Sodium in PDB 4dk4: Crystal Structure of Trypanosoma Brucei Dutpase with Dupnp, CA2+ and Na+

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

The structure of Crystal Structure of Trypanosoma Brucei Dutpase with Dupnp, CA2+ and Na+, PDB code: 4dk4 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)	61.45 / 1.90
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	58.840, 83.190, 91.180, 90.00, 90.00, 90.00
R / Rfree (%)	17.7 / 23.2

The structure of Crystal Structure of Trypanosoma Brucei Dutpase with Dupnp, CA2+ and Na+ also contains other interesting chemical elements:

Calcium

(Ca)

4 atoms

The binding sites of Sodium atom in the Crystal Structure of Trypanosoma Brucei Dutpase with Dupnp, CA2+ and Na+ (pdb code 4dk4). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structure of Trypanosoma Brucei Dutpase with Dupnp, CA2+ and Na+, PDB code: 4dk4:
Jump to Sodium binding site number: 1; 2;

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


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of Trypanosoma Brucei Dutpase with Dupnp, CA2+ and Na+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Na304 b:19.2 occ:1.00 O A:HOH407 2.2 30.7 1.0 O A:HOH405 2.3 27.7 1.0 OE2 A:GLU76 2.5 15.5 1.0 OE1 A:GLU51 2.6 14.9 1.0 O A:HOH403 2.6 16.8 1.0 O A:HOH406 2.6 25.2 1.0 CD A:GLU76 3.4 20.3 1.0 CD A:GLU51 3.5 21.0 1.0 OE1 A:GLU76 3.6 16.4 1.0 CA A:CA303 3.7 12.9 1.0 CG A:GLU51 3.9 11.6 1.0 CB A:GLU51 3.9 11.1 1.0 O A:HOH425 4.2 20.8 1.0 O1B A:DUN301 4.4 14.5 1.0 OD1 A:ASN72 4.4 18.4 1.0 OE2 A:GLU51 4.4 12.2 1.0 O3B A:DUN301 4.6 11.3 1.0 ND2 A:ASN72 4.6 11.3 1.0 OE1 A:GLU233 4.6 40.1 1.0 CG A:GLU76 4.8 13.7 1.0 CG A:ASN72 5.0 20.4 1.0 OE2 A:GLU233 5.0 77.9 1.0

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


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of Trypanosoma Brucei Dutpase with Dupnp, CA2+ and Na+ within 5.0Å range: probe atom residue distance (Å) B Occ B:Na304 b:19.6 occ:1.00 O B:HOH490 2.3 49.7 1.0 OE2 B:GLU76 2.4 15.8 1.0 OE1 B:GLU51 2.6 12.3 1.0 O B:HOH402 2.6 13.2 1.0 O B:HOH432 2.6 31.4 1.0 CD B:GLU76 3.3 14.9 1.0 CD B:GLU51 3.5 20.5 1.0 OE1 B:GLU76 3.6 18.6 1.0 CA B:CA303 3.7 10.7 1.0 CG B:GLU51 3.8 17.8 1.0 CB B:GLU51 3.9 12.7 1.0 OD1 B:ASN72 4.2 18.9 1.0 O B:HOH476 4.3 21.2 1.0 OE2 B:GLU233 4.3 24.1 1.0 NZ B:LYS227 4.4 44.6 1.0 ND2 B:ASN72 4.4 17.1 1.0 O2B B:DUN301 4.5 14.6 1.0 OE2 B:GLU51 4.5 11.6 1.0 CG B:GLU76 4.7 13.1 1.0 CG B:ASN72 4.7 17.1 1.0 O3B B:DUN301 4.8 11.4 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