Sodium in PDB 5u21: X-Ray Structure of the Wlarf Aminotransferase From Campylobacter Jejuni, K184A Mutant in Complex with Tdp-QUI3N

The structure of X-Ray Structure of the Wlarf Aminotransferase From Campylobacter Jejuni, K184A Mutant in Complex with Tdp-QUI3N, PDB code: 5u21 was solved by J.B.Thoden, H.M.Holden, G.T.Dow, M.Gilbert, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.98 / 1.60
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	108.164, 56.653, 124.802, 90.00, 90.04, 90.00
R / Rfree (%)	13.2 / 16.1

The structure of X-Ray Structure of the Wlarf Aminotransferase From Campylobacter Jejuni, K184A Mutant in Complex with Tdp-QUI3N also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Sodium atom in the X-Ray Structure of the Wlarf Aminotransferase From Campylobacter Jejuni, K184A Mutant in Complex with Tdp-QUI3N (pdb code 5u21). 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 Wlarf Aminotransferase From Campylobacter Jejuni, K184A Mutant in Complex with Tdp-QUI3N, PDB code: 5u21:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the X-Ray Structure of the Wlarf Aminotransferase From Campylobacter Jejuni, K184A Mutant in Complex with Tdp-QUI3N


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 Wlarf Aminotransferase From Campylobacter Jejuni, K184A Mutant in Complex with Tdp-QUI3N within 5.0Å range: probe atom residue distance (Å) B Occ A:Na401 b:8.2 occ:1.00 O A:HOH695 2.0 20.0 1.0 O B:HOH607 2.0 20.2 1.0 O B:HOH723 2.2 7.6 1.0 O A:HOH733 2.3 10.4 1.0 O B:HOH539 2.4 10.7 1.0 O A:HOH523 2.5 12.3 1.0 O A:HOH824 3.7 10.9 1.0 O B:HOH784 3.8 16.5 1.0 O B:HOH734 4.0 11.8 1.0 O A:HOH765 4.1 15.2 1.0 O B:ASP191 4.4 8.2 1.0 OD2 A:ASP230 4.4 8.6 1.0 O A:ASP191 4.4 8.5 1.0 OD2 B:ASP230 4.4 9.5 1.0 OD1 B:ASP230 4.5 8.0 1.0 CB B:ALA56 4.6 7.5 1.0 OD1 A:ASP230 4.6 9.5 1.0 O B:ARG228 4.6 8.5 1.0 O B:ALA56 4.7 7.5 1.0 CG B:ASP230 4.7 11.3 1.0 O A:ALA56 4.7 8.3 1.0 CG A:ASP230 4.7 8.4 1.0 O A:ARG228 4.7 7.8 1.0 CB A:ALA56 4.7 11.1 1.0 CB B:ASP191 4.9 9.4 1.0 CB A:ASP191 4.9 7.5 1.0

Sodium binding site 2 out of 2 in the X-Ray Structure of the Wlarf Aminotransferase From Campylobacter Jejuni, K184A Mutant in Complex with Tdp-QUI3N


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 Wlarf Aminotransferase From Campylobacter Jejuni, K184A Mutant in Complex with Tdp-QUI3N within 5.0Å range: probe atom residue distance (Å) B Occ C:Na401 b:7.8 occ:1.00 O D:HOH745 1.8 19.3 1.0 O C:HOH643 2.0 12.9 1.0 O C:HOH706 2.2 9.3 1.0 O D:HOH633 2.3 9.1 1.0 O D:HOH584 2.4 9.6 1.0 O C:HOH576 2.4 10.9 1.0 O D:HOH739 3.9 17.1 1.0 O C:HOH786 3.9 13.4 1.0 O C:HOH750 4.1 12.3 1.0 O D:HOH695 4.1 11.8 1.0 O C:ASP191 4.3 10.8 1.0 O D:ASP191 4.4 7.8 1.0 OD2 D:ASP230 4.4 11.5 1.0 OD2 C:ASP230 4.4 13.5 1.0 OD1 C:ASP230 4.6 9.2 1.0 OD1 D:ASP230 4.6 8.0 1.0 O D:ARG228 4.6 9.2 1.0 O D:ALA56 4.7 7.7 1.0 O C:ARG228 4.7 10.6 1.0 O C:ALA56 4.7 9.8 1.0 CG D:ASP230 4.7 11.4 1.0 CB D:ALA56 4.7 7.6 1.0 CB C:ASP191 4.7 7.9 1.0 CG C:ASP230 4.8 10.5 1.0 CB C:ALA56 4.8 11.7 1.0 CB D:ASP191 4.9 7.9 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