Calcium in PDB 4dkb: Crystal Structure of Trypanosoma Brucei Dutpase with Dupnp and CA2+

All present enzymatic activity of Crystal Structure of Trypanosoma Brucei Dutpase with Dupnp and CA2+:
3.6.1.23;

The structure of Crystal Structure of Trypanosoma Brucei Dutpase with Dupnp and CA2+, PDB code: 4dkb was solved by G.R.Hemsworth, D.Gonzalez-Pacanowska, K.S.Wilson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.42 / 1.83
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	68.470, 68.470, 123.870, 90.00, 90.00, 90.00
R / Rfree (%)	16.9 / 19.8

The binding sites of Calcium atom in the Crystal Structure of Trypanosoma Brucei Dutpase with Dupnp and CA2+ (pdb code 4dkb). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Crystal Structure of Trypanosoma Brucei Dutpase with Dupnp and CA2+, PDB code: 4dkb:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Crystal Structure of Trypanosoma Brucei Dutpase with Dupnp and CA2+


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 Trypanosoma Brucei Dutpase with Dupnp and CA2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca301 b:12.8 occ:1.00 O2A A:DUN303 2.2 10.3 1.0 OE2 A:GLU51 2.4 24.2 1.0 O A:HOH402 2.4 16.9 1.0 OE2 A:GLU48 2.4 16.4 1.0 O3B A:DUN303 2.4 13.6 1.0 O A:HOH401 2.5 13.4 1.0 OE1 A:GLU51 2.8 18.2 1.0 CD A:GLU51 2.9 18.0 1.0 CD A:GLU48 3.1 15.9 1.0 OE1 A:GLU48 3.2 11.8 1.0 PA A:DUN303 3.4 11.5 1.0 PB A:DUN303 3.6 13.6 1.0 CA A:CA302 3.6 12.6 1.0 N3A A:DUN303 3.6 10.0 1.0 O A:HOH520 4.0 13.6 1.0 C5' A:DUN303 4.4 10.7 1.0 O5' A:DUN303 4.4 11.0 1.0 O1B A:DUN303 4.4 20.0 1.0 CG A:GLU51 4.5 15.4 1.0 O A:HOH512 4.5 31.4 1.0 O A:HOH485 4.5 32.9 1.0 CG A:GLU48 4.5 14.7 1.0 O1A A:DUN303 4.5 11.7 1.0 O2B A:DUN303 4.7 22.2 1.0 O A:HOH403 4.9 16.5 1.0

Calcium binding site 2 out of 2 in the Crystal Structure of Trypanosoma Brucei Dutpase with Dupnp and CA2+


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 Trypanosoma Brucei Dutpase with Dupnp and CA2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca302 b:12.6 occ:1.00 OE1 A:GLU76 2.2 18.4 1.0 OE1 A:GLU48 2.3 11.8 1.0 O3B A:DUN303 2.3 13.6 1.0 OD2 A:ASP79 2.3 11.2 1.0 OE1 A:GLU51 2.4 18.2 1.0 O A:HOH403 2.4 16.5 1.0 CD A:GLU76 3.3 25.2 1.0 CD A:GLU48 3.4 15.9 1.0 CG A:ASP79 3.5 14.3 1.0 PB A:DUN303 3.5 13.6 1.0 CD A:GLU51 3.5 18.0 1.0 CA A:CA301 3.6 12.8 1.0 OE2 A:GLU76 3.8 17.7 1.0 OE2 A:GLU48 3.9 16.4 1.0 O2B A:DUN303 4.0 22.2 1.0 O1B A:DUN303 4.0 20.0 1.0 CB A:ASP79 4.0 10.9 1.0 OE2 A:GLU51 4.2 24.2 1.0 O A:HOH470 4.2 27.1 1.0 CB A:GLU51 4.5 10.3 1.0 OD1 A:ASP79 4.5 12.1 1.0 CA A:GLU76 4.5 10.3 1.0 CG A:GLU51 4.6 15.4 1.0 CG A:GLU76 4.6 14.9 1.0 CG A:GLU48 4.6 14.7 1.0 O A:HOH472 4.7 21.1 1.0 NZ A:LYS208 4.8 9.4 1.0 CB A:GLU76 4.9 10.9 1.0 N3A A:DUN303 4.9 10.0 1.0 CG2 A:ILE75 4.9 13.5 1.0 CB A:GLU48 5.0 15.5 1.0 O2A A:DUN303 5.0 10.3 1.0

G.R.Hemsworth, D.Gonzalez-Pacanowska, K.S.Wilson. On the Catalytic Mechanism of Dimeric Dutpases. Biochem.J. V. 456 81 2013.
ISSN: ISSN 0264-6021
PubMed: 24001052
DOI: 10.1042/BJ20130796