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Nickel in PDB 4i73: Crystal Structure of the Trypanosoma Brucei Inosine-Adenosine- Guanosine Nucleoside Hydrolase in Complex with Compound Uamc-00312

Enzymatic activity of Crystal Structure of the Trypanosoma Brucei Inosine-Adenosine- Guanosine Nucleoside Hydrolase in Complex with Compound Uamc-00312

All present enzymatic activity of Crystal Structure of the Trypanosoma Brucei Inosine-Adenosine- Guanosine Nucleoside Hydrolase in Complex with Compound Uamc-00312:
3.2.2.1;

Protein crystallography data

The structure of Crystal Structure of the Trypanosoma Brucei Inosine-Adenosine- Guanosine Nucleoside Hydrolase in Complex with Compound Uamc-00312, PDB code: 4i73 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) 71.83 / 2.18
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 63.170, 131.670, 71.850, 90.00, 91.33, 90.00
R / Rfree (%) 20 / 24.8

Other elements in 4i73:

The structure of Crystal Structure of the Trypanosoma Brucei Inosine-Adenosine- Guanosine Nucleoside Hydrolase in Complex with Compound Uamc-00312 also contains other interesting chemical elements:

Calcium (Ca) 4 atoms

Nickel Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 17;

Binding sites:

The binding sites of Nickel atom in the Crystal Structure of the Trypanosoma Brucei Inosine-Adenosine- Guanosine Nucleoside Hydrolase in Complex with Compound Uamc-00312 (pdb code 4i73). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 17 binding sites of Nickel where determined in the Crystal Structure of the Trypanosoma Brucei Inosine-Adenosine- Guanosine Nucleoside Hydrolase in Complex with Compound Uamc-00312, PDB code: 4i73:
Jump to Nickel binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Nickel binding site 1 out of 17 in 4i73

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Nickel binding site 1 out of 17 in the Crystal Structure of the Trypanosoma Brucei Inosine-Adenosine- Guanosine Nucleoside Hydrolase in Complex with Compound Uamc-00312


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 Compound Uamc-00312 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni403

b:26.7
occ:1.00
 O A:HOH628 2.0 22.0 1.0
NE2 B:HIS58 2.1 25.3 1.0
OD1 A:ASP253 2.2 34.0 1.0
O A:HOH635 2.2 19.4 1.0
O A:HOH627 2.5 19.8 1.0
CD2 B:HIS58 2.9 25.7 1.0
CG A:ASP253 3.0 33.4 1.0
OD2 A:ASP253 3.3 35.8 1.0
CE1 B:HIS58 3.3 25.1 1.0
CG B:HIS58 4.1 26.4 1.0
O A:HOH621 4.2 22.8 1.0
ND1 B:HIS58 4.3 26.4 1.0
O A:ILE250 4.4 31.2 1.0
CB A:ASP253 4.4 32.3 1.0
O A:LEU251 4.4 30.3 1.0
CA A:ASP253 5.0 32.2 1.0

Nickel binding site 2 out of 17 in 4i73

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Nickel binding site 2 out of 17 in the Crystal Structure of the Trypanosoma Brucei Inosine-Adenosine- Guanosine Nucleoside Hydrolase in Complex with Compound Uamc-00312


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 Compound Uamc-00312 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni404

b:29.2
occ:1.00
 O A:HOH696 2.1 20.6 1.0
O A:HOH631 2.2 17.2 1.0
NE2 A:HIS58 2.2 25.2 1.0
O A:HOH630 2.3 14.1 1.0
CD2 A:HIS58 3.1 25.5 1.0
CE1 A:HIS58 3.2 25.4 1.0
O A:HOH629 3.6 24.4 1.0
CG A:HIS58 4.3 26.5 1.0
ND1 A:HIS58 4.3 26.4 1.0

Nickel binding site 3 out of 17 in 4i73

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Nickel binding site 3 out of 17 in the Crystal Structure of the Trypanosoma Brucei Inosine-Adenosine- Guanosine Nucleoside Hydrolase in Complex with Compound Uamc-00312


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 Compound Uamc-00312 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni405

b:30.2
occ:1.00
 O A:HOH634 1.8 19.8 1.0
O A:HOH633 2.0 23.1 1.0
O A:HOH632 2.2 12.3 1.0
O A:HOH626 2.5 15.9 1.0
O C:HOH614 4.1 20.1 1.0
O A:HOH697 4.2 13.3 1.0

Nickel binding site 4 out of 17 in 4i73

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Nickel binding site 4 out of 17 in the Crystal Structure of the Trypanosoma Brucei Inosine-Adenosine- Guanosine Nucleoside Hydrolase in Complex with Compound Uamc-00312


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 Compound Uamc-00312 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni406

b:36.1
occ:1.00
 N A:SER-1 2.0 35.9 1.0
N A:HIS0 2.1 35.6 1.0
ND1 A:HIS0 2.1 34.3 1.0
N A:GLY-2 2.2 34.9 1.0
C A:SER-1 2.8 35.5 1.0
CA A:SER-1 2.9 35.8 1.0
C A:GLY-2 2.9 36.0 1.0
CA A:GLY-2 3.1 35.6 1.0
CG A:HIS0 3.1 34.5 1.0
CA A:HIS0 3.2 35.6 1.0
CE1 A:HIS0 3.2 33.5 1.0
CB A:HIS0 3.3 35.3 1.0
O A:HOH502 3.5 25.5 1.0
OG A:SER-1 3.7 35.0 1.0
N A:MET1 3.9 36.0 1.0
CB A:SER-1 3.9 36.0 1.0
C A:HIS0 4.0 35.9 1.0
O A:SER-1 4.0 34.6 1.0
O A:GLY-2 4.1 36.5 1.0
CD2 A:HIS0 4.2 34.2 1.0
NE2 A:HIS0 4.3 35.3 1.0
CG A:MET1 4.6 39.0 1.0

Nickel binding site 5 out of 17 in 4i73

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Nickel binding site 5 out of 17 in the Crystal Structure of the Trypanosoma Brucei Inosine-Adenosine- Guanosine Nucleoside Hydrolase in Complex with Compound Uamc-00312


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 Compound Uamc-00312 within 5.0Å range:

Nickel binding site 6 out of 17 in 4i73

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Nickel binding site 6 out of 17 in the Crystal Structure of the Trypanosoma Brucei Inosine-Adenosine- Guanosine Nucleoside Hydrolase in Complex with Compound Uamc-00312


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 Compound Uamc-00312 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni408

b:35.6
occ:0.60
 NE2 A:HIS115 2.1 27.8 1.0
CE1 A:HIS115 3.1 27.5 1.0
CD2 A:HIS115 3.2 25.8 1.0
ND1 A:HIS115 4.2 27.2 1.0
CG A:HIS115 4.3 25.8 1.0
CB A:PRO67 4.8 19.2 1.0
O A:GLU111 4.8 28.4 1.0

Nickel binding site 7 out of 17 in 4i73

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Nickel binding site 7 out of 17 in the Crystal Structure of the Trypanosoma Brucei Inosine-Adenosine- Guanosine Nucleoside Hydrolase in Complex with Compound Uamc-00312


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 Compound Uamc-00312 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ni403

b:38.4
occ:1.00
 NE2 B:HIS115 2.3 27.3 1.0
O B:HOH655 2.6 27.2 1.0
O B:HOH676 2.8 20.0 1.0
CE1 B:HIS115 3.2 27.8 1.0
CD2 B:HIS115 3.3 26.0 1.0
O B:HOH570 4.3 28.3 1.0
ND1 B:HIS115 4.4 27.9 1.0
CG B:HIS115 4.4 26.4 1.0
CB B:PRO67 4.5 19.1 1.0
CA A:PRO177 4.7 29.4 1.0
CD1 B:LEU120 4.8 14.3 1.0
O B:HOH646 4.8 29.3 1.0

Nickel binding site 8 out of 17 in 4i73

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Nickel binding site 8 out of 17 in the Crystal Structure of the Trypanosoma Brucei Inosine-Adenosine- Guanosine Nucleoside Hydrolase in Complex with Compound Uamc-00312


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 8 of Crystal Structure of the Trypanosoma Brucei Inosine-Adenosine- Guanosine Nucleoside Hydrolase in Complex with Compound Uamc-00312 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ni404

b:85.2
occ:1.00
 NE2 B:HIS317 2.3 29.2 1.0
O B:HOH617 3.1 42.5 1.0
CE1 B:HIS317 3.1 30.8 1.0
CD2 B:HIS317 3.4 28.0 1.0
O B:HOH615 3.5 34.3 1.0
ND1 B:HIS317 4.3 28.6 1.0
CG B:HIS317 4.4 25.7 1.0
O B:HOH518 4.7 19.2 1.0
O B:HOH571 4.9 15.9 1.0
OD1 B:ASP318 5.0 25.1 1.0

Nickel binding site 9 out of 17 in 4i73

Go back to Nickel Binding Sites List in 4i73
Nickel binding site 9 out of 17 in the Crystal Structure of the Trypanosoma Brucei Inosine-Adenosine- Guanosine Nucleoside Hydrolase in Complex with Compound Uamc-00312


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 9 of Crystal Structure of the Trypanosoma Brucei Inosine-Adenosine- Guanosine Nucleoside Hydrolase in Complex with Compound Uamc-00312 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ni403

b:36.5
occ:0.60
 NE2 C:HIS58 2.5 25.3 1.0
CD2 C:HIS58 3.4 26.4 1.0
CE1 C:HIS58 3.5 25.7 1.0
O C:HOH586 3.6 32.8 1.0
CG C:HIS58 4.6 26.6 1.0
ND1 C:HIS58 4.6 26.6 1.0
CD1 C:LEU65 4.8 20.1 1.0

Nickel binding site 10 out of 17 in 4i73

Go back to Nickel Binding Sites List in 4i73
Nickel binding site 10 out of 17 in the Crystal Structure of the Trypanosoma Brucei Inosine-Adenosine- Guanosine Nucleoside Hydrolase in Complex with Compound Uamc-00312


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 10 of Crystal Structure of the Trypanosoma Brucei Inosine-Adenosine- Guanosine Nucleoside Hydrolase in Complex with Compound Uamc-00312 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ni404

b:51.7
occ:1.00
 ND1 C:HIS0 1.8 38.5 1.0
N C:GLY-2 1.9 51.9 1.0
N C:HIS0 2.7 45.9 1.0
N C:SER-1 2.7 50.8 1.0
CE1 C:HIS0 2.7 40.9 1.0
CG C:HIS0 2.8 42.0 1.0
CA C:GLY-2 3.1 52.0 1.0
CB C:HIS0 3.2 43.9 1.0
CA C:HIS0 3.3 44.1 1.0
C C:GLY-2 3.4 51.7 1.0
C C:SER-1 3.5 48.6 1.0
N C:MET1 3.6 40.9 1.0
CA C:SER-1 3.7 50.0 1.0
C C:HIS0 3.7 43.2 1.0
NE2 C:HIS0 3.8 39.7 1.0
OG C:SER-1 3.8 50.5 1.0
CD2 C:HIS0 3.9 41.0 1.0
CB C:SER-1 4.2 50.4 1.0
O C:GLY-2 4.5 51.9 1.0
O C:SER-1 4.6 49.6 1.0
O C:HIS0 4.6 43.2 1.0
CA C:MET1 4.8 39.9 1.0
CB C:MET1 4.8 40.8 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 18:12:43 2024

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