Sodium in PDB 5d5d: In Meso in Situ Serial X-Ray Crystallography Structure of Alge at 100 K

The structure of In Meso in Situ Serial X-Ray Crystallography Structure of Alge at 100 K, PDB code: 5d5d 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)	25.22 / 2.40
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	46.330, 66.350, 176.840, 90.00, 90.00, 90.00
R / Rfree (%)	21.9 / 26

The structure of In Meso in Situ Serial X-Ray Crystallography Structure of Alge at 100 K also contains other interesting chemical elements:

Calcium

(Ca)

1 atom

The binding sites of Sodium atom in the In Meso in Situ Serial X-Ray Crystallography Structure of Alge at 100 K (pdb code 5d5d). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the In Meso in Situ Serial X-Ray Crystallography Structure of Alge at 100 K, PDB code: 5d5d:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the In Meso in Situ Serial X-Ray Crystallography Structure of Alge at 100 K


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of In Meso in Situ Serial X-Ray Crystallography Structure of Alge at 100 K within 5.0Å range: probe atom residue distance (Å) B Occ A:Na501 b:25.8 occ:1.00 O A:ALA136 2.4 44.1 1.0 O A:TYR141 2.6 41.2 1.0 O A:GLU144 2.6 42.8 1.0 O A:THR139 2.7 47.7 1.0 OE1 A:GLU144 2.7 59.1 1.0 C A:ALA136 3.5 43.1 1.0 C A:GLU144 3.6 41.8 1.0 C A:TYR141 3.6 43.5 1.0 C A:THR139 3.7 49.1 1.0 CD A:GLU144 3.8 65.5 1.0 CB A:GLU144 4.0 39.5 1.0 OG1 A:THR139 4.0 48.4 1.0 CA A:ALA136 4.0 41.1 1.0 CA A:GLU144 4.1 38.4 1.0 CB A:ALA136 4.1 41.8 1.0 N A:TYR141 4.2 42.3 1.0 N A:GLU144 4.2 39.8 1.0 N A:THR139 4.3 46.0 1.0 CA A:TYR141 4.4 41.0 1.0 CG A:GLU144 4.5 48.7 1.0 C A:ALA140 4.5 47.7 1.0 N A:PRO142 4.5 42.8 1.0 CA A:THR139 4.5 45.4 1.0 CA A:PRO142 4.5 42.7 1.0 N A:GLY137 4.6 38.5 1.0 O A:HOH605 4.6 41.6 1.0 N A:HIS145 4.6 38.3 1.0 N A:ALA140 4.7 46.4 1.0 OE2 A:GLU144 4.7 51.9 1.0 C A:PRO142 4.8 48.6 1.0 CB A:THR139 4.9 48.8 1.0 CA A:ALA140 4.9 45.4 1.0 O A:ALA140 4.9 46.9 1.0 CB A:TYR141 4.9 41.9 1.0 N A:LEU138 5.0 45.5 1.0 CA A:GLY137 5.0 39.1 1.0

Sodium binding site 2 out of 2 in the In Meso in Situ Serial X-Ray Crystallography Structure of Alge at 100 K


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of In Meso in Situ Serial X-Ray Crystallography Structure of Alge at 100 K within 5.0Å range: probe atom residue distance (Å) B Occ A:Na502 b:67.1 occ:1.00 O A:ASN265 2.7 61.7 1.0 NE A:ARG317 3.1 33.0 1.0 NZ A:LYS325 3.1 58.8 1.0 OD1 A:ASN273 3.1 48.7 1.0 OD1 A:ASN319 3.1 58.3 1.0 CD A:LYS325 3.2 52.8 1.0 NH2 A:ARG317 3.4 29.3 1.0 CA A:GLY358 3.5 35.9 1.0 CZ A:ARG317 3.6 46.0 1.0 CE A:LYS325 3.7 55.8 1.0 O A:GLY358 3.7 42.5 1.0 C A:ASN265 3.8 60.6 1.0 CG A:ASN319 3.8 56.9 1.0 ND2 A:ASN319 3.9 45.9 1.0 CB A:SER268 3.9 61.9 1.0 CA A:TYR266 4.1 60.7 1.0 CD A:ARG317 4.1 30.7 1.0 C A:GLY358 4.1 42.1 1.0 C A:TYR266 4.2 63.9 1.0 CG A:LYS325 4.3 47.4 1.0 O A:TYR266 4.3 62.6 1.0 CG A:ASN273 4.3 54.9 1.0 N A:TYR266 4.4 59.2 1.0 N A:SER268 4.5 61.4 1.0 N A:ARG267 4.7 61.9 1.0 N A:GLY358 4.7 35.6 1.0 NH1 A:ARG317 4.9 31.1 1.0 CA A:SER268 4.9 61.2 1.0 CG A:ARG317 4.9 37.4 1.0 OG A:SER268 4.9 61.9 1.0 CA A:ASN265 5.0 51.6 1.0

C.Y.Huang, V.Olieric, P.Ma, N.Howe, L.Vogeley, X.Liu, R.Warshamanage, T.Weinert, E.Panepucci, B.Kobilka, K.Diederichs, M.Wang, M.Caffrey. In Meso in Situ Serial X-Ray Crystallography of Soluble and Membrane Proteins at Cryogenic Temperatures. Acta Crystallogr D Struct V. 72 93 2016BIOL.
ISSN: ISSN 2059-7983
PubMed: 26894538
DOI: 10.1107/S2059798315021683