Atomistry » Nickel » PDB 4guh-4jz4 » 4i75
Atomistry »
  Nickel »
    PDB 4guh-4jz4 »
      4i75 »

Nickel in PDB 4i75: Crystal Structure of the Trypanosoma Brucei Inosine-Adenosine- Guanosine Nucleoside Hydrolase in Complex with the Nitris Metalorganic Complex

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

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

Protein crystallography data

The structure of Crystal Structure of the Trypanosoma Brucei Inosine-Adenosine- Guanosine Nucleoside Hydrolase in Complex with the Nitris Metalorganic Complex, PDB code: 4i75 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) 48.80 / 1.80
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 70.700, 134.890, 60.990, 90.00, 90.00, 90.00
R / Rfree (%) 18 / 22.3

Other elements in 4i75:

The structure of Crystal Structure of the Trypanosoma Brucei Inosine-Adenosine- Guanosine Nucleoside Hydrolase in Complex with the Nitris Metalorganic Complex 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 the Nitris Metalorganic Complex (pdb code 4i75). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 9 binding sites of Nickel where determined in the Crystal Structure of the Trypanosoma Brucei Inosine-Adenosine- Guanosine Nucleoside Hydrolase in Complex with the Nitris Metalorganic Complex, PDB code: 4i75:
Jump to Nickel binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Nickel binding site 1 out of 9 in 4i75

Go back to Nickel Binding Sites List in 4i75
Nickel binding site 1 out of 9 in the Crystal Structure of the Trypanosoma Brucei Inosine-Adenosine- Guanosine Nucleoside Hydrolase in Complex with the Nitris Metalorganic Complex


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 the Nitris Metalorganic Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni402

b:9.8
occ:1.00
 O A:HOH697 2.0 9.1 1.0
O1 A:TRS403 2.0 13.6 1.0
OD2 A:ASP14 2.1 12.0 1.0
O A:HOH698 2.1 12.1 1.0
N A:TRS403 2.1 11.8 1.0
O3 A:TRS403 2.2 16.3 1.0
C A:TRS403 2.7 14.9 1.0
C1 A:TRS403 2.8 15.2 1.0
C3 A:TRS403 2.9 13.8 1.0
CG A:ASP14 3.0 12.7 1.0
OD1 A:ASP14 3.2 11.8 1.0
OD2 A:ASP40 3.5 13.9 1.0
O A:HOH521 3.7 7.4 1.0
CA A:CA401 3.8 9.0 1.0
OD1 A:ASP261 4.0 11.5 1.0
OD2 A:ASP261 4.0 9.5 1.0
O A:HOH742 4.1 22.6 1.0
C2 A:TRS403 4.2 15.9 1.0
CE3 A:TRP260 4.2 20.1 1.0
CG A:ASP261 4.3 11.3 1.0
CB A:ASP14 4.4 11.8 1.0
O A:HOH539 4.5 18.0 1.0
O A:HOH716 4.5 24.8 1.0
CG A:ASP40 4.6 14.6 1.0
CD2 A:TRP260 4.7 17.3 1.0
CZ3 A:TRP260 4.8 23.3 1.0
OD2 A:ASP15 4.8 10.3 1.0
CB A:TRP260 4.8 15.2 1.0
CG A:TRP260 5.0 15.3 1.0

Nickel binding site 2 out of 9 in 4i75

Go back to Nickel Binding Sites List in 4i75
Nickel binding site 2 out of 9 in the Crystal Structure of the Trypanosoma Brucei Inosine-Adenosine- Guanosine Nucleoside Hydrolase in Complex with the Nitris Metalorganic Complex


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 the Nitris Metalorganic Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni404

b:25.4
occ:1.00
 ND1 A:HIS0 1.9 24.7 1.0
N A:SER-1 1.9 32.6 1.0
N A:GLY-2 2.1 32.6 1.0
N A:HIS0 2.1 30.5 1.0
CG A:HIS0 2.8 28.4 1.0
C A:GLY-2 2.8 33.5 1.0
C A:SER-1 2.9 31.9 1.0
CA A:SER-1 2.9 33.5 1.0
CA A:GLY-2 2.9 33.6 1.0
CE1 A:HIS0 3.0 26.6 1.0
CA A:HIS0 3.1 30.0 1.0
CB A:HIS0 3.1 29.4 1.0
N A:MET1 3.8 28.2 1.0
C A:HIS0 3.9 29.6 1.0
O A:GLY-2 4.0 34.4 1.0
CD2 A:HIS0 4.0 27.0 1.0
NE2 A:HIS0 4.0 27.9 1.0
O A:SER-1 4.1 33.1 1.0
CB A:SER-1 4.1 34.0 1.0
OG A:SER-1 4.2 36.7 1.0
CG A:MET1 4.9 29.7 0.5
O A:HIS0 4.9 30.9 1.0
CA A:MET1 5.0 27.5 0.5
CA A:MET1 5.0 27.3 0.5
CB A:MET1 5.0 27.8 0.5

Nickel binding site 3 out of 9 in 4i75

Go back to Nickel Binding Sites List in 4i75
Nickel binding site 3 out of 9 in the Crystal Structure of the Trypanosoma Brucei Inosine-Adenosine- Guanosine Nucleoside Hydrolase in Complex with the Nitris Metalorganic Complex


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 the Nitris Metalorganic Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni405

b:42.0
occ:1.00
 O A:HOH704 2.0 24.2 1.0
NE2 A:HIS115 2.1 20.9 1.0
O A:HOH744 2.2 28.2 1.0
O A:HOH712 2.4 25.6 1.0
O A:HOH700 2.9 15.9 1.0
CE1 A:HIS115 3.0 19.9 1.0
CD2 A:HIS115 3.1 19.8 1.0
O A:HOH556 4.0 15.2 1.0
ND1 A:HIS115 4.2 17.4 1.0
CG A:HIS115 4.2 16.7 1.0
O A:GLU111 4.4 23.2 1.0

Nickel binding site 4 out of 9 in 4i75

Go back to Nickel Binding Sites List in 4i75
Nickel binding site 4 out of 9 in the Crystal Structure of the Trypanosoma Brucei Inosine-Adenosine- Guanosine Nucleoside Hydrolase in Complex with the Nitris Metalorganic Complex


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 the Nitris Metalorganic Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni406

b:66.0
occ:1.00
 NE2 A:HIS317 2.3 34.4 1.0
O A:HOH681 2.6 29.6 1.0
CE1 A:HIS317 3.1 33.2 1.0
CD2 A:HIS317 3.4 32.6 1.0
ND1 A:HIS317 4.3 32.8 1.0
CG A:HIS317 4.5 27.8 1.0
O A:HOH724 4.9 28.5 1.0
CD1 A:PHE321 4.9 26.2 1.0
CG A:PHE321 5.0 23.4 1.0

Nickel binding site 5 out of 9 in 4i75

Go back to Nickel Binding Sites List in 4i75
Nickel binding site 5 out of 9 in the Crystal Structure of the Trypanosoma Brucei Inosine-Adenosine- Guanosine Nucleoside Hydrolase in Complex with the Nitris Metalorganic Complex


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 the Nitris Metalorganic Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ni404

b:23.8
occ:1.00
 O3 B:TRS403 1.8 41.6 1.0
O1 B:TRS402 2.1 30.0 1.0
N B:TRS402 2.1 29.0 1.0
NE2 B:HIS58 2.2 17.9 1.0
O2 B:TRS403 2.6 41.5 1.0
C B:TRS402 2.9 30.3 1.0
C1 B:TRS402 3.0 30.2 1.0
CD2 B:HIS58 3.0 18.4 1.0
C3 B:TRS403 3.1 43.0 1.0
C2 B:TRS403 3.2 43.0 1.0
CE1 B:HIS58 3.3 18.7 1.0
C2 B:TRS402 3.4 31.2 1.0
C B:TRS403 3.6 43.0 1.0
CG B:HIS58 4.2 16.2 1.0
C3 B:TRS402 4.3 29.5 1.0
ND1 B:HIS58 4.3 15.5 1.0
O1 B:TRS403 4.4 42.4 1.0
C1 B:TRS403 4.6 43.8 1.0
N B:TRS403 4.8 43.1 1.0
O2 B:TRS402 4.8 34.0 1.0

Nickel binding site 6 out of 9 in 4i75

Go back to Nickel Binding Sites List in 4i75
Nickel binding site 6 out of 9 in the Crystal Structure of the Trypanosoma Brucei Inosine-Adenosine- Guanosine Nucleoside Hydrolase in Complex with the Nitris Metalorganic Complex


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 the Nitris Metalorganic Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ni405

b:20.1
occ:1.00
 O B:HOH700 2.0 12.9 1.0
O1 B:TRS401 2.0 23.7 1.0
OD1 B:ASP253 2.1 23.2 1.0
N B:TRS401 2.1 22.6 1.0
O3 B:TRS401 2.1 21.8 1.0
C B:TRS401 2.7 23.5 1.0
C1 B:TRS401 2.9 23.1 1.0
C3 B:TRS401 3.0 22.6 1.0
CG B:ASP253 3.1 27.2 1.0
OD2 B:ASP253 3.3 28.9 1.0
O B:HOH604 4.0 15.9 1.0
C2 B:TRS401 4.2 24.8 1.0
O B:ILE250 4.4 22.8 1.0
CB B:ASP253 4.4 26.6 1.0
CA B:ASP253 4.9 26.6 1.0

Nickel binding site 7 out of 9 in 4i75

Go back to Nickel Binding Sites List in 4i75
Nickel binding site 7 out of 9 in the Crystal Structure of the Trypanosoma Brucei Inosine-Adenosine- Guanosine Nucleoside Hydrolase in Complex with the Nitris Metalorganic Complex


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 the Nitris Metalorganic Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ni406

b:43.2
occ:1.00
 O B:HOH709 2.0 22.9 1.0
NE2 B:HIS115 2.1 24.1 1.0
O B:HOH710 2.3 23.9 1.0
CE1 B:HIS115 3.0 22.6 1.0
CD2 B:HIS115 3.1 23.8 1.0
ND1 B:HIS115 4.1 20.1 1.0
CG B:HIS115 4.2 20.4 1.0
O B:HOH650 4.4 16.4 1.0
O B:GLU111 4.6 26.3 1.0

Nickel binding site 8 out of 9 in 4i75

Go back to Nickel Binding Sites List in 4i75
Nickel binding site 8 out of 9 in the Crystal Structure of the Trypanosoma Brucei Inosine-Adenosine- Guanosine Nucleoside Hydrolase in Complex with the Nitris Metalorganic Complex


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 the Nitris Metalorganic Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ni407

b:32.4
occ:0.80
 NE2 B:HIS317 2.1 32.2 1.0
O B:HOH707 2.1 9.4 0.8
O B:HOH708 2.4 28.0 0.8
CE1 B:HIS317 3.0 31.9 1.0
CD2 B:HIS317 3.1 31.1 1.0
O B:HOH580 4.2 13.4 1.0
ND1 B:HIS317 4.2 30.5 1.0
CG B:HIS317 4.2 25.8 1.0
O B:HOH502 4.3 21.8 1.0
O B:HOH595 4.4 25.2 1.0

Nickel binding site 9 out of 9 in 4i75

Go back to Nickel Binding Sites List in 4i75
Nickel binding site 9 out of 9 in the Crystal Structure of the Trypanosoma Brucei Inosine-Adenosine- Guanosine Nucleoside Hydrolase in Complex with the Nitris Metalorganic Complex


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 the Nitris Metalorganic Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ni409

b:11.2
occ:1.00
 O B:HOH698 2.0 8.1 1.0
O3 B:TRS410 2.1 14.5 1.0
O1 B:TRS410 2.1 14.7 1.0
O B:HOH699 2.1 5.4 1.0
OD2 B:ASP14 2.1 12.8 1.0
N B:TRS410 2.2 15.0 1.0
C B:TRS410 2.8 16.2 1.0
C1 B:TRS410 2.8 17.1 1.0
C3 B:TRS410 2.9 16.4 1.0
CG B:ASP14 3.0 12.8 1.0
OD1 B:ASP14 3.2 14.0 1.0
OD2 B:ASP40 3.4 15.9 1.0
CA B:CA408 3.7 10.6 1.0
O B:HOH507 3.7 9.7 1.0
OD1 B:ASP261 3.9 14.9 1.0
OD2 B:ASP261 4.0 11.8 1.0
CG B:ASP261 4.3 12.5 1.0
O B:HOH590 4.3 18.8 1.0
C2 B:TRS410 4.3 16.6 1.0
O B:HOH715 4.3 26.4 1.0
CE3 B:TRP260 4.4 20.9 1.0
CB B:ASP14 4.4 12.5 1.0
O B:HOH725 4.5 33.8 1.0
CG B:ASP40 4.6 15.7 1.0
CD2 B:TRP260 4.8 16.8 1.0
OD2 B:ASP15 4.8 11.2 1.0
CB B:TRP260 4.9 15.7 1.0
CZ3 B:TRP260 5.0 23.7 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 18:12:58 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy