Calcium in PDB 6mc9: Crystal Structure of Human NAV1.4 C-Terminal (1599-1754) Domain in Complex with Calcium-Bound Calmodulin

The structure of Crystal Structure of Human NAV1.4 C-Terminal (1599-1754) Domain in Complex with Calcium-Bound Calmodulin, PDB code: 6mc9 was solved by J.B.Yoder, S.B.Gabelli, L.M.Amzel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.83 / 3.30
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	72.615, 72.615, 134.661, 90.00, 90.00, 90.00
R / Rfree (%)	24 / 28.5

The binding sites of Calcium atom in the Crystal Structure of Human NAV1.4 C-Terminal (1599-1754) Domain in Complex with Calcium-Bound Calmodulin (pdb code 6mc9). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Crystal Structure of Human NAV1.4 C-Terminal (1599-1754) Domain in Complex with Calcium-Bound Calmodulin, PDB code: 6mc9:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Crystal Structure of Human NAV1.4 C-Terminal (1599-1754) Domain in Complex with Calcium-Bound Calmodulin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of Human NAV1.4 C-Terminal (1599-1754) Domain in Complex with Calcium-Bound Calmodulin within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1001 b:77.8 occ:1.00 OD1 B:ASP133 2.3 0.3 1.0 O B:GLN135 2.4 0.1 1.0 OD1 B:ASP129 2.7 95.7 1.0 OE1 B:GLU140 2.9 98.2 1.0 OE2 B:GLU140 2.9 99.4 1.0 CD B:GLU140 3.3 98.7 1.0 CG B:ASP133 3.4 0.9 1.0 C B:GLN135 3.5 0.9 1.0 CB B:ASP131 3.5 0.8 1.0 CG B:ASP129 3.8 0.4 1.0 OD2 B:ASP133 3.9 0.3 1.0 CG B:ASP131 4.1 0.8 1.0 CA B:GLN135 4.2 0.1 1.0 N B:GLN135 4.3 0.1 1.0 CB B:GLN135 4.4 0.1 1.0 OD1 B:ASP131 4.4 0.7 1.0 N B:VAL136 4.4 0.5 1.0 OD2 B:ASP129 4.5 0.8 1.0 N B:ASN137 4.5 0.1 1.0 N B:ASP133 4.5 0.1 1.0 CB B:ASP133 4.5 0.5 1.0 CA B:VAL136 4.6 0.1 1.0 CA B:ASP131 4.6 0.7 1.0 N B:GLY132 4.7 0.8 1.0 N B:ASP131 4.7 0.2 1.0 CG B:GLU140 4.7 0.3 1.0 OD2 B:ASP131 4.8 0.6 1.0 CB B:ASP129 4.8 93.4 1.0 CA B:ASP129 4.8 0.9 1.0 C B:VAL136 4.9 99.9 1.0 CA B:ASP133 4.9 1.0 1.0 OD1 B:ASN137 5.0 1.0 1.0 CG B:ASN137 5.0 88.9 1.0

Calcium binding site 2 out of 4 in the Crystal Structure of Human NAV1.4 C-Terminal (1599-1754) Domain in Complex with Calcium-Bound Calmodulin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of Human NAV1.4 C-Terminal (1599-1754) Domain in Complex with Calcium-Bound Calmodulin within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1002 b:76.5 occ:1.00 O B:TYR99 2.6 0.2 1.0 OE2 B:GLU104 2.6 0.5 1.0 OE1 B:GLU104 2.7 99.5 1.0 OD1 B:ASP95 2.7 0.1 1.0 OD1 B:ASP93 2.7 0.9 1.0 OD2 B:ASP95 2.7 0.5 1.0 OD1 B:ASN97 2.7 0.3 1.0 CG B:ASP95 2.9 0.3 1.0 CD B:GLU104 3.0 0.4 1.0 CG B:ASN97 3.6 0.9 1.0 C B:TYR99 3.8 0.9 1.0 CG B:ASP93 3.9 0.9 1.0 ND2 B:ASN97 4.1 0.9 1.0 N B:ASP95 4.2 0.1 1.0 N B:ASN97 4.2 0.4 1.0 CB B:ASP95 4.3 0.4 1.0 CG B:GLU104 4.5 0.1 1.0 CA B:ASP93 4.5 93.1 1.0 N B:GLY96 4.5 0.4 1.0 CA B:ILE100 4.5 0.3 1.0 N B:TYR99 4.5 0.2 1.0 CB B:ASN97 4.6 0.2 1.0 N B:SER101 4.6 0.7 1.0 N B:LYS94 4.6 98.8 1.0 CA B:ASP95 4.6 0.6 1.0 N B:ILE100 4.7 0.3 1.0 C B:ASP93 4.7 99.2 1.0 OD2 B:ASP93 4.7 0.5 1.0 CA B:TYR99 4.8 0.1 1.0 CB B:ASP93 4.8 99.6 1.0 C B:ASP95 4.9 0.3 1.0 CA B:ASN97 4.9 0.4 1.0

Calcium binding site 3 out of 4 in the Crystal Structure of Human NAV1.4 C-Terminal (1599-1754) Domain in Complex with Calcium-Bound Calmodulin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of Human NAV1.4 C-Terminal (1599-1754) Domain in Complex with Calcium-Bound Calmodulin within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1003 b:0.1 occ:1.00 OE1 B:GLU31 2.3 0.5 1.0 OD1 B:ASP24 2.4 0.5 1.0 OD1 B:ASP20 2.4 0.5 1.0 O B:THR26 2.5 0.6 1.0 OE2 B:GLU31 2.6 0.2 1.0 OD1 B:ASP22 2.6 0.8 1.0 CD B:GLU31 2.7 0.8 1.0 CG B:ASP24 3.0 1.0 1.0 OD2 B:ASP24 3.2 0.8 1.0 CG B:ASP20 3.5 1.0 1.0 CG B:ASP22 3.5 0.2 1.0 C B:THR26 3.6 0.3 1.0 OD2 B:ASP22 3.7 0.7 1.0 OD2 B:ASP20 4.0 0.2 1.0 CG B:GLU31 4.1 0.1 1.0 OG1 B:THR26 4.1 0.2 1.0 CB B:ASP24 4.3 0.4 1.0 N B:ASP24 4.3 0.3 1.0 N B:THR26 4.4 0.2 1.0 N B:ILE27 4.4 0.6 1.0 CA B:ILE27 4.5 0.9 1.0 CA B:THR26 4.5 0.5 1.0 CA B:ASP20 4.5 0.8 1.0 CB B:ASP20 4.6 0.1 1.0 N B:THR28 4.7 0.8 1.0 CA B:ASP24 4.8 0.3 1.0 OG1 B:THR28 4.8 0.4 1.0 N B:LYS21 4.8 0.4 1.0 N B:ASP22 4.8 0.2 1.0 N B:GLY23 4.9 0.3 1.0 CB B:THR26 5.0 0.8 1.0 CB B:ASP22 5.0 0.3 1.0

Calcium binding site 4 out of 4 in the Crystal Structure of Human NAV1.4 C-Terminal (1599-1754) Domain in Complex with Calcium-Bound Calmodulin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of Human NAV1.4 C-Terminal (1599-1754) Domain in Complex with Calcium-Bound Calmodulin within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1004 b:97.9 occ:1.00 OE2 B:GLU67 2.3 0.1 1.0 OE1 B:GLU67 2.3 0.6 1.0 OD1 B:ASP58 2.4 0.4 1.0 O B:THR62 2.4 0.2 1.0 CD B:GLU67 2.6 0.7 1.0 OD1 B:ASP56 2.9 0.0 1.0 CB B:ASN60 3.2 0.6 1.0 CG B:ASP58 3.3 1.0 1.0 OD2 B:ASP58 3.5 0.7 1.0 C B:THR62 3.6 0.7 1.0 ND2 B:ASN60 3.9 0.6 1.0 CG B:GLU67 4.0 0.2 1.0 CG B:ASN60 4.1 0.7 1.0 CG B:ASP56 4.1 0.7 1.0 CA B:ILE63 4.3 0.4 1.0 N B:ASN60 4.3 0.6 1.0 N B:ILE63 4.3 0.8 1.0 CA B:ASN60 4.3 0.6 1.0 N B:THR62 4.5 0.2 1.0 OD1 B:ASP64 4.5 0.9 1.0 N B:ASP58 4.6 0.7 1.0 CA B:THR62 4.7 0.3 1.0 CB B:ASP58 4.7 0.2 1.0 N B:ASP64 4.7 0.2 1.0 N B:GLY61 4.8 0.4 1.0 OD2 B:ASP56 4.8 0.7 1.0 CG2 B:THR62 4.8 0.9 1.0 CA B:ASP56 4.9 0.3 1.0 C B:ASN60 5.0 1.0 1.0 N B:ALA57 5.0 0.5 1.0

J.B.Yoder, M.Ben-Johny, F.Farinelli, L.Srinivasan, S.R.Shoemaker, G.F.Tomaselli, S.B.Gabelli, L.M.Amzel. CA2+-Dependent Regulation of Sodium Channels NAV1.4 and NAV1.5 Is Controlled By the Post-Iq Motif. Nat Commun V. 10 1514 2019.
ISSN: ESSN 2041-1723
PubMed: 30944319
DOI: 10.1038/S41467-019-09570-7