Calcium in PDB 1qiw: Calmodulin Complexed with N-(3,3,-Diphenylpropyl)-N'-[1-R-(3,4-Bis- Butoxyphenyl)-Ethyl]-Propylenediamine (Dpd)

The structure of Calmodulin Complexed with N-(3,3,-Diphenylpropyl)-N'-[1-R-(3,4-Bis- Butoxyphenyl)-Ethyl]-Propylenediamine (Dpd), PDB code: 1qiw was solved by V.Harmat, Z.S.Bocskei, B.G.Vertessy, J.Ovadi, G.Naray-Szabo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	54.23 / 2.30
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	41.960, 56.200, 35.270, 99.52, 114.47, 96.86
R / Rfree (%)	23.2 / 31.7

The binding sites of Calcium atom in the Calmodulin Complexed with N-(3,3,-Diphenylpropyl)-N'-[1-R-(3,4-Bis- Butoxyphenyl)-Ethyl]-Propylenediamine (Dpd) (pdb code 1qiw). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 8 binding sites of Calcium where determined in the Calmodulin Complexed with N-(3,3,-Diphenylpropyl)-N'-[1-R-(3,4-Bis- Butoxyphenyl)-Ethyl]-Propylenediamine (Dpd), PDB code: 1qiw:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in the Calmodulin Complexed with N-(3,3,-Diphenylpropyl)-N'-[1-R-(3,4-Bis- Butoxyphenyl)-Ethyl]-Propylenediamine (Dpd)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Calmodulin Complexed with N-(3,3,-Diphenylpropyl)-N'-[1-R-(3,4-Bis- Butoxyphenyl)-Ethyl]-Propylenediamine (Dpd) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca149 b:30.9 occ:1.00 OD1 A:ASP22 2.3 32.5 1.0 OD1 A:ASP20 2.3 27.6 1.0 OE2 A:GLU31 2.3 13.2 1.0 O A:THR26 2.3 19.7 1.0 OE1 A:GLU31 2.3 13.2 1.0 OD1 A:ASP24 2.3 53.7 1.0 CD A:GLU31 2.6 13.2 1.0 CG A:ASP22 2.9 32.5 1.0 OD2 A:ASP22 2.9 32.5 1.0 CG A:ASP24 3.4 53.7 1.0 CG A:ASP20 3.4 27.6 1.0 C A:THR26 3.5 19.7 1.0 OD2 A:ASP24 3.8 53.7 1.0 CA A:ASP20 4.1 17.1 1.0 CG A:GLU31 4.1 13.2 1.0 CB A:ASP20 4.2 17.1 1.0 N A:THR26 4.2 19.7 1.0 OD2 A:ASP20 4.3 27.6 1.0 OG1 A:THR26 4.3 34.5 1.0 N A:ASP24 4.3 39.1 1.0 CB A:ASP22 4.3 39.2 1.0 N A:ASP22 4.3 39.2 1.0 N A:GLY23 4.4 36.6 1.0 CA A:THR26 4.5 19.7 1.0 C A:ASP20 4.5 17.1 1.0 N A:ILE27 4.5 11.0 1.0 N A:LYS21 4.5 35.1 1.0 CA A:ILE27 4.5 11.0 1.0 CB A:ASP24 4.6 39.1 1.0 N A:GLY25 4.8 10.8 1.0 CA A:ASP22 4.8 39.2 1.0 N A:THR28 4.9 22.5 1.0 CA A:ASP24 4.9 39.1 1.0 CG2 A:THR28 5.0 19.8 1.0 CB A:THR26 5.0 19.7 1.0

Calcium binding site 2 out of 8 in the Calmodulin Complexed with N-(3,3,-Diphenylpropyl)-N'-[1-R-(3,4-Bis- Butoxyphenyl)-Ethyl]-Propylenediamine (Dpd)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Calmodulin Complexed with N-(3,3,-Diphenylpropyl)-N'-[1-R-(3,4-Bis- Butoxyphenyl)-Ethyl]-Propylenediamine (Dpd) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca150 b:18.5 occ:1.00 OD1 A:ASN60 2.3 28.8 1.0 OD1 A:ASP58 2.3 28.2 1.0 OD1 A:ASP56 2.3 16.7 1.0 OE2 A:GLU67 2.3 26.2 1.0 O A:THR62 2.3 28.9 1.0 OE1 A:GLU67 2.3 26.2 1.0 CD A:GLU67 2.6 26.2 1.0 CG A:ASP58 3.3 28.2 1.0 CG A:ASN60 3.4 28.8 1.0 CG A:ASP56 3.5 16.7 1.0 C A:THR62 3.5 28.9 1.0 OD2 A:ASP58 3.7 28.2 1.0 OD2 A:ASP64 3.8 26.9 1.0 ND2 A:ASN60 3.9 28.8 1.0 CA A:ASP56 4.1 20.2 1.0 CG A:GLU67 4.2 26.2 1.0 N A:ASN60 4.2 36.8 1.0 N A:ASP58 4.2 23.2 1.0 N A:THR62 4.3 28.9 1.0 OD2 A:ASP56 4.3 16.7 1.0 CB A:ASP56 4.4 20.2 1.0 N A:ILE63 4.4 12.9 1.0 CA A:ILE63 4.4 12.9 1.0 C A:ASP56 4.4 20.2 1.0 N A:GLY59 4.4 24.0 1.0 CA A:THR62 4.5 28.9 1.0 CB A:ASP58 4.5 23.2 1.0 OG1 A:THR62 4.5 37.7 1.0 N A:ALA57 4.6 21.3 1.0 CB A:ASN60 4.6 36.8 1.0 CA A:ASP58 4.7 23.2 1.0 CG A:ASP64 4.8 26.9 1.0 C A:ASP58 4.8 23.2 1.0 CD1 A:ILE63 4.9 6.2 1.0 CA A:ASN60 4.9 36.8 1.0 N A:ASP64 4.9 21.0 1.0

Calcium binding site 3 out of 8 in the Calmodulin Complexed with N-(3,3,-Diphenylpropyl)-N'-[1-R-(3,4-Bis- Butoxyphenyl)-Ethyl]-Propylenediamine (Dpd)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Calmodulin Complexed with N-(3,3,-Diphenylpropyl)-N'-[1-R-(3,4-Bis- Butoxyphenyl)-Ethyl]-Propylenediamine (Dpd) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca151 b:27.2 occ:1.00 OD1 A:ASN97 2.3 57.4 1.0 OD1 A:ASP95 2.3 36.6 1.0 O A:TYR99 2.3 28.6 1.0 OD1 A:ASP93 2.3 27.0 1.0 OE2 A:GLU104 2.3 23.6 1.0 OE1 A:GLU104 2.3 23.6 1.0 CD A:GLU104 2.6 23.6 1.0 CG A:ASP95 3.3 36.6 1.0 CG A:ASN97 3.4 57.4 1.0 C A:TYR99 3.5 28.6 1.0 CG A:ASP93 3.5 27.0 1.0 OD2 A:ASP95 3.7 36.6 1.0 CG A:GLU104 4.1 23.6 1.0 ND2 A:ASN97 4.2 57.4 1.0 CA A:ASP93 4.2 34.7 1.0 CA A:ILE100 4.3 36.6 1.0 N A:ASP95 4.3 15.8 1.0 N A:ILE100 4.3 36.6 1.0 OD2 A:ASP93 4.4 27.0 1.0 CB A:ASN97 4.4 31.1 1.0 CB A:ASP93 4.5 34.7 1.0 N A:LYS94 4.5 37.3 1.0 N A:SER101 4.5 20.8 1.0 N A:TYR99 4.5 28.6 1.0 C A:ASP93 4.5 34.7 1.0 CA A:TYR99 4.5 28.6 1.0 CB A:ASP95 4.6 15.8 1.0 N A:ASN97 4.6 31.1 1.0 CA A:ASP95 4.8 15.8 1.0 C A:ILE100 4.9 36.6 1.0 C A:ASP95 4.9 15.8 1.0 OG A:SER101 5.0 21.9 1.0

Calcium binding site 4 out of 8 in the Calmodulin Complexed with N-(3,3,-Diphenylpropyl)-N'-[1-R-(3,4-Bis- Butoxyphenyl)-Ethyl]-Propylenediamine (Dpd)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Calmodulin Complexed with N-(3,3,-Diphenylpropyl)-N'-[1-R-(3,4-Bis- Butoxyphenyl)-Ethyl]-Propylenediamine (Dpd) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca152 b:43.6 occ:1.00 OE2 A:GLU140 2.3 22.9 1.0 O A:GLN135 2.3 28.8 1.0 OD1 A:ASP133 2.3 43.2 1.0 OD2 A:ASP131 2.3 65.8 1.0 OD1 A:ASP129 2.3 47.2 1.0 OE1 A:GLU140 2.3 22.9 1.0 CD A:GLU140 2.6 22.9 1.0 CG A:ASP131 2.8 65.8 1.0 CG A:ASP133 2.8 43.2 1.0 OD1 A:ASP131 2.9 65.8 1.0 OD2 A:ASP133 3.0 43.2 1.0 CG A:ASP129 3.3 47.2 1.0 C A:GLN135 3.5 28.8 1.0 OD2 A:ASP129 3.9 47.2 1.0 N A:ASP133 4.0 46.7 1.0 N A:ASP131 4.0 53.0 1.0 N A:GLN135 4.0 28.8 1.0 CB A:ASP133 4.1 46.7 1.0 CB A:ASP131 4.1 53.0 1.0 CG A:GLU140 4.2 22.9 1.0 N A:ILE130 4.2 53.5 1.0 ND2 A:ASN137 4.2 28.8 1.0 CA A:ASP129 4.2 50.0 1.0 CB A:ASP129 4.3 50.0 1.0 CA A:GLN135 4.3 28.8 1.0 N A:GLY132 4.4 21.4 1.0 N A:VAL136 4.4 23.8 1.0 CA A:VAL136 4.5 23.8 1.0 CA A:ASP133 4.5 46.7 1.0 CA A:ASP131 4.5 53.0 1.0 N A:GLY134 4.5 27.2 1.0 N A:ASN137 4.6 31.7 1.0 C A:ASP131 4.6 53.0 1.0 C A:ASP129 4.7 50.0 1.0 C A:ASP133 4.8 46.7 1.0 CB A:GLN135 4.9 28.8 1.0 C A:GLY132 5.0 21.4 1.0

Calcium binding site 5 out of 8 in the Calmodulin Complexed with N-(3,3,-Diphenylpropyl)-N'-[1-R-(3,4-Bis- Butoxyphenyl)-Ethyl]-Propylenediamine (Dpd)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Calmodulin Complexed with N-(3,3,-Diphenylpropyl)-N'-[1-R-(3,4-Bis- Butoxyphenyl)-Ethyl]-Propylenediamine (Dpd) within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca149 b:27.9 occ:1.00 OD1 B:ASP22 2.2 51.0 1.0 OD1 B:ASP20 2.3 21.0 1.0 OE2 B:GLU31 2.3 15.5 1.0 O B:THR26 2.3 25.2 1.0 OE1 B:GLU31 2.3 15.5 1.0 OD1 B:ASP24 2.3 32.0 1.0 CD B:GLU31 2.6 15.5 1.0 CG B:ASP22 2.9 51.0 1.0 OD2 B:ASP22 3.0 51.0 1.0 CG B:ASP20 3.4 21.0 1.0 CG B:ASP24 3.5 32.0 1.0 C B:THR26 3.5 25.2 1.0 OD2 B:ASP24 3.9 32.0 1.0 CG B:GLU31 4.1 15.5 1.0 OG1 B:THR26 4.2 27.7 1.0 OD2 B:ASP20 4.2 21.0 1.0 CA B:ASP20 4.2 19.9 1.0 N B:THR26 4.3 25.2 1.0 CB B:ASP20 4.4 19.9 1.0 CB B:ASP22 4.4 21.3 1.0 N B:ASP24 4.4 11.0 1.0 N B:ASP22 4.4 21.3 1.0 N B:GLY23 4.4 16.8 1.0 N B:ILE27 4.4 20.9 1.0 CA B:ILE27 4.5 20.9 1.0 CA B:THR26 4.5 25.2 1.0 N B:LYS21 4.6 40.0 1.0 C B:ASP20 4.6 19.9 1.0 CG2 B:THR28 4.7 23.8 1.0 CB B:ASP24 4.7 11.0 1.0 CA B:ASP22 4.8 21.3 1.0 N B:THR28 4.8 21.9 1.0 N B:GLY25 4.9 29.3 1.0 CB B:THR26 5.0 25.2 1.0 CA B:ASP24 5.0 11.0 1.0

Calcium binding site 6 out of 8 in the Calmodulin Complexed with N-(3,3,-Diphenylpropyl)-N'-[1-R-(3,4-Bis- Butoxyphenyl)-Ethyl]-Propylenediamine (Dpd)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Calmodulin Complexed with N-(3,3,-Diphenylpropyl)-N'-[1-R-(3,4-Bis- Butoxyphenyl)-Ethyl]-Propylenediamine (Dpd) within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca150 b:23.1 occ:1.00 OD1 B:ASP56 2.3 17.6 1.0 OD1 B:ASP58 2.3 20.4 1.0 O B:THR62 2.3 28.6 1.0 OD1 B:ASN60 2.3 31.2 1.0 OE2 B:GLU67 2.3 23.4 1.0 OE1 B:GLU67 2.3 23.4 1.0 CD B:GLU67 2.7 23.4 1.0 CG B:ASP58 3.2 20.4 1.0 CG B:ASN60 3.4 31.2 1.0 C B:THR62 3.4 28.6 1.0 OD2 B:ASP58 3.5 20.4 1.0 CG B:ASP56 3.5 17.6 1.0 ND2 B:ASN60 3.8 31.2 1.0 CG B:GLU67 4.2 23.4 1.0 CA B:ASP56 4.2 34.7 1.0 OD2 B:ASP56 4.2 17.6 1.0 N B:ILE63 4.3 16.3 1.0 CA B:ILE63 4.3 16.3 1.0 N B:THR62 4.3 28.6 1.0 N B:ASN60 4.3 28.9 1.0 N B:ASP58 4.4 12.1 1.0 OG1 B:THR62 4.4 40.6 1.0 CB B:ASP56 4.4 34.7 1.0 CA B:THR62 4.4 28.6 1.0 N B:ALA57 4.6 33.0 1.0 CB B:ASP58 4.6 12.1 1.0 C B:ASP56 4.6 34.7 1.0 CB B:ASN60 4.6 28.9 1.0 N B:ASP64 4.7 23.2 1.0 N B:GLY59 4.7 31.2 1.0 C B:ILE63 4.9 16.3 1.0 CA B:ASP58 4.9 12.1 1.0 CA B:ASN60 4.9 28.9 1.0 OD1 B:ASP64 4.9 25.4 1.0 C B:ASP58 5.0 12.1 1.0

Calcium binding site 7 out of 8 in the Calmodulin Complexed with N-(3,3,-Diphenylpropyl)-N'-[1-R-(3,4-Bis- Butoxyphenyl)-Ethyl]-Propylenediamine (Dpd)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Calmodulin Complexed with N-(3,3,-Diphenylpropyl)-N'-[1-R-(3,4-Bis- Butoxyphenyl)-Ethyl]-Propylenediamine (Dpd) within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca151 b:50.7 occ:1.00 OD1 B:ASN97 2.2 58.9 1.0 OD1 B:ASP93 2.3 27.7 1.0 O B:TYR99 2.3 29.4 1.0 OE2 B:GLU104 2.3 21.6 1.0 OE1 B:GLU104 2.3 21.6 1.0 OD1 B:ASP95 2.3 53.9 1.0 CD B:GLU104 2.6 21.6 1.0 CG B:ASN97 3.2 58.9 1.0 ND2 B:ASN97 3.3 58.9 1.0 CG B:ASP95 3.4 53.9 1.0 CG B:ASP93 3.5 27.7 1.0 C B:TYR99 3.5 29.4 1.0 CA B:ASP93 3.9 32.2 1.0 OD2 B:ASP95 3.9 53.9 1.0 CG B:GLU104 4.0 21.6 1.0 C B:ASP93 4.2 32.2 1.0 CB B:ASP93 4.2 32.2 1.0 N B:ASP95 4.2 33.6 1.0 CA B:ILE100 4.2 20.2 1.0 N B:ILE100 4.3 20.2 1.0 N B:LYS94 4.3 64.8 1.0 OD2 B:ASP93 4.4 27.7 1.0 N B:TYR99 4.5 29.4 1.0 CB B:ASN97 4.5 33.5 1.0 N B:SER101 4.5 28.5 1.0 CA B:TYR99 4.5 29.4 1.0 N B:ASN97 4.6 33.5 1.0 CB B:ASP95 4.7 33.6 1.0 CA B:ASP95 4.8 33.6 1.0 O B:ASP93 4.8 32.2 1.0 C B:ASP95 4.8 33.6 1.0 C B:ILE100 4.8 20.2 1.0 CB B:GLU104 5.0 18.9 1.0

Calcium binding site 8 out of 8 in the Calmodulin Complexed with N-(3,3,-Diphenylpropyl)-N'-[1-R-(3,4-Bis- Butoxyphenyl)-Ethyl]-Propylenediamine (Dpd)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Calmodulin Complexed with N-(3,3,-Diphenylpropyl)-N'-[1-R-(3,4-Bis- Butoxyphenyl)-Ethyl]-Propylenediamine (Dpd) within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca152 b:44.7 occ:1.00 OE2 B:GLU140 2.3 22.4 1.0 OD1 B:ASP133 2.3 31.2 1.0 OD1 B:ASP129 2.3 50.6 1.0 O B:GLN135 2.3 45.3 1.0 OE1 B:GLU140 2.3 22.4 1.0 OD1 B:ASP131 2.3 44.1 1.0 CD B:GLU140 2.6 22.4 1.0 CG B:ASP133 2.7 31.2 1.0 OD2 B:ASP133 2.7 31.2 1.0 CG B:ASP131 3.0 44.1 1.0 OD2 B:ASP131 3.1 44.1 1.0 CG B:ASP129 3.4 50.6 1.0 C B:GLN135 3.5 45.3 1.0 ND2 B:ASN137 3.9 55.1 1.0 OD2 B:ASP129 4.0 50.6 1.0 CB B:ASP133 4.0 50.5 1.0 CG B:GLU140 4.1 22.4 1.0 N B:ASP133 4.1 50.5 1.0 N B:ASP131 4.1 40.7 1.0 N B:GLN135 4.2 45.3 1.0 N B:ILE130 4.2 42.0 1.0 CA B:ASP129 4.3 49.2 1.0 CB B:ASP131 4.3 40.7 1.0 CB B:ASP129 4.4 49.2 1.0 CA B:GLN135 4.4 45.3 1.0 N B:VAL136 4.4 40.9 1.0 CA B:VAL136 4.4 40.9 1.0 N B:ASN137 4.5 34.3 1.0 N B:GLY132 4.5 28.9 1.0 CA B:ASP133 4.5 50.5 1.0 CA B:ASP131 4.6 40.7 1.0 N B:GLY134 4.7 46.1 1.0 C B:ASP131 4.7 40.7 1.0 C B:ASP129 4.7 49.2 1.0 CG B:ASN137 4.8 55.1 1.0 C B:ASP133 4.9 50.5 1.0 CB B:GLN135 4.9 45.3 1.0 CE1 B:TYR99 5.0 56.0 1.0 CB B:GLU140 5.0 44.0 1.0

V.Harmat, Z.S.Bocskei, G.Naray-Szabo, I.Bata, A.S.Csutor, I.Hermecz, P.Aranyi, B.Szabo, K.Liliom, B.G.Vertessy, J.Ovadi. A New Potent Calmodulin Antagonist with Arylalkylamine Structure: Crystallographic, Spectroscopic and Functional Studies J.Mol.Biol. V. 297 747 2000.
ISSN: ISSN 0022-2836
PubMed: 10731425
DOI: 10.1006/JMBI.2000.3607