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Iron in PDB 3nvy: Crystal Structure of Bovine Xanthine Oxidase in Complex with Quercetin

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

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

Protein crystallography data

The structure of Crystal Structure of Bovine Xanthine Oxidase in Complex with Quercetin, PDB code: 3nvy 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) 101.50 / 2.00
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 132.686, 73.398, 138.210, 90.00, 97.13, 90.00
R / Rfree (%) 19.2 / 23.7

Other elements in 3nvy:

The structure of Crystal Structure of Bovine Xanthine Oxidase in Complex with Quercetin 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 Quercetin (pdb code 3nvy). 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 Quercetin, PDB code: 3nvy:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iron binding site 1 out of 8 in 3nvy

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


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 Quercetin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe601

b:15.3
occ:1.00
 FE1 A:FES601 0.0 15.3 1.0
S1 A:FES601 2.2 14.5 1.0
S2 A:FES601 2.2 15.5 1.0
SG A:CYS150 2.3 14.0 1.0
SG A:CYS113 2.3 15.0 1.0
FE2 A:FES601 2.7 15.5 1.0
CB A:CYS150 3.3 14.9 1.0
CB A:CYS113 3.3 13.2 1.0
N A:CYS113 3.6 13.7 1.0
O C:HOH127 3.7 15.7 1.0
CA A:CYS113 3.8 13.8 1.0
N A:GLY114 3.9 13.2 1.0
N A:CYS150 4.1 13.9 1.0
C A:CYS113 4.2 13.3 1.0
CA A:CYS150 4.3 13.1 1.0
SG A:CYS148 4.5 15.9 1.0
N A:PHE115 4.5 11.7 1.0
SG A:CYS116 4.7 12.2 1.0
C A:GLN112 4.7 14.7 1.0
N A:ARG149 4.8 14.1 1.0
CB A:GLN112 4.8 13.8 1.0
CA A:GLY114 4.9 13.1 1.0

Iron binding site 2 out of 8 in 3nvy

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


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 Quercetin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe601

b:15.5
occ:1.00
 FE2 A:FES601 0.0 15.5 1.0
S2 A:FES601 2.2 15.5 1.0
S1 A:FES601 2.2 14.5 1.0
SG A:CYS116 2.3 12.2 1.0
SG A:CYS148 2.4 15.9 1.0
FE1 A:FES601 2.7 15.3 1.0
CB A:CYS148 3.3 15.5 1.0
CB A:CYS116 3.4 11.3 1.0
CA A:CYS148 3.7 15.3 1.0
O A:HOH177 4.1 15.0 1.0
N A:ARG149 4.1 14.1 1.0
N A:CYS116 4.3 11.4 1.0
C A:CYS148 4.3 14.9 1.0
N A:CYS150 4.4 13.9 1.0
CA A:CYS116 4.4 12.3 1.0
CB A:CYS150 4.4 14.9 1.0
SG A:CYS150 4.5 14.0 1.0
SG A:CYS113 4.7 15.0 1.0
CG2 A:THR151 4.7 12.1 1.0
O A:LEU147 4.9 16.5 1.0
N A:CYS148 5.0 16.1 1.0

Iron binding site 3 out of 8 in 3nvy

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


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 Quercetin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe602

b:15.8
occ:1.00
 FE1 A:FES602 0.0 15.8 1.0
S1 A:FES602 2.2 18.6 1.0
S2 A:FES602 2.2 17.7 1.0
SG A:CYS51 2.3 14.5 1.0
SG A:CYS73 2.3 16.9 1.0
FE2 A:FES602 2.8 15.1 1.0
CB A:CYS73 3.1 20.0 1.0
CB A:CYS51 3.4 15.1 1.0
CB A:ASN71 4.2 19.1 1.0
N A:CYS73 4.2 19.6 1.0
CA A:CYS73 4.3 19.8 1.0
N A:CYS51 4.3 16.3 1.0
N A:GLY46 4.3 21.4 1.0
OD1 A:ASN71 4.3 18.9 1.0
CG A:ASN71 4.4 19.3 1.0
SG A:CYS43 4.5 16.1 1.0
N A:GLY44 4.5 17.8 1.0
CA A:CYS51 4.5 15.4 1.0
CA A:GLY46 4.5 21.0 1.0
SG A:CYS48 4.5 14.8 1.0
CA A:GLY44 4.7 18.6 1.0
N A:GLY49 4.8 16.4 1.0
CA A:ASN71 4.9 18.8 1.0
N A:GLU45 4.9 20.5 1.0
N A:ALA50 5.0 14.9 1.0

Iron binding site 4 out of 8 in 3nvy

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


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 Quercetin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe602

b:15.1
occ:1.00
 FE2 A:FES602 0.0 15.1 1.0
SG A:CYS48 2.2 14.8 1.0
S2 A:FES602 2.2 17.7 1.0
S1 A:FES602 2.2 18.6 1.0
SG A:CYS43 2.4 16.1 1.0
FE1 A:FES602 2.8 15.8 1.0
N A:CYS43 3.3 16.1 1.0
CB A:CYS48 3.4 16.8 1.0
CB A:CYS43 3.5 15.6 1.0
N A:CYS48 3.6 16.9 1.0
CA A:CYS43 3.8 16.2 1.0
N A:GLY49 3.9 16.4 1.0
CA A:CYS48 3.9 17.0 1.0
N A:GLY44 3.9 17.8 1.0
C A:GLY42 4.0 17.0 1.0
N A:GLY42 4.2 17.0 1.0
CA A:GLY42 4.2 16.6 1.0
C A:CYS48 4.3 16.7 1.0
C A:CYS43 4.3 17.1 1.0
N A:GLY46 4.3 21.4 1.0
N A:ALA50 4.4 14.9 1.0
N A:GLY47 4.4 19.9 1.0
SG A:CYS73 4.5 16.9 1.0
SG A:CYS51 4.6 14.5 1.0
N A:GLU45 4.7 20.5 1.0
CA A:GLY46 4.7 21.0 1.0
C A:GLY47 4.7 19.0 1.0
C A:GLY46 4.8 21.5 1.0
CA A:GLY49 4.8 15.6 1.0
O A:GLY42 4.9 15.9 1.0
CA A:GLY44 4.9 18.6 1.0
CB A:ALA50 5.0 14.2 1.0

Iron binding site 5 out of 8 in 3nvy

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


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 Quercetin within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Fe601

b:16.5
occ:1.00
 FE1 J:FES601 0.0 16.5 1.0
S2 J:FES601 2.2 17.1 1.0
S1 J:FES601 2.2 18.4 1.0
SG J:CYS150 2.3 15.6 1.0
SG J:CYS113 2.4 18.2 1.0
FE2 J:FES601 2.6 15.5 1.0
CB J:CYS150 3.2 16.1 1.0
CB J:CYS113 3.4 14.8 1.0
N J:CYS113 3.7 14.7 1.0
O L:HOH468 3.8 15.0 1.0
N J:GLY114 3.9 14.8 1.0
CA J:CYS113 4.0 15.0 1.0
N J:CYS150 4.0 17.7 1.0
CA J:CYS150 4.2 16.4 1.0
SG J:CYS148 4.3 19.4 1.0
C J:CYS113 4.4 14.1 1.0
N J:PHE115 4.5 15.9 1.0
SG J:CYS116 4.6 16.0 1.0
N J:ARG149 4.7 19.1 1.0
C J:GLN112 4.8 15.3 1.0
CB J:GLN112 4.8 14.0 1.0
CA J:GLY114 4.9 14.8 1.0
C J:ARG149 5.0 18.6 1.0
N J:CYS116 5.0 16.2 1.0

Iron binding site 6 out of 8 in 3nvy

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


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 Quercetin within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Fe601

b:15.5
occ:1.00
 FE2 J:FES601 0.0 15.5 1.0
S2 J:FES601 2.2 17.1 1.0
S1 J:FES601 2.2 18.4 1.0
SG J:CYS116 2.3 16.0 1.0
SG J:CYS148 2.4 19.4 1.0
FE1 J:FES601 2.6 16.5 1.0
CB J:CYS116 3.4 17.0 1.0
CB J:CYS148 3.4 19.2 1.0
CA J:CYS148 3.7 19.0 1.0
N J:CYS116 4.2 16.2 1.0
N J:ARG149 4.2 19.1 1.0
O J:HOH307 4.3 19.9 1.0
C J:CYS148 4.3 19.4 1.0
CA J:CYS116 4.3 16.4 1.0
N J:CYS150 4.4 17.7 1.0
CB J:CYS150 4.4 16.1 1.0
SG J:CYS150 4.5 15.6 1.0
SG J:CYS113 4.6 18.2 1.0
CG2 J:THR151 4.7 15.1 1.0
O J:LEU147 4.9 21.1 1.0
N J:CYS148 4.9 20.3 1.0
CA J:CYS150 5.0 16.4 1.0
N J:PHE115 5.0 15.9 1.0

Iron binding site 7 out of 8 in 3nvy

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Iron binding site 7 out of 8 in the Crystal Structure of Bovine Xanthine Oxidase in Complex with Quercetin


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 Quercetin within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Fe602

b:18.6
occ:1.00
 FE1 J:FES602 0.0 18.6 1.0
S1 J:FES602 2.2 17.5 1.0
SG J:CYS73 2.2 17.5 1.0
S2 J:FES602 2.2 18.1 1.0
SG J:CYS51 2.3 19.4 1.0
FE2 J:FES602 2.9 17.7 1.0
CB J:CYS73 3.1 17.9 1.0
CB J:CYS51 3.3 19.6 1.0
N J:CYS73 4.1 18.0 1.0
CB J:ASN71 4.2 17.7 1.0
CA J:CYS73 4.2 18.8 1.0
N J:CYS51 4.3 18.5 1.0
N J:GLY46 4.4 24.0 1.0
SG J:CYS43 4.4 17.4 1.0
CG J:ASN71 4.4 18.4 1.0
N J:GLY44 4.4 20.4 1.0
CA J:CYS51 4.5 19.1 1.0
OD1 J:ASN71 4.5 19.8 1.0
CA J:GLY46 4.5 23.1 1.0
SG J:CYS48 4.7 18.5 1.0
CA J:GLY44 4.7 20.8 1.0
N J:GLY49 4.8 19.1 1.0
CA J:ASN71 4.8 17.0 1.0
N J:GLU45 4.9 23.0 1.0

Iron binding site 8 out of 8 in 3nvy

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


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 Quercetin within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Fe602

b:17.7
occ:1.00
 FE2 J:FES602 0.0 17.7 1.0
S2 J:FES602 2.2 18.1 1.0
S1 J:FES602 2.2 17.5 1.0
SG J:CYS48 2.2 18.5 1.0
SG J:CYS43 2.3 17.4 1.0
FE1 J:FES602 2.9 18.6 1.0
N J:CYS43 3.3 19.5 1.0
CB J:CYS43 3.4 18.2 1.0
N J:CYS48 3.5 20.6 1.0
CB J:CYS48 3.5 19.3 1.0
CA J:CYS43 3.7 19.3 1.0
N J:GLY44 3.8 20.4 1.0
N J:GLY49 3.8 19.1 1.0
CA J:CYS48 3.9 18.8 1.0
C J:GLY42 4.0 19.9 1.0
C J:CYS43 4.2 20.2 1.0
C J:CYS48 4.2 18.2 1.0
N J:GLY42 4.2 19.1 1.0
N J:GLY47 4.3 24.0 1.0
CA J:GLY42 4.4 19.0 1.0
SG J:CYS73 4.4 17.5 1.0
N J:ALA50 4.4 17.8 1.0
N J:GLY46 4.5 24.0 1.0
C J:GLY47 4.6 23.1 1.0
N J:GLU45 4.6 23.0 1.0
SG J:CYS51 4.7 19.4 1.0
CA J:GLY44 4.8 20.8 1.0
O J:GLY42 4.8 17.9 1.0
C J:GLY46 4.8 23.8 1.0
CA J:GLY49 4.9 17.9 1.0
CA J:GLY46 4.9 23.1 1.0
CA J:GLY47 5.0 24.0 1.0
CB J:ALA50 5.0 17.0 1.0

Reference:

H.Cao, J.M.Pauff, R.Hille. X-Ray Crystal Structure of A Xanthine Oxidase Complex with the Flavonoid Inhibitor Quercetin. J Nat Prod V. 77 1693 2014.
PubMed: 25060641
DOI: 10.1021/NP500320G
Page generated: Sun Aug 4 16:45:52 2024

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