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Nickel in PDB 4i71: Crystal Structure of the Trypanosoma Brucei Inosine-Adenosine- Guanosine Nucleoside Hydrolase in Complex with A Trypanocidal Compound

Enzymatic activity of Crystal Structure of the Trypanosoma Brucei Inosine-Adenosine- Guanosine Nucleoside Hydrolase in Complex with A Trypanocidal Compound

All present enzymatic activity of Crystal Structure of the Trypanosoma Brucei Inosine-Adenosine- Guanosine Nucleoside Hydrolase in Complex with A Trypanocidal Compound:
3.2.2.1;

Protein crystallography data

The structure of Crystal Structure of the Trypanosoma Brucei Inosine-Adenosine- Guanosine Nucleoside Hydrolase in Complex with A Trypanocidal Compound, PDB code: 4i71 was solved by F.Giannese, M.Degano, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 133.30 / 1.28
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 66.360, 72.350, 133.280, 90.00, 90.00, 90.00
R / Rfree (%) 12.6 / 14.7

Other elements in 4i71:

The structure of Crystal Structure of the Trypanosoma Brucei Inosine-Adenosine- Guanosine Nucleoside Hydrolase in Complex with A Trypanocidal Compound also contains other interesting chemical elements:

Calcium (Ca) 1 atom

Nickel Binding Sites:

The binding sites of Nickel atom in the Crystal Structure of the Trypanosoma Brucei Inosine-Adenosine- Guanosine Nucleoside Hydrolase in Complex with A Trypanocidal Compound (pdb code 4i71). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 4 binding sites of Nickel where determined in the Crystal Structure of the Trypanosoma Brucei Inosine-Adenosine- Guanosine Nucleoside Hydrolase in Complex with A Trypanocidal Compound, PDB code: 4i71:
Jump to Nickel binding site number: 1; 2; 3; 4;

Nickel binding site 1 out of 4 in 4i71

Go back to Nickel Binding Sites List in 4i71
Nickel binding site 1 out of 4 in the Crystal Structure of the Trypanosoma Brucei Inosine-Adenosine- Guanosine Nucleoside Hydrolase in Complex with A Trypanocidal Compound


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Crystal Structure of the Trypanosoma Brucei Inosine-Adenosine- Guanosine Nucleoside Hydrolase in Complex with A Trypanocidal Compound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni403

b:12.1
occ:1.00
 O1 A:TRS405 2.0 12.7 0.7
NE2 A:HIS58 2.0 11.4 1.0
O A:HOH501 2.1 14.8 1.0
N A:TRS405 2.1 10.1 0.7
O2 A:TRS405 2.1 10.7 0.7
O3 A:TRS405 2.3 21.0 0.3
O1 A:TRS405 2.3 18.0 0.3
O2 A:TRS405 2.4 20.1 0.3
C3 A:TRS405 2.6 20.7 0.3
C A:TRS405 2.7 14.2 0.7
C1 A:TRS405 2.8 15.3 0.7
C2 A:TRS405 2.9 13.3 0.7
C1 A:TRS405 3.0 19.6 0.3
C A:TRS405 3.0 20.0 0.3
CE1 A:HIS58 3.0 11.6 1.0
CD2 A:HIS58 3.1 10.8 1.0
C2 A:TRS405 3.2 19.2 0.3
O A:HOH687 4.1 21.1 1.0
NZ A:LYS62 4.1 16.5 0.7
ND1 A:HIS58 4.1 10.9 1.0
C3 A:TRS405 4.2 14.5 0.7
CG A:HIS58 4.2 9.9 1.0
O A:HOH719 4.3 30.6 1.0
CE A:LYS62 4.3 16.2 0.7
N A:TRS405 4.4 21.0 0.3
O A:HOH773 4.7 24.0 1.0

Nickel binding site 2 out of 4 in 4i71

Go back to Nickel Binding Sites List in 4i71
Nickel binding site 2 out of 4 in the Crystal Structure of the Trypanosoma Brucei Inosine-Adenosine- Guanosine Nucleoside Hydrolase in Complex with A Trypanocidal Compound


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Crystal Structure of the Trypanosoma Brucei Inosine-Adenosine- Guanosine Nucleoside Hydrolase in Complex with A Trypanocidal Compound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni404

b:20.5
occ:0.70
 ND1 A:HIS0 1.9 20.0 1.0
N A:GLY-2 2.0 25.7 1.0
N A:SER-1 2.0 28.2 1.0
N A:HIS0 2.0 25.2 1.0
C A:SER-1 2.8 27.4 1.0
C A:GLY-2 2.8 28.6 1.0
CE1 A:HIS0 2.9 26.7 1.0
CG A:HIS0 2.9 23.6 1.0
CA A:GLY-2 2.9 28.6 1.0
CA A:SER-1 2.9 28.2 1.0
CA A:HIS0 3.0 25.4 1.0
CB A:HIS0 3.2 25.1 1.0
N A:MET1 3.7 24.1 1.0
OG A:SER-1 3.8 31.1 1.0
C A:HIS0 3.8 25.4 1.0
O A:HOH666 3.8 30.6 1.0
CB A:SER-1 3.9 30.3 1.0
NE2 A:HIS0 4.0 28.2 1.0
O A:SER-1 4.0 29.2 1.0
CD2 A:HIS0 4.0 27.7 1.0
O A:GLY-2 4.0 31.3 1.0
CG A:MET1 4.8 35.5 1.0
O A:HIS0 4.8 27.8 1.0
CA A:MET1 4.9 24.4 1.0

Nickel binding site 3 out of 4 in 4i71

Go back to Nickel Binding Sites List in 4i71
Nickel binding site 3 out of 4 in the Crystal Structure of the Trypanosoma Brucei Inosine-Adenosine- Guanosine Nucleoside Hydrolase in Complex with A Trypanocidal Compound


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 3 of Crystal Structure of the Trypanosoma Brucei Inosine-Adenosine- Guanosine Nucleoside Hydrolase in Complex with A Trypanocidal Compound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni406

b:36.2
occ:1.00
 NE2 A:HIS115 2.0 18.4 1.0
CE1 A:HIS115 3.0 16.9 1.0
CD2 A:HIS115 3.1 16.5 1.0
ND1 A:HIS115 4.1 15.6 1.0
CG A:HIS115 4.2 15.0 1.0
O A:HOH625 4.2 25.2 1.0
O A:GLU111 4.8 19.2 1.0
CB A:PRO67 4.9 12.1 1.0

Nickel binding site 4 out of 4 in 4i71

Go back to Nickel Binding Sites List in 4i71
Nickel binding site 4 out of 4 in the Crystal Structure of the Trypanosoma Brucei Inosine-Adenosine- Guanosine Nucleoside Hydrolase in Complex with A Trypanocidal Compound


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 4 of Crystal Structure of the Trypanosoma Brucei Inosine-Adenosine- Guanosine Nucleoside Hydrolase in Complex with A Trypanocidal Compound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni407

b:36.8
occ:1.00
 NE2 A:HIS317 2.1 20.4 1.0
O A:HOH701 2.2 33.1 1.0
O A:HOH656 2.2 33.4 1.0
CE1 A:HIS317 2.9 20.3 1.0
CD2 A:HIS317 3.1 20.2 1.0
ND1 A:HIS317 4.1 19.1 1.0
CG A:HIS317 4.2 17.6 1.0
O A:HOH631 4.7 26.6 1.0
CD1 A:PHE321 4.9 14.4 1.0
CE1 A:PHE321 5.0 15.4 1.0

Reference:

F.Giannese, M.Berg, P.Van Der Veken, V.Castagna, P.Tornaghi, K.Augustyns, M.Degano. Structures of Purine Nucleosidase From Trypanosoma Brucei Bound to Isozyme-Specific Trypanocidals and A Novel Metalorganic Inhibitor Acta Crystallogr.,Sect.D V. 69 1553 2013.
ISSN: ISSN 0907-4449
PubMed: 23897478
DOI: 10.1107/S0907444913010792
Page generated: Wed Oct 9 18:12:33 2024

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