Calcium in PDB 7kl5: Structure of Calmodulin Bound to the Cardiac Ryanodine Receptor (RYR2) at Residues: PHE4246 to VAL4271

The structure of Structure of Calmodulin Bound to the Cardiac Ryanodine Receptor (RYR2) at Residues: PHE4246 to VAL4271, PDB code: 7kl5 was solved by A.J.Fisher, J.B.Ames, Q.Yu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	41.19 / 1.65
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	33.169, 62.403, 43.19, 90, 107.49, 90
R / Rfree (%)	20.9 / 24.6

The binding sites of Calcium atom in the Structure of Calmodulin Bound to the Cardiac Ryanodine Receptor (RYR2) at Residues: PHE4246 to VAL4271 (pdb code 7kl5). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 5 binding sites of Calcium where determined in the Structure of Calmodulin Bound to the Cardiac Ryanodine Receptor (RYR2) at Residues: PHE4246 to VAL4271, PDB code: 7kl5:
Jump to Calcium binding site number: 1; 2; 3; 4; 5;

Calcium binding site 1 out of 5 in the Structure of Calmodulin Bound to the Cardiac Ryanodine Receptor (RYR2) at Residues: PHE4246 to VAL4271


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structure of Calmodulin Bound to the Cardiac Ryanodine Receptor (RYR2) at Residues: PHE4246 to VAL4271 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca201 b:27.8 occ:1.00 O A:THR27 2.2 28.1 1.0 OD1 A:ASP21 2.3 31.3 1.0 OD1 A:ASP25 2.3 27.3 1.0 OD1 A:ASP23 2.4 26.3 1.0 OE1 A:GLU32 2.5 28.4 1.0 O A:HOH322 2.5 28.9 1.0 OE2 A:GLU32 2.6 29.6 1.0 CD A:GLU32 2.9 29.6 1.0 CG A:ASP25 3.3 30.0 1.0 CG A:ASP23 3.3 28.9 1.0 CG A:ASP21 3.4 30.1 1.0 C A:THR27 3.4 28.7 1.0 OD2 A:ASP23 3.7 29.4 1.0 OG1 A:THR27 4.0 30.3 1.0 OD2 A:ASP25 4.0 31.1 1.0 N A:THR27 4.1 28.8 1.0 N A:ASP25 4.1 28.3 1.0 CA A:ASP21 4.1 29.7 1.0 CB A:ASP25 4.2 30.3 1.0 CB A:ASP21 4.2 29.5 1.0 CA A:THR27 4.3 28.4 1.0 OD2 A:ASP21 4.3 30.2 1.0 N A:ILE28 4.4 25.8 1.0 CG A:GLU32 4.4 29.7 1.0 N A:ASP23 4.4 29.9 1.0 C A:ASP21 4.4 31.2 1.0 CB A:ASP23 4.5 28.6 1.0 CA A:ILE28 4.5 26.1 1.0 CA A:ASP25 4.6 29.8 1.0 N A:GLY24 4.6 30.1 1.0 N A:GLY26 4.7 26.5 1.0 CA A:ASP23 4.8 30.3 1.0 N A:LYS22 4.8 31.4 1.0 O A:HOH318 4.8 30.6 1.0 CB A:THR27 4.8 31.0 1.0 CG2 A:THR29 4.8 28.0 1.0 C A:ASP25 4.8 28.7 1.0 N A:THR29 4.9 26.2 1.0 C A:ASP23 4.9 30.4 1.0 O A:ASP21 5.0 32.2 1.0

Calcium binding site 2 out of 5 in the Structure of Calmodulin Bound to the Cardiac Ryanodine Receptor (RYR2) at Residues: PHE4246 to VAL4271


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structure of Calmodulin Bound to the Cardiac Ryanodine Receptor (RYR2) at Residues: PHE4246 to VAL4271 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca202 b:30.3 occ:1.00 OD1 A:ASP57 1.9 36.9 1.0 O A:HOH309 2.0 47.7 1.0 O A:THR63 2.3 28.9 1.0 OE1 A:GLU68 2.4 30.2 1.0 OD1 A:ASN61 2.4 34.5 1.0 OE2 A:GLU68 2.4 32.3 1.0 OD1 A:ASP59 2.5 43.4 1.0 CD A:GLU68 2.7 32.0 1.0 CG A:ASP57 3.3 38.3 1.0 CG A:ASN61 3.3 41.7 1.0 CG A:ASP59 3.4 43.9 1.0 C A:THR63 3.6 27.9 1.0 OD2 A:ASP59 3.6 47.7 1.0 ND2 A:ASN61 3.8 43.7 1.0 OD2 A:ASP57 4.1 41.0 1.0 CA A:ASP57 4.2 42.9 1.0 CB A:ASP57 4.2 42.4 1.0 CG A:GLU68 4.3 32.2 1.0 N A:THR63 4.3 29.0 1.0 N A:ASP65 4.4 30.1 1.0 N A:ASN61 4.4 47.5 1.0 OG1 A:THR63 4.4 31.7 1.0 N A:ILE64 4.4 29.1 1.0 CB A:ASN61 4.5 41.9 1.0 CA A:ILE64 4.5 28.9 1.0 OD2 A:ASP65 4.5 38.0 1.0 CA A:THR63 4.5 29.7 1.0 N A:ASP59 4.5 48.2 1.0 C A:ASP57 4.6 48.9 1.0 CG A:ASP65 4.7 37.4 1.0 CB A:ASP59 4.7 49.1 1.0 N A:ALA58 4.7 47.9 1.0 CA A:ASN61 4.8 40.6 1.0 N A:GLY60 4.8 57.5 1.0 N A:GLY62 4.8 33.4 1.0 C A:ILE64 4.9 29.9 1.0 OD1 A:ASP65 4.9 35.8 1.0 CA A:ASP59 5.0 50.6 1.0

Calcium binding site 3 out of 5 in the Structure of Calmodulin Bound to the Cardiac Ryanodine Receptor (RYR2) at Residues: PHE4246 to VAL4271


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Structure of Calmodulin Bound to the Cardiac Ryanodine Receptor (RYR2) at Residues: PHE4246 to VAL4271 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca203 b:33.7 occ:1.00 O A:HOH346 2.2 43.1 1.0 OD1 A:ASP81 2.3 33.8 1.0 O A:LYS78 2.3 34.9 1.0 O A:HOH358 2.3 31.4 1.0 O A:HOH326 2.4 36.9 1.0 OE1 A:GLU85 2.5 31.8 1.0 OE2 A:GLU85 2.6 36.9 1.0 CD A:GLU85 2.9 32.4 1.0 CG A:ASP81 3.4 36.7 1.0 C A:LYS78 3.5 35.9 1.0 OD2 A:ASP81 3.9 40.5 1.0 CA A:LYS78 4.3 38.3 1.0 N A:ASP81 4.4 32.7 1.0 CG A:GLU85 4.4 31.8 1.0 N A:SER82 4.4 32.3 1.0 N A:ASP79 4.5 33.6 1.0 CB A:SER82 4.5 32.9 1.0 CA A:ASP79 4.5 33.6 1.0 C A:ASP79 4.6 31.3 1.0 CB A:LYS78 4.6 40.4 1.0 CB A:ASP81 4.6 35.2 1.0 OG A:SER82 4.7 31.8 1.0 N A:THR80 4.9 32.4 1.0 CA A:ASP81 4.9 34.4 1.0 O A:ASP79 4.9 30.6 1.0 O A:HOH311 4.9 43.4 1.0 C A:ASP81 5.0 35.0 1.0

Calcium binding site 4 out of 5 in the Structure of Calmodulin Bound to the Cardiac Ryanodine Receptor (RYR2) at Residues: PHE4246 to VAL4271


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Structure of Calmodulin Bound to the Cardiac Ryanodine Receptor (RYR2) at Residues: PHE4246 to VAL4271 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca204 b:31.2 occ:1.00 O A:TYR100 2.0 28.0 1.0 OD1 A:ASN98 2.3 36.8 1.0 OD1 A:ASP94 2.3 30.4 1.0 OD1 A:ASP96 2.4 37.0 1.0 O A:HOH330 2.4 31.7 1.0 OE2 A:GLU105 2.5 35.6 1.0 OE1 A:GLU105 2.7 41.0 1.0 CD A:GLU105 2.9 38.0 1.0 CG A:ASP96 3.3 39.2 1.0 C A:TYR100 3.3 30.3 1.0 CG A:ASN98 3.4 39.4 1.0 CG A:ASP94 3.5 30.4 1.0 OD2 A:ASP96 3.7 41.0 1.0 ND2 A:ASN98 4.0 39.0 1.0 N A:TYR100 4.1 33.5 1.0 N A:ASN98 4.2 34.8 1.0 CA A:ASP94 4.2 30.3 1.0 N A:ILE101 4.2 30.7 1.0 CA A:TYR100 4.2 35.0 1.0 N A:ASP96 4.3 35.8 1.0 OD2 A:ASP94 4.3 29.2 1.0 C A:ASP94 4.4 32.0 1.0 CB A:ASP94 4.4 29.7 1.0 CG A:GLU105 4.4 38.1 1.0 O A:HOH316 4.4 43.1 1.0 CB A:ASN98 4.4 38.5 1.0 CA A:ILE101 4.5 32.2 1.0 N A:LYS95 4.5 34.4 1.0 CB A:ASP96 4.5 40.4 1.0 N A:GLY97 4.6 32.7 1.0 N A:GLY99 4.6 34.2 1.0 CA A:ASN98 4.6 36.3 1.0 O A:HOH328 4.7 44.4 1.0 CA A:ASP96 4.8 37.8 1.0 CB A:TYR100 4.8 36.6 1.0 C A:ASN98 4.8 35.1 1.0 N A:SER102 4.8 34.9 1.0 O A:ASP94 4.8 33.2 1.0 C A:ASP96 4.9 37.5 1.0

Calcium binding site 5 out of 5 in the Structure of Calmodulin Bound to the Cardiac Ryanodine Receptor (RYR2) at Residues: PHE4246 to VAL4271


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Structure of Calmodulin Bound to the Cardiac Ryanodine Receptor (RYR2) at Residues: PHE4246 to VAL4271 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca205 b:44.1 occ:1.00 OE2 A:GLU141 2.1 40.2 1.0 OD1 A:ASP132 2.1 53.7 1.0 OD1 A:ASP130 2.2 40.7 1.0 O A:HOH329 2.4 33.2 1.0 OE1 A:GLU141 2.4 38.7 1.0 O A:GLN136 2.4 40.3 1.0 OD1 A:ASP134 2.5 52.2 1.0 CD A:GLU141 2.6 40.2 1.0 CG A:ASP132 3.2 57.4 1.0 CG A:ASP134 3.2 50.1 1.0 CG A:ASP130 3.4 43.8 1.0 C A:GLN136 3.5 39.4 1.0 OD2 A:ASP132 3.6 55.0 1.0 OD2 A:ASP134 3.6 48.9 1.0 CG A:GLU141 4.1 39.5 1.0 CA A:ASP130 4.2 42.9 1.0 OD2 A:ASP130 4.2 45.4 1.0 N A:ASP134 4.2 57.8 1.0 N A:ASP132 4.3 55.1 1.0 N A:GLN136 4.3 43.1 1.0 CB A:ASP130 4.3 42.7 1.0 CA A:VAL137 4.3 37.0 1.0 N A:VAL137 4.4 36.8 1.0 N A:ASN138 4.4 36.3 1.0 CB A:ASP134 4.4 54.8 1.0 CA A:GLN136 4.5 41.1 1.0 N A:ILE131 4.5 49.5 1.0 N A:GLY133 4.5 56.4 1.0 C A:ASP130 4.5 46.1 1.0 CB A:ASP132 4.5 57.8 1.0 CA A:ASP132 4.8 59.1 1.0 CA A:ASP134 4.8 55.9 1.0 C A:VAL137 4.8 36.7 1.0 C A:ASP132 4.9 59.0 1.0 N A:GLY135 4.9 49.5 1.0 CG A:ASN138 4.9 37.7 1.0

Q.Yu, D.E.Anderson, R.Kaur, A.J.Fisher, J.B.Ames. The Crystal Structure of Calmodulin Bound to the Cardiac Ryanodine Receptor (RYR2) at Residues PHE4246-VAL4270 Reveals A Fifth Calcium Binding Site. Biochemistry 2021.
ISSN: ISSN 0006-2960
PubMed: 33754699
DOI: 10.1021/ACS.BIOCHEM.1C00152