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Iron in PDB 3nvz: Crystal Structure of Bovine Xanthine Oxidase in Complex with Indole-3- Aldehyde

Enzymatic activity of Crystal Structure of Bovine Xanthine Oxidase in Complex with Indole-3- Aldehyde

All present enzymatic activity of Crystal Structure of Bovine Xanthine Oxidase in Complex with Indole-3- Aldehyde:
1.17.1.4; 1.17.3.2;

Protein crystallography data

The structure of Crystal Structure of Bovine Xanthine Oxidase in Complex with Indole-3- Aldehyde, PDB code: 3nvz 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) 45.20 / 1.60
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 133.409, 73.704, 138.922, 90.00, 97.12, 90.00
R / Rfree (%) 21.5 / 24.6

Other elements in 3nvz:

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

Iron binding site 1 out of 8 in 3nvz

Go back to Iron Binding Sites List in 3nvz
Iron binding site 1 out of 8 in the Crystal Structure of Bovine Xanthine Oxidase in Complex with Indole-3- Aldehyde


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 Indole-3- Aldehyde within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe601

b:11.8
occ:1.00
 FE1 A:FES601 0.0 11.8 1.0
S1 A:FES601 2.2 13.9 1.0
S2 A:FES601 2.3 13.2 1.0
SG A:CYS113 2.4 12.0 1.0
SG A:CYS150 2.5 14.4 1.0
FE2 A:FES601 2.7 11.4 1.0
CB A:CYS150 3.3 11.3 1.0
CB A:CYS113 3.4 11.8 1.0
O C:HOH419 3.6 12.0 1.0
N A:CYS113 3.7 12.5 1.0
CA A:CYS113 3.9 12.3 1.0
N A:GLY114 3.9 12.8 1.0
N A:CYS150 4.1 10.9 1.0
C A:CYS113 4.3 12.8 1.0
CA A:CYS150 4.4 10.4 1.0
N A:PHE115 4.4 10.3 1.0
SG A:CYS148 4.4 11.8 1.0
SG A:CYS116 4.6 13.2 1.0
N A:ARG149 4.7 11.9 1.0
C A:GLN112 4.7 12.0 1.0
CB A:GLN112 4.8 12.8 1.0
N A:CYS116 4.9 9.2 1.0
CA A:GLY114 4.9 11.8 1.0

Iron binding site 2 out of 8 in 3nvz

Go back to Iron Binding Sites List in 3nvz
Iron binding site 2 out of 8 in the Crystal Structure of Bovine Xanthine Oxidase in Complex with Indole-3- Aldehyde


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 Indole-3- Aldehyde within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe601

b:11.4
occ:1.00
 FE2 A:FES601 0.0 11.4 1.0
S2 A:FES601 2.2 13.2 1.0
S1 A:FES601 2.2 13.9 1.0
SG A:CYS116 2.3 13.2 1.0
SG A:CYS148 2.4 11.8 1.0
FE1 A:FES601 2.7 11.8 1.0
CB A:CYS148 3.3 10.8 1.0
CB A:CYS116 3.4 10.7 1.0
CA A:CYS148 3.6 11.0 1.0
N A:ARG149 4.0 11.9 1.0
N A:CYS116 4.2 9.2 1.0
C A:CYS148 4.2 11.7 1.0
N A:CYS150 4.3 10.9 1.0
O A:HOH177 4.4 10.8 1.0
CA A:CYS116 4.4 10.3 1.0
CB A:CYS150 4.4 11.3 1.0
SG A:CYS150 4.6 14.4 1.0
CG2 A:THR151 4.7 10.2 1.0
SG A:CYS113 4.7 12.0 1.0
O A:LEU147 4.9 11.0 1.0
N A:CYS148 4.9 11.0 1.0
CA A:CYS150 5.0 10.4 1.0

Iron binding site 3 out of 8 in 3nvz

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


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 Indole-3- Aldehyde within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe602

b:12.9
occ:1.00
 FE1 A:FES602 0.0 12.9 1.0
S1 A:FES602 2.2 14.4 1.0
S2 A:FES602 2.2 14.4 1.0
SG A:CYS51 2.3 12.8 1.0
SG A:CYS73 2.3 14.8 1.0
FE2 A:FES602 2.8 12.5 1.0
CB A:CYS73 3.1 14.0 1.0
CB A:CYS51 3.4 12.5 1.0
N A:CYS73 4.2 14.5 1.0
CA A:CYS73 4.2 14.3 1.0
CB A:ASN71 4.3 15.6 1.0
N A:GLY46 4.4 15.2 1.0
OD1 A:ASN71 4.4 19.4 1.0
N A:CYS51 4.4 11.7 1.0
N A:GLY44 4.4 13.2 1.0
SG A:CYS43 4.4 12.8 1.0
CA A:CYS51 4.5 11.9 1.0
CG A:ASN71 4.5 17.6 1.0
CA A:GLY46 4.6 14.8 1.0
SG A:CYS48 4.7 13.2 1.0
CA A:GLY44 4.7 13.2 1.0
N A:GLY49 4.8 12.0 1.0
N A:GLU45 4.9 13.8 1.0
CA A:ASN71 4.9 14.9 1.0

Iron binding site 4 out of 8 in 3nvz

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Iron binding site 4 out of 8 in the Crystal Structure of Bovine Xanthine Oxidase in Complex with Indole-3- Aldehyde


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 Indole-3- Aldehyde within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe602

b:12.5
occ:1.00
 FE2 A:FES602 0.0 12.5 1.0
S1 A:FES602 2.3 14.4 1.0
S2 A:FES602 2.3 14.4 1.0
SG A:CYS48 2.3 13.2 1.0
SG A:CYS43 2.4 12.8 1.0
FE1 A:FES602 2.8 12.9 1.0
N A:CYS43 3.3 13.8 1.0
CB A:CYS48 3.4 13.7 1.0
CB A:CYS43 3.5 13.8 1.0
N A:CYS48 3.5 13.9 1.0
N A:GLY49 3.8 12.0 1.0
CA A:CYS43 3.8 13.9 1.0
CA A:CYS48 3.9 13.0 1.0
N A:GLY44 3.9 13.2 1.0
C A:GLY42 4.0 14.0 1.0
C A:CYS48 4.2 12.5 1.0
C A:CYS43 4.3 14.0 1.0
N A:GLY42 4.3 13.6 1.0
CA A:GLY42 4.3 13.2 1.0
N A:GLY47 4.4 14.8 1.0
N A:GLY46 4.4 15.2 1.0
N A:ALA50 4.5 11.6 1.0
SG A:CYS73 4.5 14.8 1.0
SG A:CYS51 4.6 12.8 1.0
N A:GLU45 4.7 13.8 1.0
C A:GLY47 4.7 14.4 1.0
C A:GLY46 4.8 15.0 1.0
CA A:GLY49 4.8 12.1 1.0
CA A:GLY46 4.8 14.8 1.0
O A:GLY42 4.9 13.3 1.0
CA A:GLY44 4.9 13.2 1.0

Iron binding site 5 out of 8 in 3nvz

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Iron binding site 5 out of 8 in the Crystal Structure of Bovine Xanthine Oxidase in Complex with Indole-3- Aldehyde


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 Indole-3- Aldehyde within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Fe601

b:13.3
occ:1.00
 FE1 J:FES601 0.0 13.3 1.0
S1 J:FES601 2.2 15.3 1.0
S2 J:FES601 2.2 15.3 1.0
SG J:CYS113 2.4 13.2 1.0
SG J:CYS150 2.5 16.1 1.0
FE2 J:FES601 2.7 13.4 1.0
CB J:CYS113 3.4 13.1 1.0
CB J:CYS150 3.4 14.1 1.0
N J:CYS113 3.6 13.4 1.0
O L:HOH372 3.7 13.8 1.0
CA J:CYS113 3.9 13.0 1.0
N J:GLY114 3.9 13.4 1.0
N J:CYS150 4.2 13.2 1.0
C J:CYS113 4.3 12.9 1.0
N J:PHE115 4.4 11.4 1.0
CA J:CYS150 4.4 13.6 1.0
SG J:CYS148 4.4 14.4 1.0
SG J:CYS116 4.6 15.7 1.0
C J:GLN112 4.7 12.6 1.0
N J:ARG149 4.7 14.4 1.0
CB J:GLN112 4.9 13.4 1.0
CA J:GLY114 4.9 12.3 1.0
N J:CYS116 4.9 11.7 1.0

Iron binding site 6 out of 8 in 3nvz

Go back to Iron Binding Sites List in 3nvz
Iron binding site 6 out of 8 in the Crystal Structure of Bovine Xanthine Oxidase in Complex with Indole-3- Aldehyde


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 Indole-3- Aldehyde within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Fe601

b:13.4
occ:1.00
 FE2 J:FES601 0.0 13.4 1.0
S2 J:FES601 2.2 15.3 1.0
S1 J:FES601 2.2 15.3 1.0
SG J:CYS116 2.4 15.7 1.0
SG J:CYS148 2.4 14.4 1.0
FE1 J:FES601 2.7 13.3 1.0
CB J:CYS148 3.3 14.9 1.0
CB J:CYS116 3.5 11.8 1.0
CA J:CYS148 3.7 14.6 1.0
N J:ARG149 4.1 14.4 1.0
N J:CYS116 4.3 11.7 1.0
C J:CYS148 4.3 14.5 1.0
O J:HOH183 4.3 15.7 1.0
N J:CYS150 4.4 13.2 1.0
CB J:CYS150 4.4 14.1 1.0
CA J:CYS116 4.5 11.9 1.0
SG J:CYS150 4.5 16.1 1.0
SG J:CYS113 4.7 13.2 1.0
CG2 J:THR151 4.8 14.4 1.0
O J:LEU147 4.9 14.3 1.0
CA J:CYS150 5.0 13.6 1.0

Iron binding site 7 out of 8 in 3nvz

Go back to Iron Binding Sites List in 3nvz
Iron binding site 7 out of 8 in the Crystal Structure of Bovine Xanthine Oxidase in Complex with Indole-3- Aldehyde


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 Indole-3- Aldehyde within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Fe602

b:13.9
occ:1.00
 FE1 J:FES602 0.0 13.9 1.0
S2 J:FES602 2.2 14.8 1.0
S1 J:FES602 2.2 15.4 1.0
SG J:CYS51 2.3 14.3 1.0
SG J:CYS73 2.4 15.0 1.0
FE2 J:FES602 2.7 14.2 1.0
CB J:CYS73 3.1 14.5 1.0
CB J:CYS51 3.4 14.0 1.0
N J:CYS73 4.2 13.9 1.0
CA J:CYS73 4.3 14.5 1.0
CB J:ASN71 4.3 14.9 1.0
N J:CYS51 4.3 12.6 1.0
N J:GLY46 4.4 15.9 1.0
N J:GLY44 4.4 14.6 1.0
OD1 J:ASN71 4.4 17.8 1.0
SG J:CYS43 4.4 15.3 1.0
CG J:ASN71 4.5 15.0 1.0
CA J:CYS51 4.5 13.5 1.0
CA J:GLY46 4.6 16.2 1.0
SG J:CYS48 4.6 15.6 1.0
CA J:GLY44 4.7 14.1 1.0
N J:GLY49 4.7 13.1 1.0
N J:GLU45 4.9 15.0 1.0
CA J:ASN71 5.0 14.8 1.0

Iron binding site 8 out of 8 in 3nvz

Go back to Iron Binding Sites List in 3nvz
Iron binding site 8 out of 8 in the Crystal Structure of Bovine Xanthine Oxidase in Complex with Indole-3- Aldehyde


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 Indole-3- Aldehyde within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Fe602

b:14.2
occ:1.00
 FE2 J:FES602 0.0 14.2 1.0
S2 J:FES602 2.2 14.8 1.0
S1 J:FES602 2.3 15.4 1.0
SG J:CYS48 2.3 15.6 1.0
SG J:CYS43 2.4 15.3 1.0
FE1 J:FES602 2.7 13.9 1.0
CB J:CYS48 3.4 16.1 1.0
N J:CYS43 3.4 14.8 1.0
CB J:CYS43 3.5 14.4 1.0
N J:CYS48 3.5 17.5 1.0
N J:GLY49 3.8 13.1 1.0
CA J:CYS48 3.8 15.2 1.0
CA J:CYS43 3.9 14.6 1.0
N J:GLY44 3.9 14.6 1.0
C J:GLY42 4.1 14.2 1.0
C J:CYS48 4.2 14.2 1.0
C J:CYS43 4.3 15.2 1.0
N J:GLY42 4.3 13.2 1.0
N J:GLY47 4.3 17.2 1.0
CA J:GLY42 4.4 13.7 1.0
N J:ALA50 4.5 13.4 1.0
N J:GLY46 4.5 15.9 1.0
SG J:CYS73 4.5 15.0 1.0
SG J:CYS51 4.6 14.3 1.0
N J:GLU45 4.7 15.0 1.0
C J:GLY47 4.7 17.7 1.0
C J:GLY46 4.8 17.2 1.0
CA J:GLY49 4.8 13.0 1.0
O J:GLY42 4.9 13.2 1.0
CA J:GLY46 4.9 16.2 1.0
CA J:GLY44 4.9 14.1 1.0
CB J:ALA50 5.0 12.8 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 16:46:32 2024

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