Sodium in PDB 5u1z: X-Ray Structure of the Wlarg Aminotransferase, Apo Form, From Campylobacter Jejune

The structure of X-Ray Structure of the Wlarg Aminotransferase, Apo Form, From Campylobacter Jejune, PDB code: 5u1z 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)	29.97 / 1.60
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	107.726, 56.837, 124.797, 90.00, 90.04, 90.00
R / Rfree (%)	14.8 / 18.8

The structure of X-Ray Structure of the Wlarg Aminotransferase, Apo Form, From Campylobacter Jejune also contains other interesting chemical elements:

Chlorine

(Cl)

3 atoms

The binding sites of Sodium atom in the X-Ray Structure of the Wlarg Aminotransferase, Apo Form, From Campylobacter Jejune (pdb code 5u1z). 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, Apo Form, From Campylobacter Jejune, PDB code: 5u1z:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the X-Ray Structure of the Wlarg Aminotransferase, Apo Form, From Campylobacter Jejune


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, Apo Form, From Campylobacter Jejune within 5.0Å range: probe atom residue distance (Å) B Occ B:Na401 b:8.3 occ:1.00 O A:HOH672 2.0 9.7 1.0 O B:HOH615 2.1 7.5 1.0 O B:HOH527 2.1 8.2 1.0 O A:HOH519 2.1 9.8 1.0 O A:HOH587 2.1 12.1 1.0 O B:HOH565 2.2 9.3 1.0 O B:HOH622 3.9 15.1 1.0 OD2 B:ASP230 4.1 6.7 1.0 O A:HOH617 4.1 13.4 1.0 O B:ASP191 4.1 5.2 1.0 OD2 A:ASP230 4.1 5.7 1.0 O A:ASP191 4.2 5.7 1.0 O A:HOH670 4.2 11.0 1.0 OD1 B:ASP230 4.3 7.0 1.0 O B:HOH614 4.3 11.9 1.0 OD1 A:ASP230 4.4 6.5 1.0 CG A:ASP230 4.5 6.3 1.0 CG B:ASP230 4.5 6.4 1.0 O B:ARG228 4.7 9.9 1.0 CB B:ASP191 4.7 7.4 1.0 O A:ALA56 4.7 7.0 1.0 O B:ALA56 4.7 9.0 1.0 O A:ARG228 4.8 10.4 1.0 CB A:ALA56 4.9 12.6 1.0 CB A:ASP191 4.9 8.2 1.0 C B:ASP191 4.9 5.3 1.0 CB B:ALA56 4.9 6.9 1.0

Sodium binding site 2 out of 2 in the X-Ray Structure of the Wlarg Aminotransferase, Apo Form, From Campylobacter Jejune


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, Apo Form, From Campylobacter Jejune within 5.0Å range: probe atom residue distance (Å) B Occ C:Na401 b:9.3 occ:1.00 O D:HOH586 2.0 15.5 1.0 O C:HOH585 2.0 9.9 1.0 O C:HOH535 2.1 10.4 1.0 O D:HOH507 2.1 9.8 1.0 O C:HOH578 2.1 9.3 1.0 O D:HOH579 2.1 8.1 1.0 O D:HOH582 3.9 15.2 1.0 O C:HOH546 3.9 13.1 1.0 OD2 D:ASP230 4.0 8.9 1.0 O D:ASP191 4.2 7.0 1.0 OD2 C:ASP230 4.2 7.2 1.0 O C:HOH606 4.2 12.4 1.0 O C:ASP191 4.2 7.9 1.0 OD1 D:ASP230 4.3 7.0 1.0 OD1 C:ASP230 4.3 7.4 1.0 CG D:ASP230 4.4 8.1 1.0 O D:HOH539 4.5 11.7 1.0 CG C:ASP230 4.5 6.8 1.0 CB C:ASP191 4.7 8.4 1.0 O D:ALA56 4.7 8.3 1.0 O D:ARG228 4.7 8.8 1.0 CB D:ASP191 4.7 8.7 1.0 O C:ALA56 4.8 9.6 1.0 O C:ARG228 4.8 8.6 1.0 C D:ASP191 4.9 7.6 1.0 C C:ASP191 4.9 7.8 1.0 CB D:ALA56 5.0 11.3 1.0 CB C:ALA56 5.0 8.1 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