Sodium in PDB 4xnk: X-Ray Structure of ALGE1

The structure of X-Ray Structure of ALGE1, PDB code: 4xnk was solved by P.Ma, C.Y.Huang, V.Olieric, K.Diederichs, M.Wang, M.Caffrey, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.42 / 2.80
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	48.010, 74.340, 184.690, 90.00, 90.00, 90.00
R / Rfree (%)	22.6 / 27.4

The structure of X-Ray Structure of ALGE1 also contains other interesting chemical elements:

Calcium

(Ca)

1 atom

The binding sites of Sodium atom in the X-Ray Structure of ALGE1 (pdb code 4xnk). 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 ALGE1, PDB code: 4xnk:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the X-Ray Structure of ALGE1


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 ALGE1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na508 b:60.3 occ:1.00 O A:ASN265 2.7 50.0 1.0 NZ A:LYS325 3.1 52.7 1.0 NH2 A:ARG317 3.2 33.0 1.0 OD1 A:ASN273 3.4 71.0 1.0 NE A:ARG317 3.7 43.3 1.0 OD1 A:ASN319 3.7 45.4 1.0 C A:ASN265 3.8 50.9 1.0 CA A:TYR266 3.8 50.5 1.0 C A:TYR266 3.8 54.6 1.0 CZ A:ARG317 3.8 51.3 1.0 CD A:LYS325 4.0 46.9 1.0 O A:TYR266 4.0 54.3 1.0 OG A:SER268 4.1 61.4 1.0 O A:GLY358 4.1 43.2 1.0 CE A:LYS325 4.1 48.8 1.0 CA A:GLY358 4.1 39.1 1.0 ND2 A:ASN319 4.2 36.4 1.0 CG A:ASN319 4.2 49.4 1.0 N A:TYR266 4.2 49.6 1.0 N A:SER268 4.3 50.1 1.0 N A:ARG267 4.3 51.4 1.0 CB A:SER268 4.3 52.4 1.0 C A:GLY358 4.6 43.1 1.0 CG A:ASN273 4.6 71.9 1.0 CA A:SER268 4.9 49.5 1.0 CD A:ARG317 4.9 39.8 1.0 O A:ASP262 5.0 40.2 1.0

Sodium binding site 2 out of 2 in the X-Ray Structure of ALGE1


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 ALGE1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na509 b:53.4 occ:1.00 O A:ALA136 2.6 49.7 1.0 O A:TYR141 2.8 42.2 1.0 O A:GLU144 2.9 41.5 1.0 O A:THR139 3.1 48.6 1.0 OE1 A:GLU144 3.3 48.6 1.0 C A:ALA136 3.4 50.2 1.0 C A:TYR141 3.9 43.1 1.0 CB A:ALA136 4.0 45.7 1.0 CA A:ALA136 4.0 45.0 1.0 C A:GLU144 4.0 42.5 1.0 C A:THR139 4.2 49.4 1.0 OG1 A:THR139 4.3 52.6 1.0 N A:GLY137 4.4 48.1 1.0 CD A:GLU144 4.4 60.2 1.0 CB A:GLU144 4.5 39.2 1.0 N A:GLU144 4.6 38.0 1.0 CA A:GLU144 4.6 37.8 1.0 N A:TYR141 4.6 41.8 1.0 N A:THR139 4.6 48.0 1.0 CA A:PRO142 4.7 38.4 1.0 CA A:GLY137 4.8 48.1 1.0 N A:PRO142 4.8 38.8 1.0 CA A:TYR141 4.8 41.0 1.0 O A:PRO142 4.9 42.8 1.0 C A:ALA140 4.9 46.7 1.0 C A:PRO142 4.9 42.3 1.0 CA A:THR139 4.9 46.8 1.0

C.Y.Huang, V.Olieric, P.Ma, E.Panepucci, K.Diederichs, M.Wang, M.Caffrey. In Meso in Situ Serial X-Ray Crystallography of Soluble and Membrane Proteins. Acta Crystallogr.,Sect.D V. 71 1238 2015.
ISSN: ESSN 1399-0047
PubMed: 26057665
DOI: 10.1107/S1399004715005210