Sodium in PDB 3v7z: Carboxypeptidase T with Gemsa

All present enzymatic activity of Carboxypeptidase T with Gemsa:
3.4.17.18;

The structure of Carboxypeptidase T with Gemsa, PDB code: 3v7z was solved by S.A.Kuznetsov, V.I.Timofeev, V.K.Akparov, I.P.Kuranova, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	10.00 / 1.61
Space group	P 63 2 2
Cell size a, b, c (Å), α, β, γ (°)	157.890, 157.890, 104.195, 90.00, 90.00, 120.00
R / Rfree (%)	13.3 / 15.2

The structure of Carboxypeptidase T with Gemsa also contains other interesting chemical elements:

Calcium	(Ca)	4 atoms
Zinc	(Zn)	1 atom

The binding sites of Sodium atom in the Carboxypeptidase T with Gemsa (pdb code 3v7z). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the Carboxypeptidase T with Gemsa, PDB code: 3v7z:

Sodium binding site 1 out of 1 in the Carboxypeptidase T with Gemsa


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Carboxypeptidase T with Gemsa within 5.0Å range: probe atom residue distance (Å) B Occ A:Na404 b:21.2 occ:1.00 O A:TYR5 2.3 19.2 1.0 O A:HOH704 2.4 31.2 1.0 O A:HOH570 2.4 21.6 1.0 OE2 A:GLU292 2.4 28.9 1.0 OD1 A:ASP291 2.5 16.0 1.0 O A:HOH530 2.6 39.0 1.0 OE1 A:GLU292 2.6 20.1 1.0 CD A:GLU292 2.9 21.6 1.0 O A:HOH637 3.3 34.3 1.0 CG A:ASP291 3.5 15.4 1.0 C A:TYR5 3.5 18.8 1.0 OD2 A:ASP291 3.9 15.9 1.0 CA A:TYR5 4.3 19.6 1.0 CG A:GLU292 4.4 20.5 1.0 OD1 A:ASP6 4.4 16.3 1.0 N A:ASP291 4.4 13.2 1.0 O A:HOH531 4.5 35.4 1.0 CB A:TYR5 4.5 20.8 1.0 N A:ASP6 4.6 16.4 1.0 N A:GLU292 4.6 13.4 1.0 CB A:ASP291 4.7 13.4 1.0 CA A:ASP6 4.8 15.1 1.0 O A:HOH821 4.9 19.4 0.5 O A:HOH790 4.9 44.1 0.8 CA A:ASP291 5.0 13.1 1.0

V.K.H.Akparov, V.I.Timofeev, I.G.Khaliullin, V.Svedas, G.G.Chestukhina, I.P.Kuranova. Structural Insights Into the Broad Substrate Specificity of Carboxypeptidase T From Thermoactinomyces Vulgaris. Febs J. V. 282 1214 2015.
ISSN: ISSN 1742-464X
PubMed: 25619204
DOI: 10.1111/FEBS.13210