Sodium in PDB 3trq: Crystal Structure of Native Rabbit Skeletal Calsequestrin

The structure of Crystal Structure of Native Rabbit Skeletal Calsequestrin, PDB code: 3trq was solved by E.J.Sanchez, K.M.Lewis, G.R.Munske, M.S.Nissen, C.Kang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.70 / 1.76
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	59.271, 144.565, 111.170, 90.00, 90.00, 90.00
R / Rfree (%)	17.8 / 21.3

The structure of Crystal Structure of Native Rabbit Skeletal Calsequestrin also contains other interesting chemical elements:

Calcium

(Ca)

6 atoms

The binding sites of Sodium atom in the Crystal Structure of Native Rabbit Skeletal Calsequestrin (pdb code 3trq). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Crystal Structure of Native Rabbit Skeletal Calsequestrin, PDB code: 3trq:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Crystal Structure of Native Rabbit Skeletal Calsequestrin


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of Native Rabbit Skeletal Calsequestrin within 5.0Å range: probe atom residue distance (Å) B Occ A:Na364 b:28.8 occ:1.00 OD1 A:ASP290 2.5 40.5 1.0 OD2 A:ASP288 2.6 17.7 1.0 O A:HOH498 2.8 46.9 1.0 N A:ALA258 3.2 15.1 1.0 N A:GLU257 3.2 16.0 1.0 OD1 A:ASP288 3.2 15.6 1.0 CG A:ASP288 3.3 16.5 1.0 CG A:ASP290 3.4 47.9 1.0 CB A:ALA258 3.6 21.2 1.0 CB A:ASP290 3.7 14.7 1.0 C A:GLU256 3.8 13.3 1.0 CA A:GLU257 3.9 14.5 1.0 CA A:GLU256 4.0 13.7 1.0 CB A:GLU257 4.0 17.2 1.0 CA A:ALA258 4.0 20.6 1.0 C A:GLU257 4.0 16.1 1.0 O A:HOH841 4.1 18.9 1.0 CB A:GLU256 4.2 18.3 1.0 O A:HOH377 4.3 42.9 1.0 O A:HOH871 4.5 31.2 1.0 OD2 A:ASP290 4.6 48.5 1.0 O A:GLU256 4.6 16.5 1.0 CB A:ASP288 4.7 13.3 1.0

Sodium binding site 2 out of 3 in the Crystal Structure of Native Rabbit Skeletal Calsequestrin


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of Native Rabbit Skeletal Calsequestrin within 5.0Å range: probe atom residue distance (Å) B Occ A:Na365 b:43.7 occ:1.00 O A:HOH558 2.1 30.0 1.0 O A:PRO172 2.1 24.3 1.0 O A:HOH557 2.2 30.0 1.0 O A:HOH555 2.5 30.0 1.0 O A:HOH556 2.6 30.0 1.0 O A:HOH492 2.9 54.0 1.0 C A:PRO172 3.3 18.4 1.0 O A:TYR173 4.1 22.1 1.0 CA A:TYR173 4.1 19.9 1.0 CB A:PRO172 4.1 24.9 1.0 N A:TYR173 4.1 17.4 1.0 C A:TYR173 4.1 27.2 1.0 O A:HOH843 4.1 33.5 1.0 OD1 A:ASP121 4.3 24.1 1.0 CA A:PRO172 4.3 17.4 1.0 OE2 A:GLU236 4.4 34.1 1.0 OE1 A:GLU145 4.4 45.0 1.0 OE1 A:GLU236 4.6 53.4 1.0 CG A:ASP121 4.7 23.5 1.0 CG A:PRO172 4.8 19.1 1.0 CB A:ASP121 4.9 19.3 1.0 N A:ILE174 4.9 17.2 1.0 O A:HOH638 4.9 25.8 1.0 CD A:GLU236 4.9 55.2 1.0

Sodium binding site 3 out of 3 in the Crystal Structure of Native Rabbit Skeletal Calsequestrin


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of Native Rabbit Skeletal Calsequestrin within 5.0Å range: probe atom residue distance (Å) B Occ A:Na366 b:42.8 occ:1.00 O A:HOH559 2.5 30.0 1.0 OG1 A:THR318 2.7 26.0 1.0 O A:GLY248 2.9 21.0 1.0 OD1 A:ASN316 3.1 28.5 1.0 CA A:GLY248 3.4 23.4 1.0 C A:GLY248 3.5 22.4 1.0 N2 A:NAG900 3.8 34.6 1.0 CG2 A:VAL317 3.9 29.2 1.0 CB A:THR318 3.9 30.3 1.0 CG A:ASN316 3.9 29.2 1.0 N A:THR318 4.0 24.9 1.0 C1 A:NAG900 4.0 29.2 1.0 N A:VAL317 4.3 18.7 1.0 ND2 A:ASN316 4.3 26.1 1.0 C8 A:NAG900 4.5 44.8 1.0 C2 A:NAG900 4.5 37.8 1.0 CA A:THR318 4.5 25.0 1.0 C7 A:NAG900 4.6 36.5 1.0 N A:GLY248 4.8 22.5 1.0 C A:VAL317 4.8 26.5 1.0 N A:ILE249 4.8 20.4 1.0 CA A:VAL317 4.9 19.7 1.0 C A:ASN316 4.9 20.3 1.0 CB A:VAL317 5.0 24.4 1.0 CA A:ASN316 5.0 19.5 1.0

E.J.Sanchez, K.M.Lewis, G.R.Munske, M.S.Nissen, C.Kang. Glycosylation of Skeletal Calsequestrin: Implications For Its Function. J.Biol.Chem. V. 287 3042 2012.
ISSN: ISSN 0021-9258
PubMed: 22170046
DOI: 10.1074/JBC.M111.326363