Calcium in PDB 6mud: Voltage-Gated Sodium Channel NAV1.5 C-Terminal Domain in Complex with CA2+/Calmodulin

The structure of Voltage-Gated Sodium Channel NAV1.5 C-Terminal Domain in Complex with CA2+/Calmodulin, PDB code: 6mud was solved by B.R.Gardill, C.C.Tung, F.Van Petegem, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	34.31 / 2.69
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	65.579, 84.032, 140.684, 90.00, 90.00, 90.00
R / Rfree (%)	21.2 / 26.9

The binding sites of Calcium atom in the Voltage-Gated Sodium Channel NAV1.5 C-Terminal Domain in Complex with CA2+/Calmodulin (pdb code 6mud). 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 NAV1.5 C-Terminal Domain in Complex with CA2+/Calmodulin, PDB code: 6mud:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Voltage-Gated Sodium Channel NAV1.5 C-Terminal 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 NAV1.5 C-Terminal Domain in Complex with CA2+/Calmodulin within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1001 b:55.8 occ:1.00 OD1 A:ASP22 2.1 64.8 1.0 O A:THR26 2.3 56.0 1.0 O A:HOH1107 2.3 67.4 1.0 OD1 A:ASP24 2.3 57.2 1.0 OD1 A:ASP20 2.4 54.0 1.0 OE1 A:GLU31 2.4 52.7 1.0 OE2 A:GLU31 2.7 55.6 1.0 CD A:GLU31 2.9 53.2 1.0 CG A:ASP22 3.1 65.4 1.0 CG A:ASP24 3.3 59.6 1.0 OD2 A:ASP22 3.4 66.5 1.0 C A:THR26 3.5 53.5 1.0 CG A:ASP20 3.5 55.4 1.0 OD2 A:ASP24 3.8 61.7 1.0 CA A:ASP20 3.9 56.5 1.0 CB A:ASP20 3.9 55.8 1.0 N A:THR26 4.1 54.3 1.0 N A:ASP24 4.2 62.9 1.0 OG1 A:THR26 4.3 61.8 1.0 CA A:THR26 4.3 54.7 1.0 CG A:GLU31 4.4 51.8 1.0 N A:ILE27 4.4 50.8 1.0 C A:ASP20 4.4 58.2 1.0 CB A:ASP22 4.4 65.9 1.0 N A:ASP22 4.4 64.0 1.0 CB A:ASP24 4.5 61.1 1.0 CA A:ILE27 4.5 48.9 1.0 OD2 A:ASP20 4.5 57.1 1.0 N A:GLY25 4.5 58.8 1.0 N A:GLY23 4.5 66.8 1.0 N A:LYS21 4.7 60.0 1.0 CA A:ASP24 4.7 61.7 1.0 CA A:ASP22 4.8 65.7 1.0 C A:ASP22 4.9 66.6 1.0 O A:HOH1104 4.9 38.6 1.0 N A:THR28 4.9 50.0 1.0 C A:ASP24 4.9 61.2 1.0

Calcium binding site 2 out of 4 in the Voltage-Gated Sodium Channel NAV1.5 C-Terminal 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 NAV1.5 C-Terminal Domain in Complex with CA2+/Calmodulin within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1002 b:53.4 occ:1.00 O A:HOH1101 2.0 40.9 1.0 OD1 A:ASP56 2.2 56.5 1.0 OD1 A:ASP58 2.2 67.2 1.0 O A:THR62 2.4 52.4 1.0 OE2 A:GLU67 2.5 56.7 1.0 OE1 A:GLU67 2.7 56.7 1.0 OD1 A:ASN60 2.7 57.4 1.0 CD A:GLU67 2.9 55.4 1.0 CG A:ASP58 3.1 65.7 1.0 CG A:ASN60 3.2 56.5 1.0 OD2 A:ASP58 3.3 65.5 1.0 CG A:ASP56 3.4 58.2 1.0 ND2 A:ASN60 3.4 55.4 1.0 C A:THR62 3.5 51.1 1.0 OD2 A:ASP56 4.1 58.7 1.0 OG1 A:THR62 4.3 53.9 1.0 N A:ILE63 4.3 49.0 1.0 N A:THR62 4.3 54.6 1.0 CB A:ASP56 4.3 58.6 1.0 N A:ASP58 4.4 64.7 1.0 N A:ASN60 4.4 61.0 1.0 CB A:ASN60 4.4 59.1 1.0 CG A:GLU67 4.4 53.1 1.0 CB A:ASP58 4.5 66.4 1.0 CA A:ILE63 4.5 47.4 1.0 N A:ALA57 4.5 61.1 1.0 CA A:ASP56 4.5 59.4 1.0 CA A:THR62 4.5 52.4 1.0 N A:ASP64 4.6 47.7 1.0 CA A:ASN60 4.8 60.3 1.0 CA A:ASP58 4.8 66.5 1.0 N A:GLY59 4.9 65.6 1.0 C A:ASP56 4.9 61.1 1.0 C A:ASN60 4.9 59.6 1.0 OD1 A:ASP64 5.0 59.9 1.0 C A:ILE63 5.0 45.7 1.0

Calcium binding site 3 out of 4 in the Voltage-Gated Sodium Channel NAV1.5 C-Terminal 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 NAV1.5 C-Terminal Domain in Complex with CA2+/Calmodulin within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1003 b:76.4 occ:1.00 OD2 A:ASP131 2.1 93.7 1.0 O A:HOH1106 2.2 63.9 1.0 OD1 A:ASP133 2.2 78.8 1.0 O A:GLN135 2.3 70.4 1.0 OD1 A:ASP129 2.3 89.8 1.0 OE1 A:GLU140 2.5 83.0 1.0 OE2 A:GLU140 3.0 87.2 1.0 CG A:ASP133 3.1 80.3 1.0 CD A:GLU140 3.1 84.2 1.0 CG A:ASP131 3.3 95.7 1.0 C A:GLN135 3.4 67.6 1.0 OD2 A:ASP133 3.4 80.8 1.0 CG A:ASP129 3.5 88.9 1.0 OD1 A:ASP131 4.0 97.5 1.0 N A:VAL136 4.2 64.4 1.0 N A:ASP133 4.2 83.3 1.0 N A:GLN135 4.2 70.1 1.0 CA A:ASP129 4.2 87.2 1.0 CA A:VAL136 4.3 63.6 1.0 CB A:ASP129 4.3 87.0 1.0 CA A:GLN135 4.3 68.1 1.0 OD2 A:ASP129 4.3 88.7 1.0 N A:GLY132 4.4 90.2 1.0 CB A:ASP133 4.4 82.1 1.0 CB A:ASP131 4.5 97.6 1.0 N A:ASP131 4.6 95.8 1.0 N A:ASN137 4.6 65.5 1.0 CG A:GLU140 4.6 83.0 1.0 C A:ASP129 4.7 91.1 1.0 CA A:ASP133 4.7 81.9 1.0 CB A:GLN135 4.8 68.9 1.0 N A:ILE130 4.9 92.0 1.0 C A:VAL136 4.9 62.7 1.0 N A:GLY134 4.9 76.4 1.0 CA A:ASP131 4.9 97.2 1.0

Calcium binding site 4 out of 4 in the Voltage-Gated Sodium Channel NAV1.5 C-Terminal 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 NAV1.5 C-Terminal Domain in Complex with CA2+/Calmodulin within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1004 b:58.9 occ:1.00 O A:TYR99 2.0 56.6 1.0 OD1 A:ASP95 2.1 57.9 1.0 OD1 A:ASP93 2.2 56.5 1.0 OD1 A:ASN97 2.3 57.9 1.0 O A:HOH1103 2.4 56.3 1.0 OE2 A:GLU104 2.4 58.7 1.0 OE1 A:GLU104 2.8 58.1 1.0 CD A:GLU104 2.9 59.0 1.0 CG A:ASP95 3.1 58.4 1.0 C A:TYR99 3.3 58.7 1.0 OD2 A:ASP95 3.3 59.5 1.0 CG A:ASN97 3.4 59.3 1.0 CG A:ASP93 3.4 57.1 1.0 N A:TYR99 4.0 61.0 1.0 ND2 A:ASN97 4.1 59.9 1.0 CA A:ASP93 4.2 53.9 1.0 N A:ILE100 4.2 58.4 1.0 CA A:TYR99 4.2 61.4 1.0 CB A:ASP93 4.2 55.3 1.0 N A:ASN97 4.2 58.7 1.0 OD2 A:ASP93 4.3 59.4 1.0 CA A:ILE100 4.3 57.8 1.0 CG A:GLU104 4.4 58.2 1.0 CB A:ASN97 4.5 60.7 1.0 CB A:ASP95 4.5 57.9 1.0 N A:GLY96 4.6 57.4 1.0 C A:ASP93 4.6 54.7 1.0 N A:ASP95 4.6 55.7 1.0 CB A:TYR99 4.7 64.2 1.0 N A:SER101 4.7 58.7 1.0 N A:GLY98 4.7 59.9 1.0 CA A:ASN97 4.7 60.6 1.0 N A:LYS94 4.9 55.4 1.0 CA A:ASP95 4.9 57.0 1.0 C A:ASN97 4.9 60.8 1.0 C A:ILE100 5.0 58.8 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