Sodium in PDB 5w56: Structure of Apo Aztc

The structure of Structure of Apo Aztc, PDB code: 5w56 was solved by D.Avalos, E.T.Yukl, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.83 / 2.03
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	61.469, 106.261, 61.672, 90.00, 110.98, 90.00
R / Rfree (%)	16.5 / 20.1

The binding sites of Sodium atom in the Structure of Apo Aztc (pdb code 5w56). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Structure of Apo Aztc, PDB code: 5w56:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Structure of Apo Aztc


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of Apo Aztc within 5.0Å range: probe atom residue distance (Å) B Occ A:Na403 b:60.1 occ:1.00 OD2 A:ASP279 2.2 53.9 1.0 O A:THR60 2.4 56.9 1.0 OD1 A:ASN254 2.6 67.0 1.0 O A:HOH548 2.6 52.7 1.0 OD1 A:ASP279 2.7 48.4 1.0 CG A:ASP279 2.8 45.5 1.0 CG A:ASN254 3.4 69.6 1.0 ND2 A:ASN254 3.6 75.2 1.0 O A:SER58 3.6 66.0 1.0 C A:THR60 3.6 53.3 1.0 CA A:HIS61 4.1 51.3 1.0 O A:HOH503 4.2 75.8 1.0 CB A:ASP279 4.3 42.6 1.0 N A:VAL62 4.3 44.1 1.0 N A:HIS61 4.3 51.9 1.0 O A:HOH525 4.4 39.3 1.0 N A:THR60 4.4 63.9 1.0 CG1 A:ILE255 4.5 64.3 1.0 CA A:THR60 4.7 57.5 1.0 CB A:ALA280 4.7 45.8 1.0 C A:SER58 4.8 70.3 1.0 C A:HIS61 4.8 47.1 1.0 CB A:ASN254 4.8 58.6 1.0

Sodium binding site 2 out of 2 in the Structure of Apo Aztc


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structure of Apo Aztc within 5.0Å range: probe atom residue distance (Å) B Occ B:Na403 b:58.2 occ:1.00 OD2 B:ASP279 2.3 50.7 1.0 O B:THR60 2.3 51.5 1.0 O B:HOH509 2.5 70.6 1.0 OG B:SER58 2.6 54.2 1.0 OD1 B:ASN254 2.7 60.9 1.0 OD1 B:ASP279 2.7 48.6 1.0 CG B:ASP279 2.8 46.6 1.0 O B:SER58 3.0 74.4 0.0 O B:SER58 3.1 63.4 1.0 C B:THR60 3.5 52.2 1.0 CG B:ASN254 3.6 74.1 1.0 ND2 B:ASN254 3.8 79.8 1.0 CB B:SER58 3.9 67.8 1.0 C B:SER58 3.9 75.2 0.0 C B:SER58 4.0 68.3 1.0 CB B:SER58 4.0 78.2 0.0 CA B:HIS61 4.1 50.9 1.0 N B:HIS61 4.2 51.0 1.0 CB B:ASP279 4.3 44.8 1.0 OG B:SER58 4.3 77.6 0.0 N B:VAL62 4.3 45.2 1.0 O B:HOH521 4.4 41.7 1.0 CA B:SER58 4.4 78.9 1.0 CA B:SER58 4.5 78.7 0.0 C B:ASP59 4.6 68.5 1.0 N B:THR60 4.6 61.5 1.0 CG1 B:ILE255 4.6 61.4 1.0 O B:ASP59 4.6 75.5 1.0 CA B:THR60 4.6 57.8 1.0 CB B:ALA280 4.7 45.6 1.0 C B:HIS61 4.7 48.2 1.0 N B:SER58 4.8 82.9 0.0 N B:SER58 4.8 89.2 1.0 N B:ASP59 4.9 69.9 1.0 CB B:ASN254 4.9 64.6 1.0 O B:HOH524 5.0 74.4 1.0

D.P.Neupane, D.Avalos, S.Fullam, H.Roychowdhury, E.T.Yukl. Mechanisms of Zinc Binding to the Solute-Binding Protein Aztc and Transfer From the Metallochaperone Aztd. J. Biol. Chem. V. 292 17496 2017.
ISSN: ESSN 1083-351X
PubMed: 28887302
DOI: 10.1074/JBC.M117.804799