Calcium in PDB 6mue: Voltage-Gated Sodium Channel NAV1.4 Iq Domain in Complex with CA2+/Calmodulin

The structure of Voltage-Gated Sodium Channel NAV1.4 Iq Domain in Complex with CA2+/Calmodulin, PDB code: 6mue was solved by B.R.Gardill, F.Van Petegem, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	33.07 / 1.90
Space group	P 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	58.580, 24.433, 60.720, 90.00, 112.63, 90.00
R / Rfree (%)	21.4 / 26

The binding sites of Calcium atom in the Voltage-Gated Sodium Channel NAV1.4 Iq Domain in Complex with CA2+/Calmodulin (pdb code 6mue). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Voltage-Gated Sodium Channel NAV1.4 Iq Domain in Complex with CA2+/Calmodulin, PDB code: 6mue:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Voltage-Gated Sodium Channel NAV1.4 Iq Domain in Complex with CA2+/Calmodulin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Voltage-Gated Sodium Channel NAV1.4 Iq Domain in Complex with CA2+/Calmodulin within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca201 b:30.6 occ:1.00 O A:GLN136 2.2 28.8 0.4 OD1 A:ASP134 2.3 37.9 1.0 OE1 A:GLU141 2.3 31.7 1.0 OD1 A:ASP130 2.3 26.2 1.0 O A:GLN136 2.4 28.2 0.6 OD1 A:ASP132 2.4 34.1 1.0 O A:HOH326 2.4 31.8 1.0 OE2 A:GLU141 2.6 31.0 1.0 CD A:GLU141 2.8 29.9 1.0 CG A:ASP132 3.2 39.1 1.0 CG A:ASP134 3.3 36.8 1.0 CG A:ASP130 3.4 27.3 1.0 OD2 A:ASP132 3.4 43.5 1.0 C A:GLN136 3.4 30.2 0.4 C A:GLN136 3.5 30.8 0.6 OD2 A:ASP134 3.7 36.0 1.0 CA A:ASP130 4.1 27.4 1.0 N A:ASP134 4.2 38.0 1.0 N A:GLN136 4.2 29.7 0.4 N A:GLN136 4.2 29.7 0.6 CB A:ASP130 4.2 27.6 1.0 N A:ASP132 4.3 36.3 1.0 OD2 A:ASP130 4.3 31.3 1.0 CA A:VAL137 4.3 26.9 1.0 CG A:GLU141 4.3 26.8 1.0 N A:VAL137 4.3 29.4 1.0 CA A:GLN136 4.4 32.3 0.6 N A:GLY133 4.4 33.6 1.0 CB A:ASP132 4.4 39.2 1.0 N A:ASN138 4.4 25.2 1.0 CA A:GLN136 4.4 30.9 0.4 CB A:ASP134 4.4 35.2 1.0 C A:ASP130 4.5 27.2 1.0 N A:ILE131 4.6 25.5 1.0 CA A:ASP132 4.7 36.3 1.0 CA A:ASP134 4.7 36.4 1.0 N A:GLY135 4.8 33.4 1.0 C A:ASP132 4.8 37.3 1.0 CG A:GLN136 4.8 31.8 0.4 C A:VAL137 4.8 26.0 1.0 CB A:GLN136 4.9 32.8 0.6 ND2 A:ASN138 4.9 29.5 1.0 CG A:ASN138 4.9 29.7 1.0 C A:ASP134 5.0 35.9 1.0 O A:ASP130 5.0 31.3 1.0

Calcium binding site 2 out of 4 in the Voltage-Gated Sodium Channel NAV1.4 Iq Domain in Complex with CA2+/Calmodulin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Voltage-Gated Sodium Channel NAV1.4 Iq Domain in Complex with CA2+/Calmodulin within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca202 b:26.7 occ:1.00 OD1 A:ASP25 2.2 28.5 1.0 OE2 A:GLU32 2.3 24.2 1.0 O A:THR27 2.3 26.2 1.0 OD1 A:ASP21 2.3 28.4 1.0 OD1 A:ASP23 2.3 34.1 1.0 O A:HOH338 2.3 29.9 1.0 OE1 A:GLU32 2.5 27.3 1.0 CD A:GLU32 2.8 26.0 1.0 CG A:ASP25 3.3 33.6 1.0 CG A:ASP23 3.4 35.1 1.0 CG A:ASP21 3.4 32.0 1.0 C A:THR27 3.5 26.9 1.0 OD2 A:ASP23 3.9 39.3 1.0 OD2 A:ASP25 4.0 32.4 1.0 OG1 A:THR27 4.0 26.7 1.0 CA A:ASP21 4.1 32.2 1.0 N A:ASP25 4.2 32.3 1.0 CB A:ASP25 4.2 34.1 1.0 OD2 A:ASP21 4.2 33.8 1.0 N A:THR27 4.2 25.8 1.0 CB A:ASP21 4.2 28.6 1.0 CG A:GLU32 4.3 26.1 1.0 N A:ASP23 4.3 29.9 1.0 C A:ASP21 4.3 30.5 1.0 CA A:THR27 4.4 28.3 1.0 N A:ILE28 4.4 26.1 1.0 N A:GLY24 4.4 33.1 1.0 N A:LYS22 4.5 30.7 1.0 CB A:ASP23 4.5 35.9 1.0 CA A:ILE28 4.6 24.9 1.0 CA A:ASP25 4.7 32.7 1.0 CA A:ASP23 4.7 34.8 1.0 C A:ASP23 4.7 34.0 1.0 O A:HOH311 4.7 46.2 1.0 N A:GLY26 4.8 31.0 1.0 CB A:THR27 4.8 30.1 1.0 O A:ASP21 4.9 28.8 1.0 N A:THR29 5.0 23.9 1.0 C A:ASP25 5.0 30.9 1.0

Calcium binding site 3 out of 4 in the Voltage-Gated Sodium Channel NAV1.4 Iq Domain in Complex with CA2+/Calmodulin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Voltage-Gated Sodium Channel NAV1.4 Iq Domain in Complex with CA2+/Calmodulin within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca203 b:28.2 occ:1.00 O A:HOH308 2.2 33.4 1.0 O A:THR63 2.2 28.3 1.0 OD1 A:ASP57 2.3 28.7 1.0 OE2 A:GLU68 2.3 29.9 1.0 OD1 A:ASN61 2.4 32.5 1.0 OE1 A:GLU68 2.4 27.0 1.0 OD1 A:ASP59 2.5 38.3 1.0 CD A:GLU68 2.7 28.2 1.0 CG A:ASN61 3.3 31.1 1.0 CG A:ASP59 3.3 36.0 1.0 CG A:ASP57 3.4 31.9 1.0 C A:THR63 3.4 28.0 1.0 O A:HOH324 3.6 42.2 1.0 OD2 A:ASP59 3.6 39.2 1.0 ND2 A:ASN61 3.9 32.4 1.0 OD2 A:ASP57 4.2 31.9 1.0 N A:THR63 4.2 28.7 1.0 CG A:GLU68 4.2 29.7 1.0 N A:ASN61 4.2 35.6 1.0 N A:ILE64 4.3 25.4 0.9 N A:ILE64 4.3 27.1 0.1 CB A:ASP57 4.3 31.4 1.0 CA A:ASP57 4.3 30.9 1.0 CA A:ILE64 4.4 24.9 0.9 CA A:ILE64 4.4 26.4 0.1 CA A:THR63 4.4 29.1 1.0 N A:ASP59 4.4 36.6 1.0 CB A:ASN61 4.4 33.5 1.0 N A:ASP65 4.5 25.0 1.0 OG1 A:THR63 4.5 28.2 1.0 CB A:ASP59 4.6 39.8 1.0 C A:ASP57 4.6 34.3 1.0 N A:GLY60 4.6 39.2 1.0 CA A:ASN61 4.7 33.3 1.0 N A:ALA58 4.7 34.4 1.0 N A:GLY62 4.8 31.1 1.0 O A:HOH336 4.8 44.5 1.0 OD2 A:ASP65 4.8 38.3 1.0 CG A:ASP65 4.8 33.0 1.0 CA A:ASP59 4.9 39.9 1.0 C A:ILE64 4.9 23.7 0.9 C A:ILE64 4.9 25.8 0.1 CD1 A:ILE64 4.9 28.0 0.9 C A:ASP59 5.0 39.6 1.0 C A:ASN61 5.0 32.7 1.0

Calcium binding site 4 out of 4 in the Voltage-Gated Sodium Channel NAV1.4 Iq Domain in Complex with CA2+/Calmodulin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Voltage-Gated Sodium Channel NAV1.4 Iq Domain in Complex with CA2+/Calmodulin within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca204 b:36.5 occ:1.00 OD1 A:ASN98 2.0 32.2 1.0 OE1 A:GLU105 2.2 34.8 1.0 O A:TYR100 2.3 39.5 1.0 OD1 A:ASP96 2.3 43.4 1.0 OD1 A:ASP94 2.3 27.3 1.0 O A:HOH329 2.5 50.7 1.0 OE2 A:GLU105 2.5 31.2 1.0 CD A:GLU105 2.7 32.5 1.0 CG A:ASN98 2.9 41.9 1.0 ND2 A:ASN98 3.1 43.4 1.0 CG A:ASP96 3.2 46.8 1.0 OD2 A:ASP96 3.4 47.3 1.0 C A:TYR100 3.5 35.9 1.0 CG A:ASP94 3.5 26.8 1.0 CA A:ASP94 4.1 26.1 1.0 CG A:GLU105 4.2 29.5 1.0 CA A:ILE101 4.2 31.4 1.0 N A:ASP96 4.3 42.5 1.0 CB A:ASN98 4.3 42.0 1.0 N A:ILE101 4.3 31.3 1.0 N A:SER102 4.3 36.5 1.0 CB A:ASP94 4.3 25.8 1.0 OD2 A:ASP94 4.4 29.0 1.0 C A:ASP94 4.4 29.9 1.0 N A:ASN98 4.4 39.3 1.0 N A:TYR100 4.4 31.2 1.0 CB A:ASP96 4.5 43.9 1.0 CA A:TYR100 4.5 32.8 1.0 N A:LYS95 4.5 34.3 1.0 N A:GLY97 4.6 37.8 1.0 C A:ILE101 4.7 34.0 1.0 CA A:ASP96 4.8 41.4 1.0 CA A:ASN98 4.8 40.9 1.0 N A:GLY99 4.9 32.5 1.0 CB A:TYR100 4.9 35.5 1.0 O A:ASP94 4.9 29.4 1.0 C A:ASP96 4.9 39.9 1.0 OG A:SER102 4.9 42.1 1.0

B.R.Gardill, R.E.Rivera-Acevedo, C.C.Tung, F.Van Petegem. Crystal Structures of CA2+-Calmodulin Bound to Navc-Terminal Regions Suggest Role For Ef-Hand Domain in Binding and Inactivation. Proc.Natl.Acad.Sci.Usa V. 116 10763 2019.
ISSN: ESSN 1091-6490
PubMed: 31072926
DOI: 10.1073/PNAS.1818618116