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Iron in PDB 3nvw: Crystal Structure of Bovine Xanthine Oxidase in Complex with Guanine

Enzymatic activity of Crystal Structure of Bovine Xanthine Oxidase in Complex with Guanine

All present enzymatic activity of Crystal Structure of Bovine Xanthine Oxidase in Complex with Guanine:
1.17.1.4; 1.17.3.2;

Protein crystallography data

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

Resolution Low / High (Å) 131.70 / 1.60
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 132.683, 73.396, 138.113, 90.00, 96.97, 90.00
R / Rfree (%) 18.4 / 21.2

Other elements in 3nvw:

The structure of Crystal Structure of Bovine Xanthine Oxidase in Complex with Guanine also contains other interesting chemical elements:

Molybdenum (Mo) 2 atoms

Iron Binding Sites:

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

Iron binding site 1 out of 8 in 3nvw

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Iron binding site 1 out of 8 in the Crystal Structure of Bovine Xanthine Oxidase in Complex with Guanine


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 Bovine Xanthine Oxidase in Complex with Guanine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe601

b:8.0
occ:1.00
 FE1 A:FES601 0.0 8.0 1.0
S2 A:FES601 2.2 9.0 1.0
S1 A:FES601 2.2 9.1 1.0
SG A:CYS113 2.4 8.0 1.0
SG A:CYS150 2.4 9.0 1.0
FE2 A:FES601 2.7 8.1 1.0
CB A:CYS150 3.2 7.1 1.0
CB A:CYS113 3.4 8.4 1.0
N A:CYS113 3.6 8.2 1.0
O C:HOH206 3.6 9.2 1.0
CA A:CYS113 3.9 7.4 1.0
N A:GLY114 3.9 7.0 1.0
N A:CYS150 4.1 7.2 1.0
C A:CYS113 4.3 7.6 1.0
CA A:CYS150 4.3 7.3 1.0
N A:PHE115 4.4 6.8 1.0
SG A:CYS148 4.4 8.4 1.0
SG A:CYS116 4.6 9.1 1.0
C A:GLN112 4.7 8.0 1.0
N A:ARG149 4.8 7.9 1.0
CB A:GLN112 4.8 7.5 1.0
N A:CYS116 4.9 6.3 1.0
CA A:GLY114 4.9 7.0 1.0

Iron binding site 2 out of 8 in 3nvw

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Iron binding site 2 out of 8 in the Crystal Structure of Bovine Xanthine Oxidase in Complex with Guanine


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 Bovine Xanthine Oxidase in Complex with Guanine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe601

b:8.1
occ:1.00
 FE2 A:FES601 0.0 8.1 1.0
S2 A:FES601 2.2 9.0 1.0
S1 A:FES601 2.2 9.1 1.0
SG A:CYS116 2.3 9.1 1.0
SG A:CYS148 2.4 8.4 1.0
FE1 A:FES601 2.7 8.0 1.0
CB A:CYS116 3.3 6.2 1.0
CB A:CYS148 3.3 8.6 1.0
CA A:CYS148 3.6 8.5 1.0
N A:ARG149 4.1 7.9 1.0
N A:CYS116 4.2 6.3 1.0
C A:CYS148 4.3 8.6 1.0
O A:HOH171 4.3 9.2 1.0
CB A:CYS150 4.3 7.1 1.0
N A:CYS150 4.3 7.2 1.0
CA A:CYS116 4.4 6.5 1.0
SG A:CYS150 4.5 9.0 1.0
SG A:CYS113 4.7 8.0 1.0
CG2 A:THR151 4.7 7.5 1.0
O A:LEU147 4.9 9.0 1.0
N A:CYS148 4.9 8.9 1.0
CA A:CYS150 4.9 7.3 1.0
C A:CYS116 5.0 7.3 1.0

Iron binding site 3 out of 8 in 3nvw

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Iron binding site 3 out of 8 in the Crystal Structure of Bovine Xanthine Oxidase in Complex with Guanine


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 Bovine Xanthine Oxidase in Complex with Guanine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe602

b:9.2
occ:1.00
 FE1 A:FES602 0.0 9.2 1.0
S2 A:FES602 2.2 10.5 1.0
S1 A:FES602 2.2 10.7 1.0
SG A:CYS73 2.3 11.1 1.0
SG A:CYS51 2.3 10.4 1.0
FE2 A:FES602 2.8 9.4 1.0
CB A:CYS73 3.1 11.4 1.0
CB A:CYS51 3.4 7.7 1.0
CB A:ASN71 4.2 11.6 1.0
N A:CYS73 4.2 11.1 1.0
CA A:CYS73 4.2 11.3 1.0
N A:GLY46 4.3 11.3 1.0
N A:CYS51 4.4 8.7 1.0
N A:GLY44 4.4 9.4 1.0
SG A:CYS43 4.4 8.7 1.0
OD1 A:ASN71 4.4 14.6 1.0
CG A:ASN71 4.5 13.7 1.0
CA A:CYS51 4.5 8.2 1.0
CA A:GLY46 4.6 11.6 1.0
SG A:CYS48 4.7 10.3 1.0
CA A:GLY44 4.7 10.2 1.0
N A:GLY49 4.8 8.5 1.0
N A:GLU45 4.9 10.9 1.0
CA A:ASN71 4.9 11.5 1.0

Iron binding site 4 out of 8 in 3nvw

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Iron binding site 4 out of 8 in the Crystal Structure of Bovine Xanthine Oxidase in Complex with Guanine


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 Bovine Xanthine Oxidase in Complex with Guanine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe602

b:9.4
occ:1.00
 FE2 A:FES602 0.0 9.4 1.0
S1 A:FES602 2.2 10.7 1.0
S2 A:FES602 2.2 10.5 1.0
SG A:CYS48 2.3 10.3 1.0
SG A:CYS43 2.4 8.7 1.0
FE1 A:FES602 2.8 9.2 1.0
N A:CYS43 3.3 9.9 1.0
CB A:CYS48 3.4 9.1 1.0
CB A:CYS43 3.5 9.5 1.0
N A:CYS48 3.6 10.1 1.0
CA A:CYS43 3.8 9.7 1.0
N A:GLY44 3.8 9.4 1.0
N A:GLY49 3.8 8.5 1.0
CA A:CYS48 3.9 9.5 1.0
C A:GLY42 4.0 10.1 1.0
C A:CYS48 4.2 8.4 1.0
N A:GLY42 4.3 8.9 1.0
C A:CYS43 4.3 9.8 1.0
CA A:GLY42 4.3 9.7 1.0
N A:GLY47 4.4 11.4 1.0
N A:GLY46 4.4 11.3 1.0
SG A:CYS73 4.4 11.1 1.0
N A:ALA50 4.5 8.7 1.0
SG A:CYS51 4.6 10.4 1.0
N A:GLU45 4.7 10.9 1.0
C A:GLY47 4.7 10.8 1.0
CA A:GLY49 4.8 8.5 1.0
C A:GLY46 4.8 11.8 1.0
O A:GLY42 4.8 9.5 1.0
CA A:GLY46 4.8 11.6 1.0
CA A:GLY44 4.9 10.2 1.0

Iron binding site 5 out of 8 in 3nvw

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Iron binding site 5 out of 8 in the Crystal Structure of Bovine Xanthine Oxidase in Complex with Guanine


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 Bovine Xanthine Oxidase in Complex with Guanine within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Fe601

b:9.5
occ:1.00
 FE1 J:FES601 0.0 9.5 1.0
S1 J:FES601 2.2 10.2 1.0
S2 J:FES601 2.2 10.1 1.0
SG J:CYS113 2.3 9.9 1.0
SG J:CYS150 2.4 11.1 1.0
FE2 J:FES601 2.7 10.4 1.0
CB J:CYS150 3.2 10.0 1.0
CB J:CYS113 3.3 8.6 1.0
N J:CYS113 3.6 9.1 1.0
O L:HOH432 3.7 11.3 1.0
N J:GLY114 3.8 9.1 1.0
CA J:CYS113 3.9 8.8 1.0
N J:CYS150 4.1 9.8 1.0
C J:CYS113 4.2 8.8 1.0
CA J:CYS150 4.3 9.8 1.0
N J:PHE115 4.3 9.1 1.0
SG J:CYS148 4.4 10.6 1.0
SG J:CYS116 4.6 11.7 1.0
C J:GLN112 4.7 9.2 1.0
N J:ARG149 4.7 10.7 1.0
CB J:GLN112 4.8 10.2 1.0
CA J:GLY114 4.8 9.7 1.0
N J:CYS116 4.9 9.3 1.0

Iron binding site 6 out of 8 in 3nvw

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Iron binding site 6 out of 8 in the Crystal Structure of Bovine Xanthine Oxidase in Complex with Guanine


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 Bovine Xanthine Oxidase in Complex with Guanine within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Fe601

b:10.4
occ:1.00
 FE2 J:FES601 0.0 10.4 1.0
S2 J:FES601 2.2 10.1 1.0
S1 J:FES601 2.2 10.2 1.0
SG J:CYS116 2.3 11.7 1.0
SG J:CYS148 2.3 10.6 1.0
FE1 J:FES601 2.7 9.5 1.0
CB J:CYS148 3.3 10.8 1.0
CB J:CYS116 3.4 9.4 1.0
CA J:CYS148 3.7 10.8 1.0
N J:ARG149 4.1 10.7 1.0
N J:CYS116 4.2 9.3 1.0
C J:CYS148 4.3 10.6 1.0
N J:CYS150 4.3 9.8 1.0
CB J:CYS150 4.3 10.0 1.0
O J:HOH314 4.3 12.0 1.0
CA J:CYS116 4.4 9.3 1.0
SG J:CYS150 4.5 11.1 1.0
SG J:CYS113 4.7 9.9 1.0
CG2 J:THR151 4.7 11.2 1.0
O J:LEU147 4.9 10.6 1.0
CA J:CYS150 4.9 9.8 1.0
N J:CYS148 4.9 10.5 1.0

Iron binding site 7 out of 8 in 3nvw

Go back to Iron Binding Sites List in 3nvw
Iron binding site 7 out of 8 in the Crystal Structure of Bovine Xanthine Oxidase in Complex with Guanine


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 Bovine Xanthine Oxidase in Complex with Guanine within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Fe602

b:10.3
occ:1.00
 FE1 J:FES602 0.0 10.3 1.0
S1 J:FES602 2.2 11.1 1.0
S2 J:FES602 2.2 10.9 1.0
SG J:CYS51 2.3 11.7 1.0
SG J:CYS73 2.3 11.4 1.0
FE2 J:FES602 2.8 10.4 1.0
CB J:CYS73 3.1 11.3 1.0
CB J:CYS51 3.4 11.3 1.0
N J:CYS73 4.2 11.3 1.0
CB J:ASN71 4.2 13.0 1.0
CA J:CYS73 4.2 11.3 1.0
N J:CYS51 4.3 10.1 1.0
N J:GLY46 4.4 12.7 1.0
SG J:CYS43 4.4 10.0 1.0
CG J:ASN71 4.4 12.9 1.0
N J:GLY44 4.4 10.9 1.0
OD1 J:ASN71 4.4 14.9 1.0
CA J:CYS51 4.5 10.6 1.0
CA J:GLY46 4.5 12.9 1.0
SG J:CYS48 4.7 12.0 1.0
CA J:GLY44 4.7 11.1 1.0
N J:GLY49 4.8 10.1 1.0
CA J:ASN71 4.9 12.6 1.0
N J:GLU45 4.9 12.2 1.0
N J:ALA50 5.0 9.5 1.0

Iron binding site 8 out of 8 in 3nvw

Go back to Iron Binding Sites List in 3nvw
Iron binding site 8 out of 8 in the Crystal Structure of Bovine Xanthine Oxidase in Complex with Guanine


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 Bovine Xanthine Oxidase in Complex with Guanine within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Fe602

b:10.4
occ:1.00
 FE2 J:FES602 0.0 10.4 1.0
S1 J:FES602 2.2 11.1 1.0
S2 J:FES602 2.2 10.9 1.0
SG J:CYS48 2.3 12.0 1.0
SG J:CYS43 2.4 10.0 1.0
FE1 J:FES602 2.8 10.3 1.0
N J:CYS43 3.4 10.0 1.0
CB J:CYS48 3.4 12.1 1.0
CB J:CYS43 3.5 8.8 1.0
N J:CYS48 3.6 12.9 1.0
N J:GLY49 3.8 10.1 1.0
CA J:CYS43 3.8 9.5 1.0
N J:GLY44 3.9 10.9 1.0
CA J:CYS48 3.9 11.3 1.0
C J:GLY42 4.0 10.1 1.0
C J:CYS48 4.2 10.6 1.0
CA J:GLY42 4.3 10.1 1.0
C J:CYS43 4.3 10.6 1.0
N J:GLY42 4.3 9.7 1.0
N J:GLY47 4.3 13.3 1.0
N J:ALA50 4.4 9.5 1.0
N J:GLY46 4.4 12.7 1.0
SG J:CYS73 4.5 11.4 1.0
SG J:CYS51 4.6 11.7 1.0
N J:GLU45 4.7 12.2 1.0
C J:GLY46 4.7 13.3 1.0
C J:GLY47 4.7 13.5 1.0
CA J:GLY46 4.8 12.9 1.0
CA J:GLY49 4.8 9.6 1.0
O J:GLY42 4.9 10.1 1.0
CA J:GLY44 4.9 11.1 1.0

Reference:

H.Cao, J.Hall, R.Hille. Substrate Orientation and Specificity in Xanthine Oxidase: Crystal Structures of the Enzyme in Complex with Indole-3-Acetaldehyde and Guanine. Biochemistry V. 53 533 2014.
ISSN: ISSN 0006-2960
PubMed: 24397336
DOI: 10.1021/BI401465U
Page generated: Sun Aug 4 16:45:46 2024

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