Sodium in PDB 7y8s: Crystal Structure of Sdscam FNIII1-3 Domains, Isoform BETA2V6

The structure of Crystal Structure of Sdscam FNIII1-3 Domains, Isoform BETA2V6, PDB code: 7y8s was solved by Q.Chen, Y.Yu, J.Cheng, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.20 / 2.70
Space group	P 64 2 2
Cell size a, b, c (Å), α, β, γ (°)	171.649, 171.649, 114.933, 90, 90, 120
R / Rfree (%)	22.2 / 27.5

The binding sites of Sodium atom in the Crystal Structure of Sdscam FNIII1-3 Domains, Isoform BETA2V6 (pdb code 7y8s). 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 Sdscam FNIII1-3 Domains, Isoform BETA2V6, PDB code: 7y8s:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Crystal Structure of Sdscam FNIII1-3 Domains, Isoform BETA2V6


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 Sdscam FNIII1-3 Domains, Isoform BETA2V6 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na601 b:35.4 occ:1.00 O A:HIS539 3.4 30.3 1.0 N A:HIS539 3.5 28.6 1.0 CA A:GLY538 3.8 36.6 1.0 C A:GLY538 4.1 37.3 1.0 CD2 A:HIS539 4.1 34.5 1.0 NE2 A:HIS539 4.2 33.1 1.0 C A:HIS539 4.3 28.0 1.0 CG A:HIS539 4.3 33.1 1.0 CA A:HIS539 4.4 30.7 1.0 CE1 A:HIS539 4.5 34.5 1.0 ND1 A:HIS539 4.6 32.3 1.0 CD1 A:LEU541 4.6 34.8 1.0 N A:LYS535 4.6 33.5 1.0 CG A:LYS535 4.7 27.7 1.0 CD A:LYS535 4.7 32.3 1.0 CB A:LYS535 4.8 23.4 1.0 CG A:LEU541 4.9 36.7 1.0 CB A:HIS539 4.9 31.2 1.0

Sodium binding site 2 out of 3 in the Crystal Structure of Sdscam FNIII1-3 Domains, Isoform BETA2V6


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 Sdscam FNIII1-3 Domains, Isoform BETA2V6 within 5.0Å range: probe atom residue distance (Å) B Occ B:Na601 b:17.0 occ:1.00 OG1 B:THR382 3.0 25.3 1.0 N A:TRP540 3.3 29.5 1.0 OG B:SER380 3.4 44.3 1.0 N B:GLU381 3.4 47.3 1.0 C B:GLU381 3.6 40.9 1.0 CA B:GLU381 3.6 41.7 1.0 N B:THR382 3.6 40.2 1.0 CD1 A:TRP540 3.6 19.5 1.0 CB B:SER380 3.6 31.2 1.0 C B:SER380 3.7 45.6 1.0 CB A:HIS539 3.7 31.2 1.0 CA A:HIS539 3.7 30.7 1.0 CB B:THR382 4.0 25.9 1.0 OG1 B:THR367 4.0 43.3 1.0 C A:HIS539 4.1 28.0 1.0 O B:SER380 4.1 54.1 1.0 CB A:TRP540 4.1 23.1 1.0 CG A:TRP540 4.2 25.0 1.0 O B:GLU381 4.2 36.1 1.0 CA A:TRP540 4.3 25.3 1.0 CA B:SER380 4.3 41.9 1.0 CA B:THR382 4.3 23.7 1.0 CB B:THR367 4.6 37.1 1.0 NE1 A:TRP540 4.7 22.2 1.0 O A:GLY538 5.0 33.2 1.0

Sodium binding site 3 out of 3 in the Crystal Structure of Sdscam FNIII1-3 Domains, Isoform BETA2V6


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 Sdscam FNIII1-3 Domains, Isoform BETA2V6 within 5.0Å range: probe atom residue distance (Å) B Occ B:Na602 b:29.0 occ:1.00 O B:HOH704 2.9 21.5 1.0 OD1 B:ASP578 3.7 47.2 1.0 CG B:ASP578 3.8 35.8 1.0 OD2 B:ASP493 3.9 23.4 1.0 OD2 B:ASP578 3.9 32.9 1.0 CG B:ASP493 4.0 27.6 1.0 OD1 B:ASP493 4.0 35.3 1.0 N B:ASP493 4.3 35.4 1.0 O B:HOH710 4.4 29.4 1.0 CD1 B:LEU496 4.4 18.0 1.0 CD2 B:LEU492 4.4 23.2 1.0 CB B:LEU496 4.5 23.5 1.0 CB B:ASP578 4.6 25.0 1.0 CA B:LEU492 4.6 29.2 1.0 N B:ASP578 4.7 41.5 1.0 CB B:ASP493 4.8 15.4 1.0 CB B:LEU492 5.0 19.3 1.0 C B:LEU492 5.0 27.2 1.0

J.Cheng, Y.Yu, X.Wang, X.Zheng, T.Liu, D.Hu, Y.Jin, Y.Lai, T.M.Fu, Q.Chen. Structural Basis For the Self-Recognition of Sdscam in Chelicerata. Nat Commun V. 14 2522 2023.
ISSN: ESSN 2041-1723
PubMed: 37130844
DOI: 10.1038/S41467-023-38205-1