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Nickel in PDB 4i72: Crystal Structure of the Trypanosoma Brucei Inosine-Adenosine- Guanosine Nucleoside Hydrolase in Complex with Immucillin A

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

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

Protein crystallography data

The structure of Crystal Structure of the Trypanosoma Brucei Inosine-Adenosine- Guanosine Nucleoside Hydrolase in Complex with Immucillin A, PDB code: 4i72 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) 47.92 / 2.05
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 72.750, 130.980, 63.690, 90.00, 90.00, 90.00
R / Rfree (%) 17.7 / 23.4

Other elements in 4i72:

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

Calcium (Ca) 2 atoms

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 Immucillin A (pdb code 4i72). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 7 binding sites of Nickel where determined in the Crystal Structure of the Trypanosoma Brucei Inosine-Adenosine- Guanosine Nucleoside Hydrolase in Complex with Immucillin A, PDB code: 4i72:
Jump to Nickel binding site number: 1; 2; 3; 4; 5; 6; 7;

Nickel binding site 1 out of 7 in 4i72

Go back to Nickel Binding Sites List in 4i72
Nickel binding site 1 out of 7 in the Crystal Structure of the Trypanosoma Brucei Inosine-Adenosine- Guanosine Nucleoside Hydrolase in Complex with Immucillin A


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 Immucillin A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni403

b:32.4
occ:1.00
 O A:HOH703 1.8 27.6 1.0
O1 A:TRS406 1.9 42.2 1.0
O3 A:TRS406 2.0 39.2 1.0
OD1 A:ASP253 2.1 30.8 1.0
O2 A:TRS406 2.1 38.8 1.0
CG A:ASP253 2.9 32.1 1.0
C3 A:TRS406 3.1 40.9 1.0
OD2 A:ASP253 3.1 29.3 1.0
C1 A:TRS406 3.1 42.9 1.0
C2 A:TRS406 3.2 41.2 1.0
C A:TRS406 3.3 41.4 1.0
O A:HOH550 3.8 29.6 1.0
O A:ILE250 4.1 29.8 1.0
O A:HOH701 4.1 29.4 1.0
O A:HOH702 4.3 42.6 1.0
CB A:ASP253 4.3 31.3 1.0
O A:LEU251 4.5 27.2 1.0
N A:TRS406 4.7 42.5 1.0
CA A:ASP253 4.9 31.0 1.0
N A:ASP253 4.9 30.1 1.0
O A:HOH715 5.0 41.0 1.0

Nickel binding site 2 out of 7 in 4i72

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Nickel binding site 2 out of 7 in the Crystal Structure of the Trypanosoma Brucei Inosine-Adenosine- Guanosine Nucleoside Hydrolase in Complex with Immucillin A


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 Immucillin A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni404

b:57.6
occ:1.00
 NE2 A:HIS115 2.1 39.6 1.0
CE1 A:HIS115 3.0 38.3 1.0
CD2 A:HIS115 3.1 37.6 1.0
ND1 A:HIS115 4.1 39.3 1.0
CG A:HIS115 4.2 37.7 1.0
OE2 A:GLU111 4.6 52.5 1.0
O A:GLU111 4.7 36.9 1.0
CG A:GLU111 4.7 43.1 1.0
CB A:PRO67 4.9 28.0 1.0

Nickel binding site 3 out of 7 in 4i72

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Nickel binding site 3 out of 7 in the Crystal Structure of the Trypanosoma Brucei Inosine-Adenosine- Guanosine Nucleoside Hydrolase in Complex with Immucillin A


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 Immucillin A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni405

b:42.9
occ:1.00
 ND1 A:HIS0 1.9 43.5 1.0
N A:SER-1 2.1 49.5 1.0
N A:GLY-2 2.1 50.7 1.0
N A:HIS0 2.2 47.5 1.0
C A:GLY-2 2.9 50.1 1.0
CE1 A:HIS0 2.9 44.0 1.0
CA A:GLY-2 2.9 50.6 1.0
CG A:HIS0 2.9 45.3 1.0
C A:SER-1 3.0 48.6 1.0
CA A:SER-1 3.0 49.3 1.0
CA A:HIS0 3.2 46.5 1.0
CB A:HIS0 3.3 46.6 1.0
N A:MET1 3.7 44.5 1.0
OG A:SER-1 3.7 50.3 1.0
CB A:SER-1 3.8 49.7 1.0
C A:HIS0 3.9 45.9 1.0
NE2 A:HIS0 4.0 44.9 1.0
CD2 A:HIS0 4.1 45.1 1.0
O A:GLY-2 4.1 50.8 1.0
O A:SER-1 4.2 49.2 1.0
CA A:MET1 4.9 43.2 1.0
O A:HIS0 5.0 46.0 1.0

Nickel binding site 4 out of 7 in 4i72

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Nickel binding site 4 out of 7 in the Crystal Structure of the Trypanosoma Brucei Inosine-Adenosine- Guanosine Nucleoside Hydrolase in Complex with Immucillin A


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 Immucillin A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ni403

b:86.5
occ:1.00
 NE2 B:HIS115 2.1 40.4 1.0
O B:HOH696 2.6 44.9 1.0
CE1 B:HIS115 3.0 39.9 1.0
CD2 B:HIS115 3.2 39.4 1.0
O B:HOH564 3.6 38.8 1.0
ND1 B:HIS115 4.2 39.9 1.0
OE2 B:GLU111 4.2 55.3 1.0
CG B:HIS115 4.3 38.5 1.0
CG B:GLU111 4.3 44.0 1.0
O B:GLU111 4.6 37.2 1.0
CD B:GLU111 4.7 51.3 1.0

Nickel binding site 5 out of 7 in 4i72

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Nickel binding site 5 out of 7 in the Crystal Structure of the Trypanosoma Brucei Inosine-Adenosine- Guanosine Nucleoside Hydrolase in Complex with Immucillin A


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 5 of Crystal Structure of the Trypanosoma Brucei Inosine-Adenosine- Guanosine Nucleoside Hydrolase in Complex with Immucillin A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ni404

b:32.7
occ:1.00
 O B:HOH715 1.8 31.0 1.0
OD1 B:ASP253 2.2 32.2 1.0
CG B:ASP253 3.0 33.1 1.0
OD2 B:ASP253 3.2 31.5 1.0
O B:HOH514 4.1 43.4 1.0
O B:ILE250 4.1 29.9 1.0
CB B:ASP253 4.4 33.1 1.0
O B:LEU251 4.6 30.0 1.0
CA B:ASP253 4.9 33.2 1.0

Nickel binding site 6 out of 7 in 4i72

Go back to Nickel Binding Sites List in 4i72
Nickel binding site 6 out of 7 in the Crystal Structure of the Trypanosoma Brucei Inosine-Adenosine- Guanosine Nucleoside Hydrolase in Complex with Immucillin A


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 6 of Crystal Structure of the Trypanosoma Brucei Inosine-Adenosine- Guanosine Nucleoside Hydrolase in Complex with Immucillin A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ni405

b:44.9
occ:1.00
 ND1 B:HIS0 1.9 43.2 1.0
N B:HIS0 2.2 47.2 1.0
N B:GLY-2 2.3 50.6 1.0
N B:SER-1 2.3 50.6 1.0
CE1 B:HIS0 2.9 44.1 1.0
CG B:HIS0 2.9 44.6 1.0
C B:SER-1 3.1 48.8 1.0
C B:GLY-2 3.1 50.5 1.0
CA B:GLY-2 3.1 50.9 1.0
CA B:SER-1 3.1 49.7 1.0
CA B:HIS0 3.2 45.8 1.0
CB B:HIS0 3.3 46.0 1.0
N B:MET1 3.5 44.0 1.0
O B:HOH595 3.6 51.2 1.0
OG B:SER-1 3.7 50.6 1.0
C B:HIS0 3.8 45.3 1.0
CB B:SER-1 3.8 49.8 1.0
NE2 B:HIS0 4.0 44.7 1.0
CD2 B:HIS0 4.1 43.9 1.0
O B:GLY-2 4.2 50.7 1.0
O B:SER-1 4.3 49.3 1.0
CA B:MET1 4.8 43.2 1.0
O B:HIS0 4.9 44.6 1.0
CB B:MET1 4.9 44.1 1.0
CG B:MET1 4.9 47.8 1.0

Nickel binding site 7 out of 7 in 4i72

Go back to Nickel Binding Sites List in 4i72
Nickel binding site 7 out of 7 in the Crystal Structure of the Trypanosoma Brucei Inosine-Adenosine- Guanosine Nucleoside Hydrolase in Complex with Immucillin A


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 7 of Crystal Structure of the Trypanosoma Brucei Inosine-Adenosine- Guanosine Nucleoside Hydrolase in Complex with Immucillin A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ni406

b:84.4
occ:1.00
 NE2 B:HIS317 2.2 39.5 1.0
CE1 B:HIS317 2.8 40.0 1.0
CD2 B:HIS317 3.4 37.2 1.0
ND1 B:HIS317 4.1 39.2 1.0
O B:HOH566 4.3 35.6 1.0
CG B:HIS317 4.3 37.0 1.0
CD1 B:PHE321 4.7 31.9 1.0
CG B:PHE321 4.7 30.3 1.0
CE1 B:PHE321 5.0 31.7 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 18:12:40 2024

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