Calcium in PDB 9ed1: Cryo-Em Structure of the Human KCA3.1/Calmodulin Channel in Complex with CA2+ and 1,4-Dihydropyridine (Dhp-103)

The structure of Cryo-Em Structure of the Human KCA3.1/Calmodulin Channel in Complex with CA2+ and 1,4-Dihydropyridine (Dhp-103) also contains other interesting chemical elements:

Potassium

(K)

5 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Calcium atom in the Cryo-Em Structure of the Human KCA3.1/Calmodulin Channel in Complex with CA2+ and 1,4-Dihydropyridine (Dhp-103) (pdb code 9ed1). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 12 binding sites of Calcium where determined in the Cryo-Em Structure of the Human KCA3.1/Calmodulin Channel in Complex with CA2+ and 1,4-Dihydropyridine (Dhp-103), PDB code: 9ed1:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 12 in the Cryo-Em Structure of the Human KCA3.1/Calmodulin Channel in Complex with CA2+ and 1,4-Dihydropyridine (Dhp-103)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Cryo-Em Structure of the Human KCA3.1/Calmodulin Channel in Complex with CA2+ and 1,4-Dihydropyridine (Dhp-103) within 5.0Å range: probe atom residue distance (Å) B Occ E:Ca201 b:32.7 occ:1.00 OE2 E:GLU31 2.3 26.8 1.0 O E:THR26 2.3 23.1 1.0 OD1 E:ASP24 2.3 26.4 1.0 OD2 E:ASP24 2.5 26.4 1.0 OD1 E:ASP20 2.6 21.3 1.0 OE1 E:GLU31 2.6 26.8 1.0 CG E:ASP24 2.8 26.4 1.0 CD E:GLU31 2.8 26.8 1.0 OD1 E:ASP22 3.3 28.3 1.0 C E:THR26 3.5 23.1 1.0 CG E:ASP20 3.7 21.3 1.0 CG2 E:THR28 4.2 27.2 1.0 OD2 E:ASP20 4.2 21.3 1.0 CG E:ASP22 4.2 28.3 1.0 CG E:GLU31 4.3 26.8 1.0 CB E:ASP24 4.3 26.4 1.0 O E:ASP22 4.3 28.3 1.0 CA E:ILE27 4.3 23.0 1.0 N E:ILE27 4.4 23.0 1.0 N E:THR26 4.4 23.1 1.0 OD2 E:ASP22 4.4 28.3 1.0 N E:THR28 4.4 27.2 1.0 CA E:THR26 4.6 23.1 1.0 OG1 E:THR26 4.6 23.1 1.0 C E:ILE27 4.8 23.0 1.0 CA E:ASP20 4.8 21.3 1.0 CB E:ASP20 4.8 21.3 1.0 OG1 E:THR28 4.8 27.2 1.0

Calcium binding site 2 out of 12 in the Cryo-Em Structure of the Human KCA3.1/Calmodulin Channel in Complex with CA2+ and 1,4-Dihydropyridine (Dhp-103)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Cryo-Em Structure of the Human KCA3.1/Calmodulin Channel in Complex with CA2+ and 1,4-Dihydropyridine (Dhp-103) within 5.0Å range: probe atom residue distance (Å) B Occ E:Ca202 b:20.9 occ:1.00 O E:THR62 2.4 28.2 1.0 OE2 E:GLU67 2.4 18.8 1.0 OD1 E:ASP56 2.4 30.3 1.0 CG E:ASP56 3.2 30.3 1.0 OD2 E:ASP56 3.2 30.3 1.0 CD E:GLU67 3.4 18.8 1.0 OD1 E:ASP58 3.5 38.0 1.0 C E:THR62 3.5 28.2 1.0 OE1 E:GLU67 3.7 18.8 1.0 CB E:ASN60 3.8 34.7 1.0 CG E:ASN60 4.2 34.7 1.0 OG1 E:THR62 4.3 28.2 1.0 CA E:ILE63 4.3 23.0 1.0 N E:ILE63 4.3 23.0 1.0 N E:ASN60 4.3 34.7 1.0 N E:ASP64 4.4 22.4 1.0 CG E:ASP58 4.4 38.0 1.0 N E:THR62 4.4 28.2 1.0 CA E:THR62 4.5 28.2 1.0 OD1 E:ASN60 4.6 34.7 1.0 OD2 E:ASP58 4.6 38.0 1.0 CA E:ASN60 4.6 34.7 1.0 CB E:ASP56 4.6 30.3 1.0 C E:ILE63 4.7 23.0 1.0 ND2 E:ASN60 4.7 34.7 1.0 CG E:GLU67 4.7 18.8 1.0 N E:GLY59 5.0 32.3 1.0 CB E:THR62 5.0 28.2 1.0

Calcium binding site 3 out of 12 in the Cryo-Em Structure of the Human KCA3.1/Calmodulin Channel in Complex with CA2+ and 1,4-Dihydropyridine (Dhp-103)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Cryo-Em Structure of the Human KCA3.1/Calmodulin Channel in Complex with CA2+ and 1,4-Dihydropyridine (Dhp-103) within 5.0Å range: probe atom residue distance (Å) B Occ E:Ca203 b:24.9 occ:1.00 OD1 E:ASP95 2.4 33.9 1.0 OD2 E:ASP95 2.5 33.9 1.0 CG E:ASP95 2.7 33.9 1.0 O E:TYR99 3.1 36.9 1.0 CG E:GLU104 3.3 37.8 1.0 N E:SER101 3.4 38.5 1.0 OG E:SER101 3.5 38.5 1.0 CB E:SER101 3.6 38.5 1.0 OD1 E:ASP93 3.7 28.5 1.0 OD1 E:ASN97 3.9 32.2 1.0 CB E:ASP95 4.0 33.9 1.0 CA E:SER101 4.2 38.5 1.0 CD E:GLU104 4.2 37.8 1.0 C E:TYR99 4.2 36.9 1.0 CB E:GLU104 4.3 37.8 1.0 N E:ASP95 4.4 33.9 1.0 CA E:ASP93 4.4 28.5 1.0 C E:ILE100 4.4 34.6 1.0 CA E:ILE100 4.4 34.6 1.0 OE2 E:GLU104 4.5 37.8 1.0 N E:LYS94 4.6 32.6 1.0 CG E:ASP93 4.6 28.5 1.0 O E:PHE92 4.6 24.1 1.0 CG E:ASN97 4.7 32.2 1.0 N E:ILE100 4.8 34.6 1.0 CA E:ASP95 4.8 33.9 1.0 C E:ASP93 4.8 28.5 1.0 CB E:ASP93 4.9 28.5 1.0 ND2 E:ASN97 4.9 32.2 1.0

Calcium binding site 4 out of 12 in the Cryo-Em Structure of the Human KCA3.1/Calmodulin Channel in Complex with CA2+ and 1,4-Dihydropyridine (Dhp-103)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Cryo-Em Structure of the Human KCA3.1/Calmodulin Channel in Complex with CA2+ and 1,4-Dihydropyridine (Dhp-103) within 5.0Å range: probe atom residue distance (Å) B Occ F:Ca201 b:35.3 occ:1.00 OE2 F:GLU31 2.3 29.6 1.0 OD1 F:ASP24 2.3 31.5 1.0 O F:THR26 2.3 26.7 1.0 OE1 F:GLU31 2.4 29.6 1.0 CD F:GLU31 2.6 29.6 1.0 OD2 F:ASP24 2.8 31.5 1.0 CG F:ASP24 2.8 31.5 1.0 C F:THR26 3.5 26.7 1.0 CB F:ASP22 4.1 29.6 1.0 CG F:GLU31 4.1 29.6 1.0 N F:THR26 4.2 26.7 1.0 CB F:ASP24 4.3 31.5 1.0 CB F:ASP20 4.3 24.4 1.0 OG1 F:THR26 4.4 26.7 1.0 CA F:THR26 4.4 26.7 1.0 N F:ILE27 4.5 25.1 1.0 CA F:ASP20 4.5 24.4 1.0 CA F:ILE27 4.6 25.1 1.0 N F:ASP24 4.6 31.5 1.0 N F:GLY25 4.7 26.5 1.0 N F:ASP22 4.9 29.6 1.0 N F:THR28 4.9 27.8 1.0 N F:GLY23 5.0 26.3 1.0 CA F:ASP24 5.0 31.5 1.0 OD2 F:ASP22 5.0 29.6 1.0 CB F:GLU31 5.0 29.6 1.0 OG1 F:THR28 5.0 27.8 1.0

Calcium binding site 5 out of 12 in the Cryo-Em Structure of the Human KCA3.1/Calmodulin Channel in Complex with CA2+ and 1,4-Dihydropyridine (Dhp-103)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Cryo-Em Structure of the Human KCA3.1/Calmodulin Channel in Complex with CA2+ and 1,4-Dihydropyridine (Dhp-103) within 5.0Å range: probe atom residue distance (Å) B Occ F:Ca202 b:26.1 occ:1.00 O F:THR62 2.4 29.8 1.0 OE2 F:GLU67 2.4 18.0 1.0 OD1 F:ASP56 2.4 32.4 1.0 CG F:ASP56 3.2 32.4 1.0 OD2 F:ASP56 3.2 32.4 1.0 CD F:GLU67 3.4 18.0 1.0 C F:THR62 3.4 29.8 1.0 OE1 F:GLU67 3.6 18.0 1.0 OG1 F:THR62 3.9 29.8 1.0 N F:ILE63 4.2 23.6 1.0 CB F:ASN60 4.3 36.7 1.0 CA F:ILE63 4.3 23.6 1.0 N F:ASN60 4.3 36.7 1.0 CA F:THR62 4.4 29.8 1.0 N F:THR62 4.4 29.8 1.0 N F:GLY59 4.6 35.0 1.0 N F:ASP64 4.6 22.0 1.0 CB F:ASP56 4.6 32.4 1.0 CG F:GLU67 4.7 18.0 1.0 CB F:THR62 4.7 29.8 1.0 C F:ILE63 4.8 23.6 1.0 CA F:ASN60 4.9 36.7 1.0

Calcium binding site 6 out of 12 in the Cryo-Em Structure of the Human KCA3.1/Calmodulin Channel in Complex with CA2+ and 1,4-Dihydropyridine (Dhp-103)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Cryo-Em Structure of the Human KCA3.1/Calmodulin Channel in Complex with CA2+ and 1,4-Dihydropyridine (Dhp-103) within 5.0Å range: probe atom residue distance (Å) B Occ F:Ca203 b:25.1 occ:1.00 OD1 F:ASP95 2.4 34.0 1.0 OD2 F:ASP95 2.9 34.0 1.0 CG F:ASP95 2.9 34.0 1.0 O F:TYR99 3.0 37.7 1.0 OD1 F:ASP93 3.0 28.3 1.0 N F:SER101 3.5 37.6 1.0 OD1 F:ASN97 3.6 32.6 1.0 O F:ASP95 3.7 34.0 1.0 OG F:SER101 3.7 37.6 1.0 CG F:GLU104 3.8 35.0 1.0 CB F:SER101 3.9 37.6 1.0 C F:TYR99 4.1 37.7 1.0 CG F:ASP93 4.1 28.3 1.0 CA F:ILE100 4.3 34.3 1.0 CD F:GLU104 4.3 35.0 1.0 CG F:ASN97 4.3 32.6 1.0 CA F:SER101 4.3 37.6 1.0 C F:ILE100 4.3 34.3 1.0 CB F:ASP95 4.3 34.0 1.0 ND2 F:ASN97 4.4 32.6 1.0 OE2 F:GLU104 4.4 35.0 1.0 CA F:ASP93 4.5 28.3 1.0 N F:ASP95 4.6 34.0 1.0 C F:ASP95 4.6 34.0 1.0 N F:ILE100 4.6 34.3 1.0 CB F:ASP93 4.7 28.3 1.0 CA F:ASP95 4.8 34.0 1.0 CB F:GLU104 4.8 35.0 1.0 OE1 F:GLU104 5.0 35.0 1.0

Calcium binding site 7 out of 12 in the Cryo-Em Structure of the Human KCA3.1/Calmodulin Channel in Complex with CA2+ and 1,4-Dihydropyridine (Dhp-103)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Cryo-Em Structure of the Human KCA3.1/Calmodulin Channel in Complex with CA2+ and 1,4-Dihydropyridine (Dhp-103) within 5.0Å range: probe atom residue distance (Å) B Occ G:Ca201 b:31.1 occ:1.00 OE2 G:GLU31 2.3 26.9 1.0 OD1 G:ASP24 2.3 27.7 1.0 O G:THR26 2.3 22.0 1.0 OE1 G:GLU31 2.4 26.9 1.0 OD2 G:ASP24 2.4 27.7 1.0 CD G:GLU31 2.6 26.9 1.0 CG G:ASP24 2.7 27.7 1.0 OD1 G:ASP20 3.2 22.2 1.0 OD1 G:ASP22 3.4 27.1 1.0 C G:THR26 3.5 22.0 1.0 O G:ASP20 3.7 22.2 1.0 CG G:GLU31 4.2 26.9 1.0 CB G:ASP24 4.2 27.7 1.0 CG G:ASP22 4.2 27.1 1.0 N G:THR26 4.2 22.0 1.0 OD2 G:ASP22 4.3 27.1 1.0 O G:ASP22 4.3 27.1 1.0 N G:ILE27 4.4 22.2 1.0 CG G:ASP20 4.5 22.2 1.0 CA G:ILE27 4.5 22.2 1.0 CA G:THR26 4.5 22.0 1.0 OG1 G:THR26 4.5 22.0 1.0 C G:ASP20 4.6 22.2 1.0 CA G:ASP20 4.7 22.2 1.0 N G:GLY25 4.8 23.3 1.0 N G:THR28 4.9 25.5 1.0 CB G:GLU31 5.0 26.9 1.0 N G:ASP24 5.0 27.7 1.0

Calcium binding site 8 out of 12 in the Cryo-Em Structure of the Human KCA3.1/Calmodulin Channel in Complex with CA2+ and 1,4-Dihydropyridine (Dhp-103)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Cryo-Em Structure of the Human KCA3.1/Calmodulin Channel in Complex with CA2+ and 1,4-Dihydropyridine (Dhp-103) within 5.0Å range: probe atom residue distance (Å) B Occ G:Ca202 b:26.2 occ:1.00 O G:THR62 2.4 27.2 1.0 OE2 G:GLU67 2.4 17.4 1.0 OD1 G:ASP56 2.4 29.8 1.0 CG G:ASP56 3.2 29.8 1.0 OD2 G:ASP56 3.3 29.8 1.0 CD G:GLU67 3.4 17.4 1.0 C G:THR62 3.5 27.2 1.0 OE1 G:GLU67 3.7 17.4 1.0 OD1 G:ASP58 3.9 34.5 1.0 OG1 G:THR62 3.9 27.2 1.0 CB G:ASN60 3.9 33.5 1.0 OD2 G:ASP58 4.1 34.5 1.0 N G:ILE63 4.3 20.9 1.0 N G:ASN60 4.3 33.5 1.0 CA G:ILE63 4.3 20.9 1.0 N G:THR62 4.4 27.2 1.0 CG G:ASP58 4.4 34.5 1.0 CA G:THR62 4.4 27.2 1.0 N G:ASP64 4.6 20.6 1.0 CA G:ASN60 4.7 33.5 1.0 CB G:ASP56 4.7 29.8 1.0 CG G:GLU67 4.8 17.4 1.0 CB G:THR62 4.8 27.2 1.0 C G:ILE63 4.8 20.9 1.0 N G:GLY59 4.9 32.2 1.0 ND2 G:ASN60 5.0 33.5 1.0

Calcium binding site 9 out of 12 in the Cryo-Em Structure of the Human KCA3.1/Calmodulin Channel in Complex with CA2+ and 1,4-Dihydropyridine (Dhp-103)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of Cryo-Em Structure of the Human KCA3.1/Calmodulin Channel in Complex with CA2+ and 1,4-Dihydropyridine (Dhp-103) within 5.0Å range: probe atom residue distance (Å) B Occ G:Ca203 b:26.6 occ:1.00 OD1 G:ASP95 2.4 35.4 1.0 OE2 G:GLU104 2.6 36.5 1.0 CD G:GLU104 2.8 36.5 1.0 OD2 G:ASP95 2.8 35.4 1.0 CG G:ASP95 2.9 35.4 1.0 OE1 G:GLU104 2.9 36.5 1.0 O G:TYR99 3.0 37.9 1.0 OD1 G:ASP93 3.6 29.7 1.0 OD1 G:ASN97 3.7 32.0 1.0 OG G:SER101 3.7 39.2 1.0 CG G:GLU104 3.8 36.5 1.0 N G:SER101 3.8 39.2 1.0 C G:TYR99 4.2 37.9 1.0 CB G:SER101 4.2 39.2 1.0 CB G:ASP95 4.3 35.4 1.0 N G:ASP95 4.5 35.4 1.0 CG G:ASN97 4.5 32.0 1.0 CA G:ILE100 4.5 36.0 1.0 CA G:ASP93 4.6 29.7 1.0 N G:LYS94 4.6 34.4 1.0 CG G:ASP93 4.6 29.7 1.0 ND2 G:ASN97 4.6 32.0 1.0 CA G:SER101 4.7 39.2 1.0 CB G:GLU104 4.7 36.5 1.0 C G:ILE100 4.7 36.0 1.0 O G:PHE92 4.7 24.3 1.0 N G:ILE100 4.8 36.0 1.0 CA G:ASP95 5.0 35.4 1.0 C G:ASP93 5.0 29.7 1.0

Calcium binding site 10 out of 12 in the Cryo-Em Structure of the Human KCA3.1/Calmodulin Channel in Complex with CA2+ and 1,4-Dihydropyridine (Dhp-103)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 10 of Cryo-Em Structure of the Human KCA3.1/Calmodulin Channel in Complex with CA2+ and 1,4-Dihydropyridine (Dhp-103) within 5.0Å range: probe atom residue distance (Å) B Occ H:Ca201 b:33.7 occ:1.00 OE2 H:GLU31 2.3 30.2 1.0 O H:THR26 2.4 23.9 1.0 OD1 H:ASP24 2.4 29.4 1.0 OE1 H:GLU31 2.7 30.2 1.0 OD2 H:ASP24 2.7 29.4 1.0 OD1 H:ASP20 2.8 23.3 1.0 CD H:GLU31 2.8 30.2 1.0 CG H:ASP24 2.9 29.4 1.0 C H:THR26 3.6 23.9 1.0 CG H:ASP20 3.8 23.3 1.0 N H:THR26 4.2 23.9 1.0 CG H:GLU31 4.3 30.2 1.0 CB H:ASP24 4.4 29.4 1.0 CB H:ASP22 4.4 31.9 1.0 OD2 H:ASP20 4.4 23.3 1.0 OD2 H:ASP22 4.4 31.9 1.0 OG1 H:THR26 4.5 23.9 1.0 CA H:THR26 4.5 23.9 1.0 N H:ILE27 4.5 24.4 1.0 CA H:ILE27 4.6 24.4 1.0 N H:ASP24 4.7 29.4 1.0 N H:GLY25 4.8 23.2 1.0 CG H:ASP22 4.9 31.9 1.0 CA H:ASP20 4.9 23.3 1.0 CB H:ASP20 4.9 23.3 1.0 N H:THR28 5.0 28.1 1.0 N H:GLY23 5.0 27.2 1.0

S.T.Ong, Y.W.Nam, A.Ramanishka, J.A.Nasburg, X.R.Ng, Z.Zhuang, S.S.M.Goay, L.Singh, V.Singh, A.Rivera, Y.Xu, S.L.Alper, H.Wulff, M.Zhang, K.G.Chandy. Design and Structural Basis of Selective 1,4-Dihydropyridine Inhibitors of the Calcium-Activated Potassium Channel, KCA3.1 Proc.Natl.Acad.Sci.Usa 2025.
ISSN: ESSN 1091-6490