Mo) 4 atoms

Iron Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 16;

Binding sites:

The binding sites of Iron atom in the Crystal Structure of Desulfo-Xanthine Oxidase with Xanthine (pdb code 3eub). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 16 binding sites of Iron where determined in the Crystal Structure of Desulfo-Xanthine Oxidase with Xanthine, PDB code: 3eub:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 16 in 3eub

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Iron binding site 1 out of 16 in the Crystal Structure of Desulfo-Xanthine Oxidase with Xanthine


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 Desulfo-Xanthine Oxidase with Xanthine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe601

b:4.8
occ:1.00
 FE1 A:FES601 0.0 4.8 1.0
S2 A:FES601 2.2 2.4 1.0
S1 A:FES601 2.2 8.5 1.0
SG A:CYS113 2.2 4.3 1.0
SG A:CYS150 2.3 4.0 1.0
FE2 A:FES601 2.8 3.6 1.0
CB A:CYS150 3.2 6.6 1.0
CB A:CYS113 3.2 4.7 1.0
N A:CYS113 3.5 4.3 1.0
N A:GLY114 3.7 3.5 1.0
CA A:CYS113 3.8 4.2 1.0
N A:CYS150 4.2 6.9 1.0
C A:CYS113 4.2 4.0 1.0
SG A:CYS148 4.2 4.3 1.0
CA A:CYS150 4.3 6.6 1.0
N A:PHE115 4.4 3.1 1.0
SG A:CYS116 4.7 3.7 1.0
C A:GLN112 4.7 4.7 1.0
CA A:GLY114 4.8 2.8 1.0
N A:ARG149 4.8 6.7 1.0
CB A:GLN112 4.9 3.8 1.0
N A:CYS116 5.0 2.5 1.0

Iron binding site 2 out of 16 in 3eub

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Iron binding site 2 out of 16 in the Crystal Structure of Desulfo-Xanthine Oxidase with Xanthine


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 Desulfo-Xanthine Oxidase with Xanthine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe601

b:3.6
occ:1.00
 FE2 A:FES601 0.0 3.6 1.0
SG A:CYS148 2.1 4.3 1.0
S2 A:FES601 2.1 2.4 1.0
S1 A:FES601 2.2 8.5 1.0
SG A:CYS116 2.3 3.7 1.0
FE1 A:FES601 2.8 4.8 1.0
CB A:CYS148 3.2 5.2 1.0
CB A:CYS116 3.5 3.9 1.0
CA A:CYS148 3.8 5.4 1.0
CB A:CYS150 4.2 6.6 1.0
N A:CYS116 4.3 2.5 1.0
N A:ARG149 4.3 6.7 1.0
CA A:CYS116 4.4 3.4 1.0
SG A:CYS150 4.5 4.0 1.0
N A:CYS150 4.5 6.9 1.0
C A:CYS148 4.5 5.9 1.0
CG2 A:THR151 4.7 7.6 1.0
SG A:CYS113 4.7 4.3 1.0
N A:GLY114 4.9 3.5 1.0
N A:THR117 4.9 3.7 1.0
CA A:CYS150 4.9 6.6 1.0
C A:CYS116 5.0 3.2 1.0

Iron binding site 3 out of 16 in 3eub

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Iron binding site 3 out of 16 in the Crystal Structure of Desulfo-Xanthine Oxidase with Xanthine


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 Desulfo-Xanthine Oxidase with Xanthine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe602

b:2.1
occ:1.00
 FE1 A:FES602 0.0 2.1 1.0
S2 A:FES602 2.2 3.0 1.0
S1 A:FES602 2.2 4.2 1.0
SG A:CYS51 2.3 3.6 1.0
SG A:CYS73 2.4 3.1 1.0
FE2 A:FES602 3.0 3.7 1.0
CB A:CYS73 3.1 3.9 1.0
CB A:CYS51 3.2 4.9 1.0
N A:CYS73 4.1 4.5 1.0
CA A:CYS73 4.2 4.2 1.0
OD1 A:ASN71 4.3 7.9 1.0
N A:CYS51 4.3 5.8 1.0
CA A:CYS51 4.4 4.9 1.0
N A:GLY46 4.4 4.5 1.0
N A:GLY44 4.4 3.2 1.0
CB A:ASN71 4.5 6.7 1.0
CA A:GLY46 4.5 4.5 1.0
CG A:ASN71 4.6 7.6 1.0
SG A:CYS48 4.7 7.3 1.0
SG A:CYS43 4.7 5.3 1.0
CA A:GLY44 4.8 3.1 1.0
N A:GLY49 5.0 4.9 1.0

Iron binding site 4 out of 16 in 3eub

Go back to Iron Binding Sites List in 3eub
Iron binding site 4 out of 16 in the Crystal Structure of Desulfo-Xanthine Oxidase with Xanthine


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 Desulfo-Xanthine Oxidase with Xanthine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe602

b:3.7
occ:1.00
 FE2 A:FES602 0.0 3.7 1.0
S1 A:FES602 2.2 4.2 1.0
SG A:CYS48 2.2 7.3 1.0
S2 A:FES602 2.2 3.0 1.0
SG A:CYS43 2.4 5.3 1.0
FE1 A:FES602 3.0 2.1 1.0
N A:CYS43 3.2 3.0 1.0
CB A:CYS43 3.4 3.4 1.0
N A:CYS48 3.4 5.7 1.0
CB A:CYS48 3.5 5.7 1.0
CA A:CYS43 3.7 3.3 1.0
N A:GLY44 3.8 3.2 1.0
C A:GLY42 3.9 3.4 1.0
CA A:CYS48 3.9 5.7 1.0
N A:GLY49 4.0 4.9 1.0
N A:GLY47 4.1 5.0 1.0
CA A:GLY42 4.2 3.5 1.0
C A:CYS43 4.2 3.3 1.0
N A:GLY42 4.3 3.6 1.0
C A:CYS48 4.4 5.2 1.0
N A:GLY46 4.4 4.5 1.0
C A:GLY47 4.6 5.7 1.0
N A:ALA50 4.6 4.7 1.0
SG A:CYS73 4.6 3.1 1.0
O A:GLY42 4.7 2.9 1.0
N A:GLU45 4.7 4.6 1.0
CA A:GLY46 4.7 4.5 1.0
C A:GLY46 4.7 5.3 1.0
CA A:GLY47 4.8 5.5 1.0
CA A:GLY44 4.9 3.1 1.0
SG A:CYS51 5.0 3.6 1.0

Iron binding site 5 out of 16 in 3eub

Go back to Iron Binding Sites List in 3eub
Iron binding site 5 out of 16 in the Crystal Structure of Desulfo-Xanthine Oxidase with Xanthine


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Crystal Structure of Desulfo-Xanthine Oxidase with Xanthine within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Fe601

b:2.0
occ:1.00
 FE1 J:FES601 0.0 2.0 1.0
S1 J:FES601 2.2 2.0 1.0
S2 J:FES601 2.2 2.8 1.0
SG J:CYS150 2.2 3.7 1.0
SG J:CYS113 2.3 4.6 1.0
FE2 J:FES601 2.9 2.0 1.0
CB J:CYS150 3.1 6.5 1.0
CB J:CYS113 3.2 4.6 1.0
N J:CYS113 3.7 4.5 1.0
N J:GLY114 3.7 3.7 1.0
CA J:CYS113 3.9 4.2 1.0
N J:CYS150 4.1 6.7 1.0
C J:CYS113 4.2 4.0 1.0
CA J:CYS150 4.2 6.4 1.0
SG J:CYS148 4.5 5.8 1.0
N J:PHE115 4.5 2.8 1.0
N J:ARG149 4.8 6.9 1.0
CA J:GLY114 4.8 2.8 1.0
C J:GLN112 4.8 4.6 1.0
SG J:CYS116 4.9 3.2 1.0
CB J:GLN112 4.9 3.8 1.0

Iron binding site 6 out of 16 in 3eub

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Iron binding site 6 out of 16 in the Crystal Structure of Desulfo-Xanthine Oxidase with Xanthine


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Crystal Structure of Desulfo-Xanthine Oxidase with Xanthine within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Fe601

b:2.0
occ:1.00
 FE2 J:FES601 0.0 2.0 1.0
S2 J:FES601 2.1 2.8 1.0
S1 J:FES601 2.2 2.0 1.0
SG J:CYS148 2.3 5.8 1.0
SG J:CYS116 2.4 3.2 1.0
FE1 J:FES601 2.9 2.0 1.0
CB J:CYS148 3.3 5.7 1.0
CB J:CYS116 3.5 3.8 1.0
CA J:CYS148 3.7 5.8 1.0
CB J:CYS150 4.1 6.5 1.0
N J:ARG149 4.3 6.9 1.0
C J:CYS148 4.4 6.0 1.0
N J:CYS150 4.4 6.7 1.0
N J:CYS116 4.4 3.0 1.0
CG2 J:THR151 4.4 7.3 1.0
SG J:CYS150 4.5 3.7 1.0
CA J:CYS116 4.5 3.3 1.0
CA J:CYS150 4.8 6.4 1.0
SG J:CYS113 4.8 4.6 1.0
N J:THR151 4.8 7.4 1.0
N J:GLY114 4.9 3.7 1.0

Iron binding site 7 out of 16 in 3eub

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Iron binding site 7 out of 16 in the Crystal Structure of Desulfo-Xanthine Oxidase with Xanthine


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Crystal Structure of Desulfo-Xanthine Oxidase with Xanthine within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Fe602

b:2.0
occ:1.00
 FE1 J:FES602 0.0 2.0 1.0
S2 J:FES602 2.2 4.7 1.0
S1 J:FES602 2.2 3.2 1.0
SG J:CYS51 2.3 5.4 1.0
SG J:CYS73 2.3 4.5 1.0
CB J:CYS73 3.0 4.5 1.0
FE2 J:FES602 3.1 3.8 1.0
CB J:CYS51 3.5 5.1 1.0
N J:CYS73 4.0 4.9 1.0
CA J:CYS73 4.1 4.5 1.0
N J:GLY44 4.3 3.0 1.0
N J:GLY46 4.3 5.2 1.0
CB J:ASN71 4.4 6.7 1.0
CA J:GLY46 4.5 4.9 1.0
SG J:CYS43 4.5 5.7 1.0
OD1 J:ASN71 4.5 8.1 1.0
N J:CYS51 4.6 5.2 1.0
CA J:GLY44 4.6 3.1 1.0
CG J:ASN71 4.6 7.7 1.0
CA J:CYS51 4.6 5.0 1.0
SG J:CYS48 4.8 6.5 1.0
N J:GLU45 4.8 4.6 1.0
N J:ALA72 5.0 5.7 1.0
C J:CYS73 5.0 4.6 1.0

Iron binding site 8 out of 16 in 3eub

Go back to Iron Binding Sites List in 3eub
Iron binding site 8 out of 16 in the Crystal Structure of Desulfo-Xanthine Oxidase with Xanthine


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Crystal Structure of Desulfo-Xanthine Oxidase with Xanthine within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Fe602

b:3.8
occ:1.00
 FE2 J:FES602 0.0 3.8 1.0
SG J:CYS48 2.1 6.5 1.0
S2 J:FES602 2.2 4.7 1.0
S1 J:FES602 2.2 3.2 1.0
SG J:CYS43 2.4 5.7 1.0
FE1 J:FES602 3.1 2.0 1.0
N J:CYS43 3.3 2.8 1.0
N J:CYS48 3.3 5.5 1.0
CB J:CYS48 3.3 5.2 1.0
CB J:CYS43 3.4 3.5 1.0
CA J:CYS48 3.7 5.6 1.0
CA J:CYS43 3.8 3.5 1.0
N J:GLY49 3.9 4.6 1.0
N J:GLY44 3.9 3.0 1.0
C J:GLY42 3.9 3.5 1.0
C J:CYS48 4.2 4.9 1.0
CA J:GLY42 4.2 3.9 1.0
N J:GLY47 4.2 5.0 1.0
N J:GLY42 4.3 3.9 1.0
C J:CYS43 4.4 3.2 1.0
N J:ALA50 4.4 4.5 1.0
C J:GLY47 4.5 5.9 1.0
N J:GLY46 4.6 5.2 1.0
O J:GLY42 4.8 3.2 1.0
SG J:CYS73 4.8 4.5 1.0
C J:GLY46 4.8 5.2 1.0
CA J:GLY47 4.9 5.4 1.0
SG J:CYS51 4.9 5.4 1.0
N J:GLU45 4.9 4.6 1.0
CA J:GLY49 4.9 4.5 1.0
CA J:GLY46 4.9 4.9 1.0
CB J:ALA50 4.9 4.8 1.0

Iron binding site 9 out of 16 in 3eub

Go back to Iron Binding Sites List in 3eub
Iron binding site 9 out of 16 in the Crystal Structure of Desulfo-Xanthine Oxidase with Xanthine


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of Crystal Structure of Desulfo-Xanthine Oxidase with Xanthine within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Fe601

b:4.5
occ:1.00
 FE1 S:FES601 0.0 4.5 1.0
S1 S:FES601 2.1 9.4 1.0
SG S:CYS150 2.2 5.1 1.0
S2 S:FES601 2.2 10.5 1.0
SG S:CYS113 2.3 5.0 1.0
FE2 S:FES601 2.9 5.0 1.0
CB S:CYS113 3.3 5.0 1.0
CB S:CYS150 3.4 7.4 1.0
N S:CYS113 3.6 5.8 1.0
N S:GLY114 3.8 4.6 1.0
CA S:CYS113 3.8 5.2 1.0
N S:CYS150 4.2 7.7 1.0
C S:CYS113 4.2 5.1 1.0
CA S:CYS150 4.4 7.3 1.0
SG S:CYS148 4.5 8.4 1.0
N S:PHE115 4.5 4.7 1.0
C S:GLN112 4.7 6.4 1.0
SG S:CYS116 4.8 4.7 1.0
N S:ARG149 4.8 8.2 1.0
CB S:GLN112 4.9 6.3 1.0
CA S:GLY114 4.9 4.7 1.0

Iron binding site 10 out of 16 in 3eub

Go back to Iron Binding Sites List in 3eub
Iron binding site 10 out of 16 in the Crystal Structure of Desulfo-Xanthine Oxidase with Xanthine


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of Crystal Structure of Desulfo-Xanthine Oxidase with Xanthine within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Fe601

b:5.0
occ:1.00
 FE2 S:FES601 0.0 5.0 1.0
S2 S:FES601 2.1 10.5 1.0
S1 S:FES601 2.2 9.4 1.0
SG S:CYS148 2.2 8.4 1.0
SG S:CYS116 2.3 4.7 1.0
FE1 S:FES601 2.9 4.5 1.0
CB S:CYS148 3.3 8.1 1.0
CB S:CYS116 3.6 5.3 1.0
CA S:CYS148 3.7 7.8 1.0
N S:ARG149 4.2 8.2 1.0
N S:CYS116 4.3 5.5 1.0
C S:CYS148 4.3 8.1 1.0
SG S:CYS150 4.4 5.1 1.0
N S:CYS150 4.4 7.7 1.0
CA S:CYS116 4.5 5.2 1.0
CB S:CYS150 4.5 7.4 1.0
CG2 S:THR151 4.7 7.6 1.0
SG S:CYS113 4.8 5.0 1.0
OG1 S:THR151 4.9 7.3 1.0
O S:LEU147 5.0 9.2 1.0
N S:GLY114 5.0 4.6 1.0
N S:THR151 5.0 7.9 1.0
C S:CYS116 5.0 5.5 1.0

Reference:

J.M.Pauff, H.Cao, R.Hille. Substrate Orientation and Catalysis at the Molybdenum Site in Xanthine Oxidase: Crystal Structures in Complex with Xanthine and Lumazine. J.Biol.Chem. V. 284 8760 2009.
ISSN: ISSN 0021-9258
PubMed: 19109252
DOI: 10.1074/JBC.M804517200
Page generated: Sun Dec 13 15:05:24 2020

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