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Calcium 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:

Nickel (Ni) 17 atoms

Calcium Binding Sites:

The binding sites of Calcium 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 Calcium atom.
In total 4 binding sites of Calcium 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 Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 4i73

Go back to Calcium Binding Sites List in 4i73
Calcium binding site 1 out of 4 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 Calcium with other atoms in the Ca 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:Ca401

b:14.6
occ:1.00
 O A:THR137 2.3 16.1 1.0
OD1 A:ASP10 2.3 13.2 1.0
OD2 A:ASP261 2.4 15.3 1.0
O2' A:MBY402 2.5 14.3 1.0
OD2 A:ASP15 2.5 12.6 1.0
OD1 A:ASP15 2.5 12.5 1.0
O3' A:MBY402 2.6 16.6 1.0
O A:HOH566 2.7 12.6 1.0
CG A:ASP15 2.8 12.8 1.0
C A:THR137 3.4 15.8 1.0
CG A:ASP10 3.4 16.1 1.0
CG A:ASP261 3.4 17.6 1.0
C2' A:MBY402 3.6 14.7 1.0
C3' A:MBY402 3.6 15.7 1.0
OD1 A:ASP261 3.8 15.9 1.0
OD2 A:ASP10 3.9 15.1 1.0
OD1 A:ASP14 4.2 16.1 1.0
N A:GLY138 4.2 15.5 1.0
CA A:GLY138 4.2 15.6 1.0
CB A:ASP15 4.3 12.1 1.0
CB A:THR137 4.3 14.9 1.0
OG1 A:THR137 4.3 14.0 1.0
N4' A:MBY402 4.3 16.4 1.0
C1' A:MBY402 4.4 15.4 1.0
C4' A:MBY402 4.4 16.4 1.0
N A:ASP10 4.4 13.9 1.0
CA A:THR137 4.4 15.1 1.0
OD1 A:ASN186 4.5 17.2 1.0
ND2 A:ASN186 4.6 15.1 1.0
CB A:ASP10 4.6 14.9 1.0
OD2 A:ASP14 4.7 19.1 1.0
CB A:ASP261 4.8 17.4 1.0
CG A:ASP14 4.8 17.1 1.0
CA A:ASP10 4.9 14.7 1.0
CA A:ASP15 4.9 12.6 1.0
N A:ASP15 4.9 13.8 1.0
C A:ASP10 4.9 15.1 1.0
CG A:ASN186 5.0 17.2 1.0

Calcium binding site 2 out of 4 in 4i73

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Calcium binding site 2 out of 4 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 Calcium with other atoms in the Ca 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
B:Ca401

b:14.6
occ:1.00
 OD1 B:ASP10 2.3 14.2 1.0
OD2 B:ASP15 2.4 12.9 1.0
O B:THR137 2.4 15.6 1.0
O2' B:MBY402 2.4 14.5 1.0
OD2 B:ASP261 2.5 15.7 1.0
O3' B:MBY402 2.5 16.1 1.0
O B:HOH508 2.6 10.6 1.0
OD1 B:ASP15 2.6 12.4 1.0
CG B:ASP15 2.9 12.7 1.0
CG B:ASP10 3.4 15.8 1.0
CG B:ASP261 3.5 17.9 1.0
C2' B:MBY402 3.5 14.5 1.0
C3' B:MBY402 3.5 16.0 1.0
C B:THR137 3.5 15.2 1.0
OD1 B:ASP261 3.8 16.0 1.0
OD2 B:ASP10 4.0 14.1 1.0
N4' B:MBY402 4.2 15.9 1.0
OD1 B:ASP14 4.2 16.1 1.0
C1' B:MBY402 4.3 15.5 1.0
N B:GLY138 4.3 15.4 1.0
CA B:GLY138 4.3 15.7 1.0
C4' B:MBY402 4.3 16.1 1.0
CB B:ASP15 4.3 12.3 1.0
N B:ASP10 4.4 14.1 1.0
CB B:THR137 4.4 14.7 1.0
OD1 B:ASN186 4.4 17.1 1.0
OG1 B:THR137 4.5 13.8 1.0
CA B:THR137 4.6 14.8 1.0
CB B:ASP10 4.7 14.4 1.0
ND2 B:ASN186 4.7 16.0 1.0
OD2 B:ASP14 4.8 19.9 1.0
CB B:ASP261 4.8 17.2 1.0
CA B:ASP10 4.8 14.8 1.0
CG B:ASP14 4.8 17.3 1.0
CA B:ASP15 4.9 12.7 1.0
N B:ASP15 4.9 13.6 1.0
OD2 B:ASP40 4.9 17.2 1.0
CB B:ASN12 4.9 15.5 1.0
C B:ASP10 4.9 14.8 1.0

Calcium binding site 3 out of 4 in 4i73

Go back to Calcium Binding Sites List in 4i73
Calcium binding site 3 out of 4 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 Calcium with other atoms in the Ca 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
C:Ca401

b:16.8
occ:1.00
 OD1 C:ASP10 2.2 14.3 1.0
OD2 C:ASP261 2.4 16.3 1.0
O2' C:MBY402 2.4 14.6 0.6
OD2 C:ASP15 2.4 14.1 1.0
O3' C:MBY402 2.5 16.2 0.6
O C:THR137 2.5 16.2 1.0
OD1 C:ASP15 2.6 13.0 1.0
O C:HOH517 2.6 19.0 1.0
CG C:ASP15 2.8 12.6 1.0
CG C:ASP10 3.4 16.3 1.0
CG C:ASP261 3.4 18.1 1.0
C2' C:MBY402 3.5 15.2 0.6
C3' C:MBY402 3.5 15.8 0.6
C C:THR137 3.6 15.9 1.0
NI C:NI406 3.6 29.1 0.4
OD2 C:ASP10 3.8 14.9 1.0
OD1 C:ASP261 3.8 16.4 1.0
OD1 C:ASP14 4.2 17.4 1.0
N4' C:MBY402 4.2 16.0 0.6
C1' C:MBY402 4.3 15.8 0.6
CB C:ASP15 4.3 12.8 1.0
C4' C:MBY402 4.4 16.5 0.6
N C:GLY138 4.4 16.1 1.0
CA C:GLY138 4.4 16.1 1.0
CB C:THR137 4.4 14.7 1.0
OG1 C:THR137 4.4 13.8 1.0
N C:ASP10 4.5 14.2 1.0
OD1 C:ASN186 4.5 18.1 1.0
CA C:THR137 4.6 15.0 1.0
ND2 C:ASN186 4.6 15.4 1.0
CB C:ASP10 4.6 14.8 1.0
OD2 C:ASP14 4.7 21.1 1.0
CB C:ASP261 4.8 17.4 1.0
CG C:ASP14 4.8 17.8 1.0
N C:ASP15 4.8 13.7 1.0
CA C:ASP10 4.9 14.7 1.0
CA C:ASP15 4.9 12.7 1.0
OD2 C:ASP40 4.9 17.4 1.0
C C:ASP10 4.9 15.4 1.0
CB C:ASN12 5.0 15.6 1.0
N C:ASN12 5.0 14.5 1.0

Calcium binding site 4 out of 4 in 4i73

Go back to Calcium Binding Sites List in 4i73
Calcium binding site 4 out of 4 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 Calcium with other atoms in the Ca 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
D:Ca401

b:14.8
occ:1.00
 OD1 D:ASP10 2.4 13.7 1.0
OD2 D:ASP261 2.4 15.9 1.0
O D:THR137 2.4 16.2 1.0
OD2 D:ASP15 2.4 13.0 1.0
O2' D:MBY402 2.4 15.1 0.8
OD1 D:ASP15 2.5 12.9 1.0
O3' D:MBY402 2.6 16.0 0.8
O D:HOH521 2.7 17.1 1.0
CG D:ASP15 2.8 12.7 1.0
CG D:ASP261 3.4 17.6 1.0
C2' D:MBY402 3.5 15.2 0.8
CG D:ASP10 3.5 16.0 1.0
C D:THR137 3.5 15.5 1.0
C3' D:MBY402 3.6 15.6 0.8
NI D:NI405 3.8 13.2 0.2
OD1 D:ASP261 3.8 15.3 1.0
OD2 D:ASP10 3.9 14.1 1.0
OD1 D:ASP14 4.2 16.9 1.0
CB D:ASP15 4.2 12.4 1.0
OG1 D:THR137 4.3 14.6 1.0
N4' D:MBY402 4.3 16.0 0.8
CB D:THR137 4.3 14.8 1.0
N D:GLY138 4.3 15.6 1.0
C1' D:MBY402 4.3 15.9 0.8
CA D:GLY138 4.4 15.6 1.0
C4' D:MBY402 4.4 16.6 0.8
CA D:THR137 4.5 15.0 1.0
N D:ASP10 4.5 14.2 1.0
OD1 D:ASN186 4.6 17.4 1.0
OD2 D:ASP14 4.6 21.0 1.0
ND2 D:ASN186 4.7 15.0 1.0
N D:ASP15 4.7 13.3 1.0
CB D:ASP10 4.7 14.5 1.0
CB D:ASP261 4.7 17.4 1.0
CG D:ASP14 4.7 17.5 1.0
CA D:ASP15 4.8 12.7 1.0
CA D:ASP10 4.9 14.8 1.0
C D:ASP10 4.9 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: Sun Jul 14 08:03:08 2024

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