Calcium 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:

Sodium

(Na)

2 atoms

The binding sites of Calcium 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 Calcium atom.
In total 7 binding sites of Calcium where determined in the 1.65 Angstrom Crystal Structure of the N97S Ca-Cam:CAV1.2 Iq Domain Complex, PDB code: 6u3a:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7;

Calcium binding site 1 out of 7 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 Calcium with other atoms in the Ca 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:Ca501 b:22.0 occ:1.00 OD1 A:ASP20 2.3 23.3 1.0 O A:THR26 2.3 21.6 1.0 OD1 A:ASP22 2.4 26.1 1.0 O A:HOH707 2.4 29.4 1.0 OD1 A:ASP24 2.4 27.3 1.0 OE1 A:GLU31 2.5 26.8 1.0 OE2 A:GLU31 2.5 26.6 1.0 CD A:GLU31 2.8 21.8 1.0 CG A:ASP24 3.4 28.4 1.0 CG A:ASP22 3.4 40.3 1.0 CG A:ASP20 3.4 21.5 1.0 C A:THR26 3.5 23.0 1.0 OD2 A:ASP22 3.8 43.0 1.0 OD2 A:ASP24 3.9 34.6 1.0 OG1 A:THR26 4.0 32.1 1.0 CA A:ASP20 4.0 19.4 1.0 CB A:ASP20 4.1 19.0 1.0 N A:THR26 4.1 21.8 1.0 N A:ASP24 4.2 24.9 1.0 CG A:GLU31 4.3 20.6 1.0 OD2 A:ASP20 4.3 19.3 1.0 CA A:THR26 4.4 21.3 1.0 C A:ASP20 4.4 22.3 1.0 N A:ASP22 4.4 25.3 1.0 N A:GLY23 4.5 28.8 1.0 CB A:ASP24 4.5 34.6 1.0 N A:ILE27 4.5 17.9 1.0 CB A:ASP22 4.5 33.2 1.0 CA A:ILE27 4.6 20.4 1.0 O A:HOH681 4.6 47.0 1.0 N A:LYS21 4.7 24.1 1.0 CA A:ASP24 4.8 25.9 1.0 N A:GLY25 4.8 23.9 1.0 CA A:ASP22 4.8 27.5 1.0 CB A:THR26 4.8 27.4 1.0 CG2 A:THR28 4.8 27.3 1.0 C A:ASP22 4.8 33.6 1.0 N A:THR28 4.9 21.2 1.0 O A:ASP20 4.9 23.1 1.0 C A:ASP24 5.0 23.1 1.0

Calcium binding site 2 out of 7 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 Calcium with other atoms in the Ca 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:Ca502 b:25.3 occ:1.00 OD1 A:ASP56 2.3 26.5 1.0 OD1 A:ASN60 2.4 27.4 1.0 O A:HOH629 2.5 26.3 1.0 OD1 A:ASP58 2.5 33.3 1.0 O A:THR62 2.5 26.4 1.0 OE1 A:GLU67 2.5 22.8 1.0 O A:HOH649 2.6 25.1 1.0 OE2 A:GLU67 2.6 22.6 1.0 CD A:GLU67 2.9 21.5 1.0 CG A:ASN60 3.2 37.4 1.0 CG A:ASP56 3.3 32.0 1.0 CG A:ASP58 3.4 31.1 1.0 C A:THR62 3.6 19.6 1.0 ND2 A:ASN60 3.6 36.2 1.0 OD2 A:ASP58 3.8 30.2 1.0 OD2 A:ASP56 4.1 31.7 1.0 CB A:ASP56 4.2 29.3 1.0 CA A:ASP56 4.3 27.3 1.0 N A:ASN60 4.3 35.2 1.0 N A:ASP64 4.4 21.0 1.0 N A:THR62 4.4 28.7 1.0 CG A:GLU67 4.4 21.3 1.0 CA A:ILE63 4.4 19.8 1.0 N A:ILE63 4.4 18.6 1.0 OG1 A:THR62 4.5 28.0 1.0 N A:ASP58 4.5 26.5 1.0 CB A:ASN60 4.5 37.6 1.0 OD2 A:ASP64 4.5 22.7 1.0 CA A:THR62 4.6 23.2 1.0 O A:HOH699 4.6 34.9 1.0 N A:GLY59 4.6 33.5 1.0 CG A:ASP64 4.7 22.7 1.0 C A:ASP56 4.7 32.9 1.0 CB A:ASP58 4.7 28.6 1.0 N A:ALA57 4.7 27.5 1.0 C A:ILE63 4.8 23.0 1.0 CA A:ASN60 4.8 38.2 1.0 N A:GLY61 4.9 33.1 1.0 CA A:ASP58 4.9 27.3 1.0 OD1 A:ASP64 4.9 21.3 1.0 C A:ASP58 5.0 33.9 1.0

Calcium binding site 3 out of 7 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 Calcium with other atoms in the Ca binding site number 3 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:Ca503 b:24.6 occ:1.00 O A:GLN135 2.3 27.6 1.0 OD1 A:ASP129 2.3 25.8 1.0 OD1 A:ASP131 2.3 35.9 1.0 OD1 A:ASP133 2.4 28.7 1.0 O A:HOH676 2.4 35.1 1.0 OE2 A:GLU140 2.4 25.2 1.0 OE1 A:GLU140 2.5 23.8 1.0 CD A:GLU140 2.8 22.9 1.0 CG A:ASP133 3.3 35.4 1.0 CG A:ASP131 3.4 40.2 1.0 CG A:ASP129 3.4 30.9 1.0 C A:GLN135 3.5 25.1 1.0 OD2 A:ASP133 3.8 36.7 1.0 OD2 A:ASP131 3.9 39.9 1.0 OD2 A:ASP129 4.2 30.8 1.0 N A:ASP133 4.2 30.8 1.0 CA A:ASP129 4.2 29.0 1.0 N A:GLN135 4.2 29.0 1.0 N A:ASP131 4.3 33.5 1.0 CG A:GLU140 4.3 18.6 1.0 CB A:ASP129 4.3 28.7 1.0 CA A:GLN135 4.4 24.9 1.0 N A:GLY132 4.4 42.5 1.0 N A:VAL136 4.4 21.5 1.0 C A:ASP129 4.4 31.0 1.0 CB A:ASP133 4.5 35.8 1.0 CA A:VAL136 4.5 19.6 1.0 N A:ILE130 4.5 29.3 1.0 N A:ASN137 4.6 20.8 1.0 CB A:ASP131 4.6 39.9 1.0 CB A:GLN135 4.7 31.2 1.0 CA A:ASP133 4.8 39.1 1.0 CA A:ASP131 4.8 37.2 1.0 C A:ASP131 4.8 44.6 1.0 ND2 A:ASN137 4.8 27.1 1.0 O A:HOH673 4.9 35.7 1.0 N A:GLY134 4.9 30.0 1.0

Calcium binding site 4 out of 7 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 Calcium with other atoms in the Ca binding site number 4 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 B:Ca501 b:16.1 occ:1.00 O B:HOH688 2.3 19.0 1.0 O B:THR26 2.3 20.6 1.0 OD1 B:ASP20 2.4 15.4 1.0 OD1 B:ASP22 2.4 18.9 1.0 OE1 B:GLU31 2.5 17.4 1.0 OD1 B:ASP24 2.5 19.1 1.0 OE2 B:GLU31 2.5 18.4 1.0 CD B:GLU31 2.8 18.3 1.0 CG B:ASP24 3.4 21.5 1.0 CG B:ASP22 3.4 21.1 1.0 CG B:ASP20 3.4 18.9 1.0 C B:THR26 3.5 16.3 1.0 OD2 B:ASP22 3.7 22.3 1.0 OD2 B:ASP24 3.9 23.0 1.0 OG1 B:THR26 3.9 20.3 1.0 CA B:ASP20 4.0 15.0 1.0 CB B:ASP20 4.1 15.7 1.0 N B:THR26 4.2 14.7 1.0 N B:ASP24 4.2 15.7 1.0 CG B:GLU31 4.3 16.3 1.0 OD2 B:ASP20 4.3 15.8 1.0 CB B:ASP24 4.4 20.2 1.0 CA B:THR26 4.4 14.2 1.0 C B:ASP20 4.5 14.5 1.0 N B:ILE27 4.5 14.9 1.0 N B:ASP22 4.5 15.8 1.0 CA B:ILE27 4.6 16.4 1.0 O B:HOH628 4.6 43.0 1.0 CB B:ASP22 4.7 18.9 1.0 CA B:ASP24 4.7 16.7 1.0 N B:GLY23 4.8 17.8 1.0 N B:LYS21 4.8 17.8 1.0 O B:HOH635 4.8 20.9 1.0 CB B:THR26 4.8 15.7 1.0 O B:HOH632 4.8 33.7 1.0 CG2 B:THR28 4.8 14.9 1.0 N B:GLY25 4.9 18.6 1.0 C B:ASP24 5.0 20.1 1.0 N B:THR28 5.0 17.1 1.0 O B:ASP20 5.0 16.1 1.0 CA B:ASP22 5.0 16.9 1.0

Calcium binding site 5 out of 7 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 Calcium with other atoms in the Ca binding site number 5 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 B:Ca502 b:18.0 occ:1.00 OD1 B:ASP56 2.3 19.2 1.0 OD1 B:ASN60 2.4 18.0 1.0 OE1 B:GLU67 2.4 17.7 1.0 O B:HOH613 2.5 20.3 1.0 O B:THR62 2.5 17.7 1.0 OD1 B:ASP58 2.5 21.4 1.0 O B:HOH644 2.5 20.4 1.0 OE2 B:GLU67 2.6 19.4 1.0 CD B:GLU67 2.9 17.5 1.0 CG B:ASN60 3.3 18.4 1.0 CG B:ASP56 3.4 21.1 1.0 CG B:ASP58 3.5 21.0 1.0 C B:THR62 3.6 15.2 1.0 ND2 B:ASN60 3.6 22.2 1.0 OD2 B:ASP58 3.9 22.5 1.0 OD2 B:ASP56 4.2 20.5 1.0 CB B:ASP56 4.3 17.7 1.0 CA B:ASP56 4.3 17.8 1.0 N B:ASN60 4.3 18.0 1.0 N B:ASP64 4.4 17.2 1.0 CG B:GLU67 4.4 15.6 1.0 OG1 B:THR62 4.4 18.6 1.0 CA B:ILE63 4.4 14.2 1.0 N B:ILE63 4.4 14.8 1.0 N B:THR62 4.4 17.7 1.0 N B:ASP58 4.5 20.8 1.0 CB B:ASN60 4.5 19.0 1.0 OD2 B:ASP64 4.6 19.6 1.0 CA B:THR62 4.6 16.7 1.0 C B:ASP56 4.6 21.8 1.0 N B:GLY59 4.7 21.7 1.0 CG B:ASP64 4.7 19.5 1.0 O B:HOH717 4.7 25.9 1.0 CB B:ASP58 4.7 21.0 1.0 C B:ILE63 4.8 18.8 1.0 N B:ALA57 4.8 20.1 1.0 CA B:ASN60 4.9 19.8 1.0 CA B:ASP58 4.9 20.2 1.0 C B:ASP58 5.0 20.8 1.0 N B:GLY61 5.0 16.4 1.0 OD1 B:ASP64 5.0 19.7 1.0

Calcium binding site 6 out of 7 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 Calcium with other atoms in the Ca binding site number 6 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 B:Ca503 b:22.7 occ:1.00 OD1 B:ASP93 2.3 24.0 1.0 O B:TYR99 2.3 21.9 1.0 OD1 B:ASP95 2.4 27.1 1.0 OE2 B:GLU104 2.5 23.6 1.0 OE1 B:GLU104 2.5 27.5 1.0 OG B:SER97 2.5 24.6 1.0 CD B:GLU104 2.8 25.7 1.0 CG B:ASP95 3.3 26.7 1.0 CG B:ASP93 3.4 25.4 1.0 C B:TYR99 3.6 22.9 1.0 OD2 B:ASP95 3.6 27.9 1.0 CB B:SER97 3.6 29.2 1.0 N B:SER97 4.0 29.7 1.0 CA B:ASP93 4.0 23.3 1.0 CB B:ASP93 4.2 25.3 1.0 N B:TYR99 4.3 25.1 1.0 CG B:GLU104 4.3 23.9 1.0 CA B:SER97 4.3 28.7 1.0 OD2 B:ASP93 4.3 26.4 1.0 C B:ASP93 4.4 24.2 1.0 N B:ILE100 4.5 23.6 1.0 CA B:ILE100 4.5 22.6 1.0 CA B:TYR99 4.5 23.5 1.0 O B:HOH605 4.6 33.7 1.0 N B:ASP95 4.6 27.8 1.0 CB B:ASP95 4.7 30.8 1.0 N B:GLY98 4.7 30.6 1.0 N B:SER101 4.8 26.0 1.0 N B:LYS94 4.8 23.3 1.0 N B:GLY96 4.8 30.0 1.0 C B:SER97 4.8 33.6 1.0 O B:HOH652 4.8 28.4 1.0 O B:ASP93 4.9 25.5 1.0 CA B:ASP95 5.0 32.0 1.0

Calcium binding site 7 out of 7 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 Calcium with other atoms in the Ca binding site number 7 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 B:Ca504 b:25.5 occ:1.00 OD1 B:ASP129 2.3 27.1 1.0 OD1 B:ASP131 2.3 29.5 1.0 O B:GLN135 2.3 26.3 1.0 OD1 B:ASP133 2.4 27.2 1.0 O B:HOH650 2.4 22.1 1.0 OE2 B:GLU140 2.4 26.7 1.0 OE1 B:GLU140 2.5 30.4 1.0 CD B:GLU140 2.8 28.0 1.0 CG B:ASP131 3.2 33.1 1.0 CG B:ASP133 3.3 28.9 1.0 CG B:ASP129 3.4 36.4 1.0 C B:GLN135 3.5 26.9 1.0 OD2 B:ASP131 3.5 28.4 1.0 OD2 B:ASP133 3.8 26.8 1.0 N B:ASP133 4.0 30.8 1.0 OD2 B:ASP129 4.1 34.8 1.0 N B:GLN135 4.2 29.4 1.0 CG B:GLU140 4.3 26.6 1.0 N B:ASP131 4.3 35.0 1.0 N B:GLY132 4.3 35.3 1.0 N B:ASN137 4.4 25.9 1.0 CB B:ASP133 4.4 29.7 1.0 N B:VAL136 4.4 25.0 1.0 CA B:VAL136 4.4 25.0 1.0 CA B:ASP129 4.4 36.6 1.0 CB B:ASP129 4.5 38.5 1.0 CB B:ASP131 4.5 31.4 1.0 CA B:GLN135 4.5 28.9 1.0 N B:GLY134 4.5 35.3 1.0 N B:ILE130 4.6 31.2 1.0 CA B:ASP133 4.6 30.7 1.0 CG B:ASN137 4.6 26.5 1.0 ND2 B:ASN137 4.6 28.2 1.0 CA B:ASP131 4.7 35.8 1.0 C B:ASP131 4.8 28.0 1.0 OD1 B:ASN137 4.8 28.1 1.0 CG B:GLN135 4.8 25.6 1.0 C B:VAL136 4.8 28.4 1.0 C B:ASP129 4.9 41.6 1.0 C B:ASP133 4.9 32.6 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