Calcium in PDB 6u3d: 1.75 Angstrom Crystal Structure of the N53I Ca-Cam:CAV1.2 Iq Domain Complex

The structure of 1.75 Angstrom Crystal Structure of the N53I Ca-Cam:CAV1.2 Iq Domain Complex, PDB code: 6u3d 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)	35.56 / 1.75
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	59.400, 43.369, 66.962, 90.00, 111.93, 90.00
R / Rfree (%)	16.4 / 20.1

The binding sites of Calcium atom in the 1.75 Angstrom Crystal Structure of the N53I Ca-Cam:CAV1.2 Iq Domain Complex (pdb code 6u3d). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 8 binding sites of Calcium where determined in the 1.75 Angstrom Crystal Structure of the N53I Ca-Cam:CAV1.2 Iq Domain Complex, PDB code: 6u3d:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in the 1.75 Angstrom Crystal Structure of the N53I Ca-Cam:CAV1.2 Iq Domain Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of 1.75 Angstrom Crystal Structure of the N53I Ca-Cam:CAV1.2 Iq Domain Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca501 b:21.2 occ:1.00 OD1 A:ASP20 2.3 21.6 1.0 OD1 A:ASP24 2.3 26.8 1.0 O A:THR26 2.3 24.6 1.0 O A:HOH641 2.3 33.9 1.0 OD1 A:ASP22 2.4 33.5 1.0 OE1 A:GLU31 2.5 24.0 1.0 OE2 A:GLU31 2.5 26.3 1.0 CD A:GLU31 2.8 27.6 1.0 CG A:ASP24 3.3 36.2 1.0 CG A:ASP22 3.4 34.0 1.0 CG A:ASP20 3.4 22.2 1.0 C A:THR26 3.6 25.7 1.0 OD2 A:ASP22 3.7 41.5 1.0 OD2 A:ASP24 3.8 39.3 1.0 N A:THR26 4.2 22.1 1.0 CA A:ASP20 4.2 20.5 1.0 OG1 A:THR26 4.3 38.8 1.0 OD2 A:ASP20 4.3 19.9 1.0 N A:ASP24 4.3 18.8 1.0 CG A:GLU31 4.3 25.6 1.0 CB A:ASP20 4.4 20.9 1.0 CB A:ASP24 4.4 28.4 1.0 CA A:THR26 4.4 22.4 1.0 N A:ASP22 4.5 28.5 1.0 C A:ASP20 4.5 20.3 1.0 N A:ILE27 4.5 18.8 1.0 CA A:ILE27 4.6 18.7 1.0 N A:LYS21 4.6 22.1 1.0 CG2 A:THR28 4.6 29.1 1.0 CB A:ASP22 4.7 27.0 1.0 N A:GLY23 4.8 24.2 1.0 CA A:ASP24 4.8 25.5 1.0 N A:GLY25 4.8 18.9 1.0 O A:HOH628 4.8 35.0 1.0 N A:THR28 4.8 20.4 1.0 CA A:ASP22 4.9 29.7 1.0 C A:ASP24 5.0 26.1 1.0

Calcium binding site 2 out of 8 in the 1.75 Angstrom Crystal Structure of the N53I Ca-Cam:CAV1.2 Iq Domain Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of 1.75 Angstrom Crystal Structure of the N53I Ca-Cam:CAV1.2 Iq Domain Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca502 b:26.9 occ:1.00 OD1 A:ASP56 2.3 36.3 1.0 O A:THR62 2.4 24.1 1.0 OD1 A:ASN60 2.4 34.9 1.0 O A:HOH604 2.4 32.7 1.0 OD1 A:ASP58 2.5 41.4 1.0 OE1 A:GLU67 2.5 29.3 1.0 O A:HOH632 2.6 31.7 1.0 OE2 A:GLU67 2.6 29.2 1.0 CD A:GLU67 2.9 26.8 1.0 CG A:ASP58 3.4 44.0 1.0 CG A:ASP56 3.4 34.9 1.0 CG A:ASN60 3.4 42.0 1.0 C A:THR62 3.6 22.7 1.0 OD2 A:ASP58 3.7 47.4 1.0 ND2 A:ASN60 3.9 38.2 1.0 OD2 A:ASP56 4.1 37.4 1.0 N A:THR62 4.3 26.2 1.0 CB A:ASP56 4.3 24.8 1.0 N A:ASP64 4.4 21.2 1.0 N A:ILE63 4.4 21.1 1.0 OD2 A:ASP64 4.4 47.0 1.0 CA A:ILE63 4.4 18.2 1.0 CA A:ASP56 4.4 25.3 1.0 CG A:GLU67 4.4 23.7 1.0 OG1 A:THR62 4.5 32.8 1.0 N A:ASP58 4.5 38.1 1.0 CA A:THR62 4.5 25.1 1.0 N A:ASN60 4.6 34.1 1.0 O A:ASP58 4.6 52.6 1.0 CB A:ASN60 4.6 42.4 1.0 CB A:ASP58 4.7 40.9 1.0 CG A:ASP64 4.7 38.6 1.0 N A:ALA57 4.7 35.6 1.0 C A:ASP58 4.8 48.2 1.0 C A:ASP56 4.8 29.9 1.0 C A:ILE63 4.8 18.9 1.0 CA A:ASP58 4.9 40.3 1.0 N A:GLY61 4.9 31.6 1.0

Calcium binding site 3 out of 8 in the 1.75 Angstrom Crystal Structure of the N53I Ca-Cam:CAV1.2 Iq Domain Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of 1.75 Angstrom Crystal Structure of the N53I Ca-Cam:CAV1.2 Iq Domain Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca503 b:17.4 occ:1.00 O A:TYR99 2.2 18.5 1.0 O A:HOH630 2.2 23.7 1.0 OD1 A:ASP93 2.3 15.7 1.0 OD1 A:ASP95 2.3 27.4 1.0 OD1 A:ASN97 2.4 19.9 1.0 OE2 A:GLU104 2.5 19.4 1.0 OE1 A:GLU104 2.5 20.4 1.0 CD A:GLU104 2.8 20.9 1.0 CG A:ASP95 3.2 30.0 1.0 CG A:ASN97 3.4 27.3 1.0 C A:TYR99 3.5 17.4 1.0 CG A:ASP93 3.5 19.4 1.0 OD2 A:ASP95 3.5 38.2 1.0 ND2 A:ASN97 4.0 28.8 1.0 CA A:ASP93 4.1 16.9 1.0 N A:TYR99 4.1 15.0 1.0 CB A:ASP93 4.3 20.0 1.0 CA A:TYR99 4.3 14.5 1.0 CG A:GLU104 4.3 16.7 1.0 N A:ASN97 4.4 20.0 1.0 N A:ILE100 4.4 13.5 1.0 OD2 A:ASP93 4.4 16.0 1.0 CA A:ILE100 4.5 14.2 1.0 C A:ASP93 4.5 17.9 1.0 CB A:ASN97 4.6 21.0 1.0 N A:ASP95 4.6 22.9 1.0 CB A:ASP95 4.6 25.7 1.0 N A:GLY96 4.8 21.2 1.0 N A:LYS94 4.8 20.8 1.0 N A:GLY98 4.8 15.5 1.0 CB A:TYR99 4.8 14.8 1.0 O A:HOH634 4.9 28.4 1.0 CA A:ASN97 4.9 18.9 1.0 N A:SER101 4.9 15.8 1.0 O A:HOH610 4.9 34.0 1.0 CA A:ASP95 5.0 20.6 1.0

Calcium binding site 4 out of 8 in the 1.75 Angstrom Crystal Structure of the N53I Ca-Cam:CAV1.2 Iq Domain Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of 1.75 Angstrom Crystal Structure of the N53I Ca-Cam:CAV1.2 Iq Domain Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca504 b:17.4 occ:1.00 O A:HOH670 2.3 24.6 1.0 OD1 A:ASP129 2.3 23.9 1.0 OD1 A:ASP131 2.3 35.3 1.0 O A:GLN135 2.4 23.1 1.0 OE1 A:GLU140 2.4 15.8 1.0 OD1 A:ASP133 2.4 20.0 1.0 OE2 A:GLU140 2.6 18.5 1.0 CD A:GLU140 2.8 17.4 1.0 CG A:ASP131 3.3 37.9 1.0 CG A:ASP133 3.4 31.8 1.0 CG A:ASP129 3.5 20.9 1.0 C A:GLN135 3.5 16.0 1.0 OD2 A:ASP131 3.7 39.4 1.0 OD2 A:ASP133 3.9 28.6 1.0 CA A:ASP129 4.2 16.7 1.0 N A:ASP133 4.2 27.3 1.0 N A:GLN135 4.2 20.1 1.0 CB A:ASP129 4.3 15.2 1.0 OD2 A:ASP129 4.3 25.2 1.0 CG A:GLU140 4.4 15.1 1.0 N A:ASP131 4.4 23.4 1.0 N A:VAL136 4.4 15.8 1.0 CA A:VAL136 4.4 15.3 1.0 N A:GLY132 4.4 24.3 1.0 N A:ASN137 4.4 14.1 1.0 CA A:GLN135 4.5 16.3 1.0 C A:ASP129 4.5 18.0 1.0 CB A:ASP133 4.5 29.9 1.0 N A:ILE130 4.6 17.6 1.0 CB A:ASP131 4.6 25.9 1.0 CA A:ASP133 4.8 30.9 1.0 CA A:ASP131 4.8 24.1 1.0 N A:GLY134 4.8 20.9 1.0 C A:ASP131 4.9 25.8 1.0 C A:VAL136 4.9 13.3 1.0 CG A:ASN137 5.0 18.2 1.0

Calcium binding site 5 out of 8 in the 1.75 Angstrom Crystal Structure of the N53I Ca-Cam:CAV1.2 Iq Domain Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of 1.75 Angstrom Crystal Structure of the N53I Ca-Cam:CAV1.2 Iq Domain Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca501 b:27.9 occ:1.00 OD1 B:ASP20 2.3 28.7 1.0 O B:THR26 2.3 33.3 1.0 O B:HOH668 2.4 41.7 1.0 OE1 B:GLU31 2.4 27.0 1.0 OD1 B:ASP24 2.5 38.1 1.0 OD1 B:ASP22 2.5 35.8 1.0 OE2 B:GLU31 2.5 35.9 1.0 CD B:GLU31 2.8 31.5 1.0 CG B:ASP24 3.5 42.2 1.0 CG B:ASP20 3.5 28.6 1.0 CG B:ASP22 3.5 41.5 1.0 C B:THR26 3.5 24.2 1.0 OD2 B:ASP24 3.9 48.1 1.0 OD2 B:ASP22 4.0 45.1 1.0 CA B:ASP20 4.1 24.3 1.0 N B:THR26 4.2 24.6 1.0 CB B:ASP20 4.3 23.2 1.0 OG1 B:THR26 4.3 41.9 1.0 CG B:GLU31 4.3 25.4 1.0 N B:ASP24 4.3 33.9 1.0 OD2 B:ASP20 4.3 27.2 1.0 C B:ASP20 4.3 24.8 1.0 CA B:THR26 4.4 28.2 1.0 N B:ASP22 4.5 31.1 1.0 N B:ILE27 4.5 21.4 1.0 N B:GLY23 4.5 33.1 1.0 N B:LYS21 4.6 34.3 1.0 CB B:ASP24 4.6 38.8 1.0 CA B:ILE27 4.6 23.8 1.0 CB B:ASP22 4.8 38.5 1.0 O B:ASP20 4.8 28.9 1.0 N B:GLY25 4.8 32.7 1.0 CG2 B:THR28 4.8 32.6 1.0 CA B:ASP24 4.9 38.7 1.0 N B:THR28 4.9 22.0 1.0 C B:ASP22 4.9 38.2 1.0 CA B:ASP22 5.0 35.3 1.0 CB B:THR26 5.0 39.0 1.0

Calcium binding site 6 out of 8 in the 1.75 Angstrom Crystal Structure of the N53I Ca-Cam:CAV1.2 Iq Domain Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of 1.75 Angstrom Crystal Structure of the N53I Ca-Cam:CAV1.2 Iq Domain Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca502 b:25.7 occ:1.00 OD1 B:ASN60 2.3 33.6 1.0 OD1 B:ASP56 2.4 31.8 1.0 O B:THR62 2.4 28.1 1.0 OE1 B:GLU67 2.5 26.0 1.0 O B:HOH617 2.5 35.7 1.0 OD1 B:ASP58 2.5 42.6 1.0 OE2 B:GLU67 2.6 32.0 1.0 O B:HOH640 2.7 36.4 1.0 CD B:GLU67 2.9 30.2 1.0 CG B:ASN60 3.2 33.8 1.0 CG B:ASP56 3.4 38.3 1.0 CG B:ASP58 3.5 43.9 1.0 C B:THR62 3.6 25.3 1.0 ND2 B:ASN60 3.6 41.2 1.0 OD2 B:ASP58 3.8 46.9 1.0 OD2 B:ASP56 4.0 37.1 1.0 N B:ASP64 4.3 22.4 1.0 N B:THR62 4.3 31.6 1.0 CB B:ASP56 4.3 34.5 1.0 CA B:ILE63 4.3 23.8 1.0 N B:ASN60 4.4 38.3 1.0 N B:ILE63 4.4 25.7 1.0 CG B:GLU67 4.4 26.6 1.0 CA B:ASP56 4.4 29.1 1.0 CB B:ASN60 4.5 31.6 1.0 OG1 B:THR62 4.5 33.3 1.0 CA B:THR62 4.5 28.8 1.0 N B:ASP58 4.6 35.8 1.0 CG B:ASP64 4.7 40.1 1.0 C B:ILE63 4.7 24.3 1.0 CB B:ASP58 4.8 40.7 1.0 N B:GLY59 4.8 35.6 1.0 OD2 B:ASP64 4.8 43.8 1.0 C B:ASP56 4.8 34.9 1.0 CA B:ASN60 4.8 33.7 1.0 N B:GLY61 4.9 33.0 1.0 OD1 B:ASP64 4.9 43.9 1.0 N B:ALA57 4.9 32.5 1.0

Calcium binding site 7 out of 8 in the 1.75 Angstrom Crystal Structure of the N53I Ca-Cam:CAV1.2 Iq Domain Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of 1.75 Angstrom Crystal Structure of the N53I Ca-Cam:CAV1.2 Iq Domain Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca503 b:18.8 occ:1.00 O B:TYR99 2.3 21.2 1.0 OD1 B:ASP93 2.3 22.3 1.0 OD1 B:ASP95 2.3 25.9 1.0 O B:HOH670 2.4 24.1 1.0 OD1 B:ASN97 2.4 18.6 1.0 OE1 B:GLU104 2.5 21.3 1.0 OE2 B:GLU104 2.6 21.2 1.0 CD B:GLU104 2.9 20.9 1.0 CG B:ASP95 3.3 32.2 1.0 CG B:ASN97 3.4 20.5 1.0 CG B:ASP93 3.5 21.8 1.0 C B:TYR99 3.5 21.0 1.0 OD2 B:ASP95 3.7 37.3 1.0 ND2 B:ASN97 4.0 21.6 1.0 CA B:ASP93 4.2 23.1 1.0 N B:TYR99 4.2 19.8 1.0 OD2 B:ASP93 4.3 25.1 1.0 CB B:ASP93 4.3 20.8 1.0 N B:ASN97 4.3 24.0 1.0 O B:HOH602 4.3 23.5 1.0 CG B:GLU104 4.4 22.2 1.0 CA B:TYR99 4.4 19.8 1.0 N B:ILE100 4.4 15.8 1.0 N B:ASP95 4.4 30.2 1.0 C B:ASP93 4.5 22.3 1.0 CA B:ILE100 4.5 15.3 1.0 CB B:ASN97 4.5 19.3 1.0 CB B:ASP95 4.6 27.4 1.0 N B:GLY96 4.7 23.3 1.0 N B:LYS94 4.7 23.1 1.0 N B:SER101 4.7 19.6 1.0 CB B:TYR99 4.8 20.9 1.0 CA B:ASN97 4.8 19.5 1.0 O B:HOH638 4.9 31.5 1.0 N B:GLY98 4.9 20.9 1.0 CA B:ASP95 4.9 27.7 1.0 O B:ASP93 5.0 25.5 1.0 C B:ASP95 5.0 28.1 1.0

Calcium binding site 8 out of 8 in the 1.75 Angstrom Crystal Structure of the N53I Ca-Cam:CAV1.2 Iq Domain Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of 1.75 Angstrom Crystal Structure of the N53I Ca-Cam:CAV1.2 Iq Domain Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca504 b:23.2 occ:1.00 O B:GLN135 2.3 24.5 1.0 OD1 B:ASP133 2.3 28.5 1.0 OD1 B:ASP129 2.4 25.6 1.0 O B:HOH628 2.4 26.6 1.0 OE1 B:GLU140 2.4 23.2 1.0 OD1 B:ASP131 2.5 36.7 1.0 OE2 B:GLU140 2.5 24.4 1.0 CD B:GLU140 2.8 20.3 1.0 CG B:ASP131 3.2 37.1 1.0 CG B:ASP133 3.2 38.0 1.0 OD2 B:ASP131 3.3 43.9 1.0 C B:GLN135 3.4 20.5 1.0 CG B:ASP129 3.5 26.6 1.0 OD2 B:ASP133 3.7 39.4 1.0 N B:ASP133 4.1 29.4 1.0 N B:GLN135 4.2 23.5 1.0 CA B:ASP129 4.2 25.2 1.0 CB B:ASP129 4.2 25.8 1.0 N B:VAL136 4.3 17.7 1.0 CB B:ASP133 4.3 36.3 1.0 CA B:VAL136 4.3 16.8 1.0 OD2 B:ASP129 4.3 26.1 1.0 CG B:GLU140 4.3 21.2 1.0 N B:ASP131 4.4 31.2 1.0 CA B:GLN135 4.4 24.7 1.0 N B:ASN137 4.4 18.9 1.0 CB B:ASP131 4.5 33.5 1.0 N B:GLY132 4.5 31.3 1.0 C B:ASP129 4.5 27.1 1.0 CA B:ASP133 4.6 33.3 1.0 N B:ILE130 4.7 27.9 1.0 N B:GLY134 4.7 28.6 1.0 CA B:ASP131 4.8 29.4 1.0 C B:VAL136 4.8 17.9 1.0 C B:ASP133 4.9 34.1 1.0 C B:ASP131 4.9 34.4 1.0

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