Sodium in PDB 5u24: X-Ray Structure of the Wlarg Aminotransferase From Campylobacter Jejuni, K184A Mutant in Complex with Tdp-FUC3N

The structure of X-Ray Structure of the Wlarg Aminotransferase From Campylobacter Jejuni, K184A Mutant in Complex with Tdp-FUC3N, PDB code: 5u24 was solved by H.M.Holden, J.B.Thoden, G.T.Dow, M.Gilbert, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	28.53 / 1.70
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	109.057, 56.795, 124.306, 90.00, 90.02, 90.00
R / Rfree (%)	10.5 / 14.6

The structure of X-Ray Structure of the Wlarg Aminotransferase From Campylobacter Jejuni, K184A Mutant in Complex with Tdp-FUC3N also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Sodium atom in the X-Ray Structure of the Wlarg Aminotransferase From Campylobacter Jejuni, K184A Mutant in Complex with Tdp-FUC3N (pdb code 5u24). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the X-Ray Structure of the Wlarg Aminotransferase From Campylobacter Jejuni, K184A Mutant in Complex with Tdp-FUC3N, PDB code: 5u24:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the X-Ray Structure of the Wlarg Aminotransferase From Campylobacter Jejuni, K184A Mutant in Complex with Tdp-FUC3N


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of X-Ray Structure of the Wlarg Aminotransferase From Campylobacter Jejuni, K184A Mutant in Complex with Tdp-FUC3N within 5.0Å range: probe atom residue distance (Å) B Occ A:Na401 b:14.2 occ:1.00 O A:HOH760 1.9 18.3 1.0 O B:HOH635 2.1 21.7 1.0 O B:HOH605 2.2 18.1 1.0 O A:HOH547 2.2 19.9 1.0 O A:HOH535 2.2 13.5 1.0 O A:HOH619 2.4 19.0 1.0 O B:HOH705 3.9 17.0 1.0 O A:HOH795 4.0 19.9 1.0 O A:HOH734 4.0 17.4 1.0 O B:HOH715 4.1 20.9 1.0 OD2 B:ASP230 4.1 13.9 1.0 OD2 A:ASP230 4.2 16.6 1.0 O A:ASP191 4.2 11.8 1.0 O B:ASP191 4.2 13.7 1.0 OD1 B:ASP230 4.3 13.0 1.0 OD1 A:ASP230 4.4 16.2 1.0 CG A:ASP230 4.5 15.1 1.0 CG B:ASP230 4.5 12.4 1.0 O B:ARG228 4.6 14.3 1.0 O B:ALA56 4.7 13.1 1.0 O A:ARG228 4.8 17.5 1.0 O A:ALA56 4.8 14.6 1.0 CB A:ASP191 4.9 10.2 1.0 CB B:ASP191 4.9 14.4 1.0 CB B:ALA56 4.9 9.7 1.0 CB A:ALA56 4.9 10.1 1.0

Sodium binding site 2 out of 2 in the X-Ray Structure of the Wlarg Aminotransferase From Campylobacter Jejuni, K184A Mutant in Complex with Tdp-FUC3N


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of X-Ray Structure of the Wlarg Aminotransferase From Campylobacter Jejuni, K184A Mutant in Complex with Tdp-FUC3N within 5.0Å range: probe atom residue distance (Å) B Occ C:Na401 b:11.5 occ:1.00 O D:HOH669 2.0 22.7 1.0 O C:HOH684 2.1 18.6 1.0 O C:HOH655 2.2 13.7 1.0 O D:HOH621 2.2 12.7 1.0 O D:HOH565 2.2 13.2 1.0 O C:HOH516 2.2 15.3 1.0 O D:HOH683 3.9 15.9 1.0 O C:HOH718 3.9 13.3 1.0 O C:HOH775 4.0 20.6 1.0 O D:HOH707 4.1 18.0 1.0 OD2 D:ASP230 4.2 13.9 1.0 O C:ASP191 4.2 13.0 1.0 O D:ASP191 4.2 13.7 1.0 OD2 C:ASP230 4.3 14.6 1.0 OD1 D:ASP230 4.3 13.7 1.0 OD1 C:ASP230 4.3 14.2 1.0 CG D:ASP230 4.5 14.1 1.0 CG C:ASP230 4.6 14.0 1.0 O D:ARG228 4.7 12.5 1.0 O D:ALA56 4.8 11.1 1.0 O C:ALA56 4.8 14.2 1.0 O C:ARG228 4.8 14.0 1.0 CB C:ASP191 4.8 12.1 1.0 CB D:ASP191 4.8 11.3 1.0 CB C:ALA56 4.9 12.3 1.0 CB D:ALA56 4.9 12.7 1.0 C C:ASP191 5.0 12.2 1.0

G.T.Dow, M.Gilbert, J.B.Thoden, H.M.Holden. Structural Investigation on Wlarg From Campylobacter Jejuni: A Sugar Aminotransferase. Protein Sci. V. 26 586 2017.
ISSN: ESSN 1469-896X
PubMed: 28028852
DOI: 10.1002/PRO.3109