Calcium in PDB 6y4p: Calmodulin N53I Variant Bound to Cardiac Ryanodine Receptor (RYR2) Calmodulin Binding Domain

The structure of Calmodulin N53I Variant Bound to Cardiac Ryanodine Receptor (RYR2) Calmodulin Binding Domain, PDB code: 6y4p was solved by K.Lau, L.H.Nielsen, C.Holt, M.Brohus, A.B.Sorensen, K.T.Larsen, C.Sommer, F.Van Petegem, M.T.Overgaard, R.Wimmer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.18 / 2.13
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	37.590, 42.360, 90.360, 90.00, 90.00, 90.00
R / Rfree (%)	18.2 / 24.6

The binding sites of Calcium atom in the Calmodulin N53I Variant Bound to Cardiac Ryanodine Receptor (RYR2) Calmodulin Binding Domain (pdb code 6y4p). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Calmodulin N53I Variant Bound to Cardiac Ryanodine Receptor (RYR2) Calmodulin Binding Domain, PDB code: 6y4p:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Calmodulin N53I Variant Bound to Cardiac Ryanodine Receptor (RYR2) Calmodulin Binding Domain


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Calmodulin N53I Variant Bound to Cardiac Ryanodine Receptor (RYR2) Calmodulin Binding Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca201 b:21.1 occ:1.00 OE2 A:GLU31 2.2 29.4 1.0 OD1 A:ASP22 2.3 26.8 1.0 O A:THR26 2.3 22.5 1.0 OD1 A:ASP20 2.3 20.8 1.0 OD1 A:ASP24 2.3 29.1 1.0 O A:HOH325 2.4 27.0 1.0 OE1 A:GLU31 2.7 27.2 1.0 CD A:GLU31 2.8 25.0 1.0 CG A:ASP22 3.2 28.2 1.0 CG A:ASP24 3.3 25.3 1.0 OD2 A:ASP22 3.5 31.5 1.0 C A:THR26 3.5 20.5 1.0 CG A:ASP20 3.5 24.0 1.0 OD2 A:ASP24 3.9 30.8 1.0 OG1 A:THR26 3.9 31.3 1.0 N A:THR26 4.1 24.8 1.0 CA A:ASP20 4.2 23.1 1.0 N A:ASP24 4.2 25.8 1.0 CG A:GLU31 4.3 27.5 1.0 CA A:THR26 4.3 25.4 1.0 N A:ASP22 4.3 29.0 1.0 OD2 A:ASP20 4.3 28.4 1.0 CB A:ASP20 4.4 23.3 1.0 N A:LYS21 4.4 22.2 1.0 C A:ASP20 4.4 26.4 1.0 CB A:ASP24 4.4 23.7 1.0 N A:ILE27 4.5 22.1 1.0 O A:HOH340 4.5 36.0 1.0 CB A:ASP22 4.6 23.1 1.0 N A:GLY23 4.6 24.8 1.0 CA A:ILE27 4.6 19.7 1.0 CB A:THR26 4.7 27.5 1.0 CA A:ASP24 4.7 27.4 1.0 N A:GLY25 4.7 24.3 1.0 CA A:ASP22 4.8 21.4 1.0 C A:ASP24 4.9 27.7 1.0 C A:ASP22 4.9 29.1 1.0 CG2 A:THR28 4.9 27.8 1.0

Calcium binding site 2 out of 4 in the Calmodulin N53I Variant Bound to Cardiac Ryanodine Receptor (RYR2) Calmodulin Binding Domain


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Calmodulin N53I Variant Bound to Cardiac Ryanodine Receptor (RYR2) Calmodulin Binding Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca202 b:26.8 occ:1.00 OD1 A:ASP56 2.2 26.1 1.0 O A:THR62 2.3 23.3 1.0 O A:HOH310 2.4 27.2 1.0 OD1 A:ASN60 2.4 24.5 1.0 OE2 A:GLU67 2.5 29.8 1.0 OE1 A:GLU67 2.5 24.7 1.0 OD1 A:ASP58 2.6 26.2 1.0 CD A:GLU67 2.8 30.6 1.0 CG A:ASP56 3.3 30.2 1.0 CG A:ASN60 3.4 31.4 1.0 CG A:ASP58 3.4 30.5 1.0 C A:THR62 3.5 26.0 1.0 OD2 A:ASP58 3.6 28.2 1.0 OD2 A:ASP56 4.0 27.9 1.0 ND2 A:ASN60 4.0 29.2 1.0 N A:ASN60 4.2 33.8 1.0 N A:THR62 4.2 24.9 1.0 CA A:ASP56 4.3 25.7 1.0 CG A:GLU67 4.3 21.6 1.0 N A:ILE63 4.3 18.4 1.0 CA A:ILE63 4.3 21.3 1.0 CB A:ASP56 4.3 30.8 1.0 OD2 A:ASP64 4.4 28.2 1.0 CB A:ASN60 4.4 31.3 1.0 N A:ASP64 4.4 20.9 1.0 N A:ASP58 4.4 29.1 1.0 CA A:THR62 4.5 26.0 1.0 OG1 A:THR62 4.5 26.0 1.0 C A:ASP56 4.6 30.9 1.0 N A:GLY59 4.6 33.4 1.0 N A:ALA57 4.6 24.2 1.0 CB A:ASP58 4.7 26.2 1.0 CA A:ASN60 4.7 26.9 1.0 N A:GLY61 4.8 29.1 1.0 CG A:ASP64 4.8 28.6 1.0 C A:ILE63 4.8 23.9 1.0 CA A:ASP58 4.9 33.3 1.0 C A:ASP58 4.9 31.7 1.0 C A:ASN60 5.0 26.2 1.0

Calcium binding site 3 out of 4 in the Calmodulin N53I Variant Bound to Cardiac Ryanodine Receptor (RYR2) Calmodulin Binding Domain


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Calmodulin N53I Variant Bound to Cardiac Ryanodine Receptor (RYR2) Calmodulin Binding Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca203 b:20.6 occ:1.00 OD1 A:ASP95 2.2 20.5 1.0 O A:HOH336 2.2 17.3 1.0 O A:TYR99 2.3 24.1 1.0 OD1 A:ASP93 2.3 18.8 1.0 OE2 A:GLU104 2.4 16.5 1.0 OD1 A:ASN97 2.4 19.5 1.0 OE1 A:GLU104 2.5 25.6 1.0 CD A:GLU104 2.8 21.1 1.0 CG A:ASP95 3.2 22.2 1.0 CG A:ASN97 3.3 23.6 1.0 CG A:ASP93 3.5 21.1 1.0 C A:TYR99 3.5 22.8 1.0 ND2 A:ASN97 3.7 19.2 1.0 OD2 A:ASP95 3.7 27.4 1.0 O A:HOH313 3.8 26.1 1.0 N A:TYR99 4.1 18.3 1.0 CA A:ASP93 4.2 22.8 1.0 N A:ASN97 4.2 19.1 1.0 N A:ASP95 4.2 22.2 1.0 CB A:ASP93 4.3 21.1 1.0 CG A:GLU104 4.3 19.5 1.0 CA A:TYR99 4.3 19.4 1.0 OD2 A:ASP93 4.3 20.1 1.0 N A:GLY96 4.4 25.5 1.0 C A:ASP93 4.4 22.6 1.0 CB A:ASP95 4.5 25.2 1.0 N A:ILE100 4.5 19.4 1.0 CB A:ASN97 4.5 20.9 1.0 CA A:ILE100 4.6 18.8 1.0 OE1 A:GLN135 4.6 25.4 1.0 N A:LYS94 4.6 27.1 1.0 N A:SER101 4.6 14.8 1.0 CA A:ASP95 4.7 22.3 1.0 C A:ASP95 4.7 22.8 1.0 CB A:TYR99 4.7 20.2 1.0 CA A:ASN97 4.8 23.3 1.0 O A:HOH324 4.9 29.4 1.0 N A:GLY98 4.9 22.4 1.0 O A:ASP93 4.9 23.7 1.0 OG A:SER101 5.0 21.3 1.0

Calcium binding site 4 out of 4 in the Calmodulin N53I Variant Bound to Cardiac Ryanodine Receptor (RYR2) Calmodulin Binding Domain


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Calmodulin N53I Variant Bound to Cardiac Ryanodine Receptor (RYR2) Calmodulin Binding Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca204 b:21.3 occ:1.00 OD1 A:ASP129 2.2 19.9 1.0 O A:HOH320 2.2 24.0 1.0 O A:GLN135 2.3 21.8 1.0 OD1 A:ASP133 2.3 21.1 1.0 OD1 A:ASP131 2.4 20.4 1.0 OE1 A:GLU140 2.5 20.6 1.0 OE2 A:GLU140 2.6 22.9 1.0 CD A:GLU140 2.9 25.7 1.0 CG A:ASP133 3.1 25.4 1.0 CG A:ASP129 3.3 25.1 1.0 CG A:ASP131 3.3 20.6 1.0 C A:GLN135 3.5 22.9 1.0 OD2 A:ASP133 3.5 26.4 1.0 OD2 A:ASP131 3.7 29.7 1.0 OD2 A:ASP129 4.0 24.6 1.0 N A:ASP133 4.1 23.2 1.0 CA A:ASP129 4.1 25.0 1.0 N A:GLN135 4.2 19.2 1.0 CB A:ASP129 4.2 23.8 1.0 CB A:ASP133 4.3 24.6 1.0 N A:ASP131 4.3 25.6 1.0 N A:VAL136 4.3 21.7 1.0 N A:ASN137 4.4 22.3 1.0 CA A:GLN135 4.4 23.4 1.0 CA A:VAL136 4.4 20.8 1.0 CG A:GLU140 4.4 22.6 1.0 N A:GLY132 4.4 25.1 1.0 C A:ASP129 4.5 20.9 1.0 N A:ILE130 4.5 21.8 1.0 CB A:ASP131 4.6 21.9 1.0 CA A:ASP133 4.6 21.2 1.0 ND2 A:ASN137 4.6 33.2 1.0 CG A:ASN137 4.8 29.1 1.0 N A:GLY134 4.8 23.6 1.0 CA A:ASP131 4.8 25.6 1.0 C A:ASP131 4.8 26.3 1.0 C A:VAL136 4.9 26.0 1.0 C A:ASP133 4.9 24.1 1.0

C.Holt, L.Hamborg, K.Lau, M.Brohus, A.B.Sorensen, K.T.Larsen, C.Sommer, F.V.Petegem, M.T.Overgaard, R.Wimmer. The Arrhythmogenic N53I Variant Subtly Changes the Structure and Dynamics in the Calmodulin N-Domain, Altering Its Interaction with the Cardiac Ryanodine Receptor J.Biol.Chem. 2020.
ISSN: ESSN 1083-351X