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Iron in PDB 3nvv: Crystal Structure of Bovine Xanthine Oxidase in Complex with Arsenite

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

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

Protein crystallography data

The structure of Crystal Structure of Bovine Xanthine Oxidase in Complex with Arsenite, PDB code: 3nvv 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) 131.80 / 1.82
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 132.766, 73.418, 138.158, 90.00, 96.93, 90.00
R / Rfree (%) 19.3 / 22.9

Other elements in 3nvv:

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

Molybdenum (Mo) 2 atoms
Arsenic (As) 2 atoms

Iron Binding Sites:

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

Iron binding site 1 out of 8 in 3nvv

Go back to Iron Binding Sites List in 3nvv
Iron binding site 1 out of 8 in the Crystal Structure of Bovine Xanthine Oxidase in Complex with Arsenite


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

b:13.6
occ:1.00
FE1 A:FES601 0.0 13.6 1.0
S1 A:FES601 2.2 14.5 1.0
S2 A:FES601 2.2 15.6 1.0
SG A:CYS150 2.4 12.3 1.0
SG A:CYS113 2.4 12.1 1.0
FE2 A:FES601 2.7 14.7 1.0
CB A:CYS113 3.3 13.6 1.0
CB A:CYS150 3.3 13.0 1.0
N A:CYS113 3.5 12.5 1.0
O C:HOH136 3.7 13.0 1.0
CA A:CYS113 3.8 12.3 1.0
N A:GLY114 3.8 10.8 1.0
N A:CYS150 4.1 12.5 1.0
C A:CYS113 4.2 11.7 1.0
CA A:CYS150 4.3 12.7 1.0
N A:PHE115 4.4 10.3 1.0
SG A:CYS148 4.5 13.1 1.0
SG A:CYS116 4.6 12.8 1.0
C A:GLN112 4.7 12.1 1.0
N A:ARG149 4.8 12.0 1.0
CB A:GLN112 4.8 10.8 1.0
CA A:GLY114 4.9 10.3 1.0
N A:CYS116 4.9 9.9 1.0

Iron binding site 2 out of 8 in 3nvv

Go back to Iron Binding Sites List in 3nvv
Iron binding site 2 out of 8 in the Crystal Structure of Bovine Xanthine Oxidase in Complex with Arsenite


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

b:14.7
occ:1.00
FE2 A:FES601 0.0 14.7 1.0
S2 A:FES601 2.2 15.6 1.0
S1 A:FES601 2.2 14.5 1.0
SG A:CYS116 2.3 12.8 1.0
SG A:CYS148 2.5 13.1 1.0
FE1 A:FES601 2.7 13.6 1.0
CB A:CYS116 3.4 9.3 1.0
CB A:CYS148 3.4 12.5 1.0
CA A:CYS148 3.6 13.2 1.0
N A:ARG149 4.1 12.0 1.0
N A:CYS116 4.2 9.9 1.0
O A:HOH166 4.2 13.0 1.0
C A:CYS148 4.3 12.1 1.0
N A:CYS150 4.4 12.5 1.0
CA A:CYS116 4.4 11.1 1.0
SG A:CYS150 4.5 12.3 1.0
CB A:CYS150 4.5 13.0 1.0
SG A:CYS113 4.8 12.1 1.0
CG2 A:THR151 4.8 12.9 1.0
O A:LEU147 4.9 13.8 1.0
N A:CYS148 4.9 12.6 1.0
C A:CYS116 5.0 11.4 1.0

Iron binding site 3 out of 8 in 3nvv

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


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

b:15.3
occ:1.00
FE1 A:FES602 0.0 15.3 1.0
S2 A:FES602 2.2 16.8 1.0
S1 A:FES602 2.2 16.8 1.0
SG A:CYS51 2.3 14.4 1.0
SG A:CYS73 2.3 15.8 1.0
FE2 A:FES602 2.8 14.8 1.0
CB A:CYS73 3.1 17.5 1.0
CB A:CYS51 3.4 13.3 1.0
CB A:ASN71 4.1 17.7 1.0
N A:CYS73 4.2 17.2 1.0
CA A:CYS73 4.2 17.6 1.0
N A:CYS51 4.3 14.7 1.0
N A:GLY46 4.3 18.2 1.0
OD1 A:ASN71 4.4 18.8 1.0
CG A:ASN71 4.4 18.6 1.0
SG A:CYS43 4.5 13.5 1.0
CA A:CYS51 4.5 13.8 1.0
N A:GLY44 4.5 15.0 1.0
CA A:GLY46 4.5 17.5 1.0
SG A:CYS48 4.6 14.3 1.0
CA A:GLY44 4.8 17.2 1.0
N A:GLY49 4.9 14.3 1.0
CA A:ASN71 4.9 17.9 1.0
N A:GLU45 4.9 17.9 1.0

Iron binding site 4 out of 8 in 3nvv

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


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

b:14.8
occ:1.00
FE2 A:FES602 0.0 14.8 1.0
S1 A:FES602 2.2 16.8 1.0
SG A:CYS48 2.2 14.3 1.0
S2 A:FES602 2.2 16.8 1.0
SG A:CYS43 2.4 13.5 1.0
FE1 A:FES602 2.8 15.3 1.0
CB A:CYS48 3.3 15.0 1.0
N A:CYS43 3.4 14.4 1.0
CB A:CYS43 3.5 14.3 1.0
N A:CYS48 3.6 15.3 1.0
CA A:CYS48 3.9 15.3 1.0
N A:GLY49 3.9 14.3 1.0
CA A:CYS43 3.9 14.9 1.0
N A:GLY44 3.9 15.0 1.0
C A:GLY42 4.0 15.4 1.0
CA A:GLY42 4.2 15.2 1.0
N A:GLY42 4.2 13.9 1.0
C A:CYS48 4.2 14.7 1.0
C A:CYS43 4.4 15.6 1.0
N A:GLY47 4.4 17.3 1.0
N A:ALA50 4.4 13.5 1.0
SG A:CYS73 4.4 15.8 1.0
N A:GLY46 4.4 18.2 1.0
SG A:CYS51 4.6 14.4 1.0
C A:GLY47 4.7 16.9 1.0
N A:GLU45 4.7 17.9 1.0
C A:GLY46 4.8 18.5 1.0
CA A:GLY46 4.8 17.5 1.0
CA A:GLY49 4.9 14.1 1.0
O A:GLY42 4.9 15.8 1.0
CB A:ALA50 4.9 13.2 1.0
CA A:GLY44 4.9 17.2 1.0

Iron binding site 5 out of 8 in 3nvv

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


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

b:14.6
occ:1.00
FE1 J:FES601 0.0 14.6 1.0
S1 J:FES601 2.2 16.2 1.0
S2 J:FES601 2.2 16.5 1.0
SG J:CYS150 2.3 14.4 1.0
SG J:CYS113 2.4 15.7 1.0
FE2 J:FES601 2.6 14.6 1.0
CB J:CYS150 3.2 14.8 1.0
CB J:CYS113 3.3 14.5 1.0
N J:CYS113 3.6 13.0 1.0
O L:HOH384 3.7 15.1 1.0
CA J:CYS113 3.9 13.0 1.0
N J:GLY114 4.0 11.9 1.0
N J:CYS150 4.0 16.0 1.0
CA J:CYS150 4.2 14.7 1.0
SG J:CYS148 4.3 17.4 1.0
C J:CYS113 4.3 13.6 1.0
N J:PHE115 4.5 13.2 1.0
SG J:CYS116 4.6 14.7 1.0
C J:GLN112 4.7 13.3 1.0
N J:ARG149 4.7 16.0 1.0
CB J:GLN112 4.8 13.1 1.0
N J:CYS116 4.9 15.0 1.0
C J:ARG149 5.0 16.0 1.0
CA J:GLY114 5.0 12.8 1.0

Iron binding site 6 out of 8 in 3nvv

Go back to Iron Binding Sites List in 3nvv
Iron binding site 6 out of 8 in the Crystal Structure of Bovine Xanthine Oxidase in Complex with Arsenite


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

b:14.6
occ:1.00
FE2 J:FES601 0.0 14.6 1.0
S1 J:FES601 2.2 16.2 1.0
S2 J:FES601 2.2 16.5 1.0
SG J:CYS116 2.2 14.7 1.0
SG J:CYS148 2.4 17.4 1.0
FE1 J:FES601 2.6 14.6 1.0
CB J:CYS148 3.3 16.4 1.0
CB J:CYS116 3.4 15.3 1.0
CA J:CYS148 3.6 16.1 1.0
N J:ARG149 4.1 16.0 1.0
N J:CYS116 4.2 15.0 1.0
C J:CYS148 4.3 16.0 1.0
N J:CYS150 4.3 16.0 1.0
O J:HOH584 4.3 14.9 1.0
CA J:CYS116 4.4 15.0 1.0
SG J:CYS150 4.4 14.4 1.0
CB J:CYS150 4.5 14.8 1.0
SG J:CYS113 4.6 15.7 1.0
CG2 J:THR151 4.8 14.2 1.0
N J:CYS148 4.9 16.1 1.0
O J:LEU147 5.0 16.4 1.0
CA J:CYS150 5.0 14.7 1.0
C J:CYS116 5.0 15.2 1.0

Iron binding site 7 out of 8 in 3nvv

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


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

b:16.5
occ:1.00
FE1 J:FES602 0.0 16.5 1.0
S1 J:FES602 2.2 15.7 1.0
S2 J:FES602 2.2 15.3 1.0
SG J:CYS73 2.2 16.7 1.0
SG J:CYS51 2.2 17.6 1.0
FE2 J:FES602 2.8 16.2 1.0
CB J:CYS73 3.1 17.6 1.0
CB J:CYS51 3.4 16.5 1.0
CB J:ASN71 4.1 16.4 1.0
N J:CYS73 4.2 16.7 1.0
CA J:CYS73 4.2 17.6 1.0
N J:CYS51 4.3 15.3 1.0
N J:GLY46 4.3 20.1 1.0
SG J:CYS43 4.4 16.9 1.0
CG J:ASN71 4.4 18.2 1.0
CA J:CYS51 4.5 15.8 1.0
OD1 J:ASN71 4.5 20.7 1.0
N J:GLY44 4.5 18.1 1.0
CA J:GLY46 4.5 20.0 1.0
SG J:CYS48 4.7 16.9 1.0
CA J:GLY44 4.7 17.9 1.0
N J:GLY49 4.8 15.8 1.0
CA J:ASN71 4.8 17.1 1.0
N J:GLU45 4.9 19.2 1.0

Iron binding site 8 out of 8 in 3nvv

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


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

b:16.2
occ:1.00
FE2 J:FES602 0.0 16.2 1.0
S2 J:FES602 2.2 15.3 1.0
S1 J:FES602 2.2 15.7 1.0
SG J:CYS43 2.3 16.9 1.0
SG J:CYS48 2.3 16.9 1.0
FE1 J:FES602 2.8 16.5 1.0
N J:CYS43 3.4 18.0 1.0
CB J:CYS48 3.4 17.0 1.0
CB J:CYS43 3.5 16.0 1.0
N J:CYS48 3.5 17.4 1.0
N J:GLY49 3.8 15.8 1.0
CA J:CYS43 3.9 16.9 1.0
CA J:CYS48 3.9 17.3 1.0
N J:GLY44 3.9 18.1 1.0
C J:GLY42 4.0 17.2 1.0
C J:CYS48 4.2 16.1 1.0
N J:GLY47 4.3 20.2 1.0
N J:GLY42 4.3 16.5 1.0
C J:CYS43 4.3 18.4 1.0
CA J:GLY42 4.3 16.9 1.0
SG J:CYS73 4.4 16.7 1.0
N J:GLY46 4.5 20.1 1.0
N J:ALA50 4.5 15.8 1.0
SG J:CYS51 4.6 17.6 1.0
C J:GLY47 4.6 19.9 1.0
N J:GLU45 4.7 19.2 1.0
C J:GLY46 4.8 20.0 1.0
O J:GLY42 4.8 17.2 1.0
CA J:GLY49 4.8 15.9 1.0
CA J:GLY46 4.9 20.0 1.0
CA J:GLY44 4.9 17.9 1.0
CA J:GLY47 5.0 19.7 1.0

Reference:

H.Cao, J.Hall, R.Hille. X-Ray Crystal Structure of Arsenite-Inhibited Xanthine Oxidase: Mu-Sulfido,Mu-Oxo Double Bridge Between Molybdenum and Arsenic in the Active Site. J.Am.Chem.Soc. V. 133 12414 2011.
ISSN: ISSN 0002-7863
PubMed: 21761899
DOI: 10.1021/JA2050265
Page generated: Sun Aug 4 16:44:30 2024

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