Sodium in PDB 6u3a: 1.65 Angstrom Crystal Structure of the N97S Ca-Cam:CAV1.2 Iq Domain Complex

The structure of 1.65 Angstrom Crystal Structure of the N97S Ca-Cam:CAV1.2 Iq Domain Complex, PDB code: 6u3a was solved by K.Wang, F.Van Petegem, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	35.66 / 1.65
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	63.419, 68.077, 86.250, 90.00, 90.00, 90.00
R / Rfree (%)	17.8 / 20.9

The structure of 1.65 Angstrom Crystal Structure of the N97S Ca-Cam:CAV1.2 Iq Domain Complex also contains other interesting chemical elements:

Calcium

(Ca)

7 atoms

The binding sites of Sodium atom in the 1.65 Angstrom Crystal Structure of the N97S Ca-Cam:CAV1.2 Iq Domain Complex (pdb code 6u3a). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the 1.65 Angstrom Crystal Structure of the N97S Ca-Cam:CAV1.2 Iq Domain Complex, PDB code: 6u3a:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the 1.65 Angstrom Crystal Structure of the N97S Ca-Cam:CAV1.2 Iq Domain Complex


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of 1.65 Angstrom Crystal Structure of the N97S Ca-Cam:CAV1.2 Iq Domain Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Na504 b:31.3 occ:1.00 OD1 A:ASP93 2.3 27.5 1.0 OD1 A:ASP95 2.3 41.1 1.0 O A:TYR99 2.3 31.1 1.0 OG A:SER97 2.5 36.3 1.0 O A:HOH713 2.5 44.8 1.0 CG A:ASP93 3.3 28.2 1.0 CG A:ASP95 3.4 47.0 1.0 CB A:SER97 3.5 38.5 1.0 C A:TYR99 3.5 31.1 1.0 N A:SER97 3.8 31.1 1.0 OD2 A:ASP95 3.9 47.7 1.0 CA A:ASP93 4.1 25.5 1.0 OD2 A:ASP93 4.1 27.1 1.0 N A:TYR99 4.1 27.7 1.0 CA A:SER97 4.2 38.6 1.0 CB A:ASP93 4.2 24.4 1.0 N A:ASP95 4.3 38.5 1.0 C A:ASP93 4.3 28.8 1.0 O A:HOH608 4.3 35.8 1.0 N A:LYS94 4.3 30.9 1.0 CA A:TYR99 4.4 34.8 1.0 N A:GLY96 4.4 35.6 1.0 N A:ILE100 4.5 28.9 1.0 CA A:ILE100 4.6 25.0 1.0 N A:GLY98 4.6 29.6 1.0 CB A:ASP95 4.7 44.2 1.0 C A:SER97 4.7 37.1 1.0 CB A:TYR99 4.7 47.1 1.0 C A:ASP95 4.8 40.3 1.0 CA A:ASP95 4.8 43.0 1.0 O A:ASP93 4.9 29.9 1.0 C A:GLY96 4.9 28.2 1.0

Sodium binding site 2 out of 2 in the 1.65 Angstrom Crystal Structure of the N97S Ca-Cam:CAV1.2 Iq Domain Complex


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of 1.65 Angstrom Crystal Structure of the N97S Ca-Cam:CAV1.2 Iq Domain Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Na505 b:36.0 occ:1.00 O A:HOH630 2.3 22.6 1.0 O A:HOH714 2.4 33.7 1.0 O A:GLU114 2.4 33.5 1.0 OD1 B:ASN42 2.4 24.5 1.0 O A:LEU116 2.5 31.0 1.0 C A:GLU114 3.2 28.5 1.0 CG B:ASN42 3.4 25.5 1.0 O B:HOH638 3.4 30.2 1.0 N A:LEU116 3.4 29.6 1.0 C A:LEU116 3.5 33.9 1.0 ND2 B:ASN42 3.6 31.4 1.0 C A:LYS115 3.6 34.8 1.0 CA A:LYS115 3.7 39.9 1.0 N A:LYS115 3.8 30.3 1.0 O B:HOH702 3.9 32.4 1.0 CD B:ARG37 4.0 21.8 1.0 CA A:LEU116 4.0 27.7 1.0 O A:GLY113 4.0 35.3 1.0 CA A:GLU114 4.1 25.5 1.0 O B:HOH621 4.2 40.1 1.0 O A:LYS115 4.3 36.6 1.0 N A:THR117 4.6 30.5 1.0 NH1 B:ARG37 4.6 22.3 1.0 CB A:LEU116 4.7 25.9 1.0 O A:THR110 4.8 25.7 0.2 O A:THR110 4.8 25.3 0.8 CB B:ASN42 4.8 26.5 1.0 NE B:ARG37 4.9 24.5 1.0 O B:PRO43 4.9 24.4 1.0 C A:GLY113 4.9 32.2 1.0 CG B:ARG37 5.0 19.4 1.0 CG2 A:THR110 5.0 25.8 0.8

K.Wang, M.Brohus, C.Holt, M.T.Overgaard, R.Wimmer, F.Van Petegem. Arrhythmia Mutations in Calmodulin Can Disrupt Cooperativity of CA2+Binding and Cause Misfolding. J. Physiol. (Lond.) 2020.
ISSN: ISSN 1469-7793
PubMed: 32012279
DOI: 10.1113/JP279307