Calcium in PDB 6m7h: Structure of Calmodulin with KN93

The structure of Structure of Calmodulin with KN93, PDB code: 6m7h was solved by S.M.Damo, R.Pattanayek, C.N.Johnson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	35.08 / 1.60
Space group	P 61 2 2
Cell size a, b, c (Å), α, β, γ (°)	40.511, 40.511, 348.785, 90.00, 90.00, 120.00
R / Rfree (%)	22.8 / 26.7

The structure of Structure of Calmodulin with KN93 also contains other interesting chemical elements:

Chlorine

(Cl)

3 atoms

The binding sites of Calcium atom in the Structure of Calmodulin with KN93 (pdb code 6m7h). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Structure of Calmodulin with KN93, PDB code: 6m7h:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Structure of Calmodulin with KN93


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 with KN93 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca204 b:27.1 occ:1.00 O A:HOH339 2.0 37.7 1.0 OD1 A:ASP56 2.3 27.3 1.0 OD1 A:ASN60 2.3 28.8 1.0 OD1 A:ASP58 2.4 38.0 1.0 O A:THR62 2.4 26.7 1.0 OE1 A:GLU67 2.5 21.3 1.0 OE2 A:GLU67 2.5 35.2 1.0 CD A:GLU67 2.8 36.9 1.0 CG A:ASN60 3.4 33.8 1.0 CG A:ASP58 3.4 39.7 1.0 CG A:ASP56 3.5 33.0 1.0 C A:THR62 3.6 26.0 1.0 OD2 A:ASP58 3.8 41.1 1.0 ND2 A:ASN60 3.9 36.9 1.0 N A:THR62 4.2 28.8 1.0 N A:ASN60 4.3 30.0 1.0 OD2 A:ASP56 4.3 30.2 1.0 CA A:ASP56 4.4 28.5 1.0 CG A:GLU67 4.4 22.6 1.0 N A:ASP58 4.4 41.4 1.0 N A:ILE63 4.4 20.9 1.0 CA A:ILE63 4.5 24.3 1.0 OG1 A:THR62 4.5 28.9 1.0 CB A:ASP56 4.5 33.3 1.0 CA A:THR62 4.5 21.5 1.0 N A:ALA57 4.5 36.4 1.0 CB A:ASN60 4.5 37.5 1.0 N A:ASP64 4.7 21.5 1.0 N A:GLY59 4.7 42.4 1.0 CB A:ASP58 4.7 38.6 1.0 C A:ASP56 4.7 36.4 1.0 N A:GLY61 4.8 28.8 1.0 CA A:ASN60 4.8 31.7 1.0 CA A:ASP58 4.9 39.0 1.0 C A:ASP58 4.9 38.0 1.0 C A:ASN60 4.9 27.0 1.0 O A:HOH301 5.0 42.5 1.0

Calcium binding site 2 out of 4 in the Structure of Calmodulin with KN93


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 with KN93 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca205 b:12.9 occ:1.00 OD1 A:ASP93 2.2 16.1 1.0 O A:HOH322 2.2 16.7 1.0 O A:TYR99 2.3 13.3 1.0 OD1 A:ASP95 2.3 19.4 1.0 OE1 A:GLU104 2.5 16.8 1.0 OD1 A:ASN97 2.5 14.1 1.0 OE2 A:GLU104 2.6 18.2 1.0 CD A:GLU104 2.8 15.3 1.0 CG A:ASP95 3.3 20.4 1.0 CG A:ASP93 3.4 16.7 1.0 C A:TYR99 3.5 12.3 1.0 CG A:ASN97 3.5 14.3 1.0 OD2 A:ASP95 3.6 21.6 1.0 N A:ASN97 4.1 14.9 1.0 N A:TYR99 4.1 12.5 1.0 ND2 A:ASN97 4.2 14.8 1.0 CA A:ASP93 4.2 15.8 1.0 O A:HOH318 4.2 21.3 1.0 OD2 A:ASP93 4.3 16.4 1.0 CB A:ASP93 4.3 14.4 1.0 CG A:GLU104 4.3 15.6 1.0 CA A:TYR99 4.3 9.8 1.0 N A:ILE100 4.4 10.1 1.0 N A:ASP95 4.4 20.6 1.0 CB A:ASN97 4.5 10.9 1.0 C A:ASP93 4.5 13.0 1.0 CA A:ILE100 4.5 11.6 1.0 N A:GLY96 4.5 14.2 1.0 CB A:ASP95 4.6 22.1 1.0 O A:HOH327 4.6 27.1 1.0 N A:SER101 4.7 11.2 1.0 CA A:ASN97 4.7 12.0 1.0 N A:LYS94 4.8 20.9 1.0 CB A:TYR99 4.8 11.0 1.0 CA A:ASP95 4.8 18.2 1.0 N A:GLY98 4.8 13.2 1.0 O A:ASP93 4.9 16.3 1.0 C A:ASP95 4.9 13.4 1.0

Calcium binding site 3 out of 4 in the Structure of Calmodulin with KN93


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 with KN93 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca206 b:13.2 occ:1.00 OD1 A:ASP131 2.3 14.2 1.0 O A:GLN135 2.3 11.7 1.0 OE1 A:GLU140 2.4 15.7 1.0 OD1 A:ASP129 2.4 13.5 1.0 OD1 A:ASP133 2.4 13.4 1.0 O A:HOH321 2.5 17.6 1.0 OE2 A:GLU140 2.5 16.2 1.0 CD A:GLU140 2.8 16.1 1.0 CG A:ASP131 3.2 16.4 1.0 CG A:ASP133 3.3 11.8 1.0 CG A:ASP129 3.4 12.2 1.0 C A:GLN135 3.5 11.1 1.0 OD2 A:ASP131 3.5 21.6 1.0 OD2 A:ASP133 3.7 16.5 1.0 N A:GLN135 4.1 8.8 1.0 N A:ASP133 4.2 14.8 1.0 N A:ASP131 4.2 17.1 1.0 OD2 A:ASP129 4.3 14.5 1.0 N A:ILE130 4.3 15.0 1.0 CA A:ASP129 4.3 12.4 1.0 CB A:ASP129 4.3 14.9 1.0 N A:VAL136 4.3 11.0 1.0 CG A:GLU140 4.4 12.2 1.0 CA A:VAL136 4.4 13.1 1.0 CA A:GLN135 4.4 12.1 1.0 N A:GLY132 4.4 15.1 1.0 CB A:ASP133 4.4 13.4 1.0 CB A:ASP131 4.5 14.6 1.0 N A:ASN137 4.5 11.0 1.0 N A:GLY134 4.7 12.1 1.0 CA A:ASP133 4.7 14.4 1.0 CA A:ASP131 4.7 12.9 1.0 C A:ASP129 4.8 11.6 1.0 C A:ASP131 4.9 17.2 1.0 C A:VAL136 4.9 12.0 1.0 C A:ASP133 4.9 13.8 1.0 CB A:GLN135 5.0 12.1 1.0

Calcium binding site 4 out of 4 in the Structure of Calmodulin with KN93


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 with KN93 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca207 b:28.6 occ:1.00 O A:HOH308 2.2 35.4 1.0 OD1 A:ASP24 2.3 37.7 1.0 OD1 A:ASP20 2.3 36.3 1.0 O A:THR26 2.3 38.5 1.0 OD1 A:ASP22 2.4 35.0 1.0 OE1 A:GLU31 2.4 23.8 1.0 OE2 A:GLU31 2.5 35.4 1.0 CD A:GLU31 2.8 31.4 1.0 CG A:ASP24 3.1 42.0 1.0 CG A:ASP22 3.3 30.0 1.0 CG A:ASP20 3.5 34.3 1.0 C A:THR26 3.5 27.7 1.0 OD2 A:ASP24 3.6 41.2 1.0 OD2 A:ASP22 3.6 37.7 1.0 CB A:ASP24 4.1 34.1 1.0 N A:ASP24 4.2 31.7 1.0 OG1 A:THR26 4.2 43.4 1.0 N A:THR26 4.2 31.7 1.0 CG A:GLU31 4.3 26.1 1.0 OD2 A:ASP20 4.3 30.9 1.0 CA A:ASP20 4.4 26.5 1.0 CA A:THR26 4.4 30.6 1.0 N A:ASP22 4.5 34.9 1.0 N A:ILE27 4.5 23.3 1.0 CB A:ASP20 4.5 29.8 1.0 CA A:ILE27 4.5 22.7 1.0 CA A:ASP24 4.6 36.1 1.0 CB A:ASP22 4.6 36.9 1.0 C A:ASP20 4.7 33.0 1.0 N A:LYS21 4.7 31.9 1.0 CG2 A:THR28 4.7 27.2 1.0 N A:GLY25 4.8 36.7 1.0 N A:GLY23 4.8 33.9 1.0 O A:HOH344 4.8 31.4 1.0 C A:ASP22 4.8 40.9 1.0 N A:THR28 4.9 20.9 1.0 CA A:ASP22 4.9 32.5 1.0 O A:HOH313 4.9 29.9 1.0 C A:ASP24 4.9 40.4 1.0 CB A:THR26 5.0 31.9 1.0

C.N.Johnson, R.Pattanayek, F.Potet, R.T.Rebbeck, D.J.Blackwell, R.Nikolaienko, V.Sequeira, R.Le Meur, P.B.Radwanski, J.P.Davis, A.V.Zima, R.L.Cornea, S.M.Damo, S.Gyorke, A.L.George Jr., B.C.Knollmann. The Camkii Inhibitor KN93-Calmodulin Interaction and Implications For Calmodulin Tuning of NAV1.5 and RYR2 Function. Cell Calcium V. 82 02063 2019.
ISSN: ISSN 1532-1991
PubMed: 31401388
DOI: 10.1016/J.CECA.2019.102063