Calcium in PDB 1up5: Chicken Calmodulin

The structure of Chicken Calmodulin, PDB code: 1up5 was solved by M.A.Wilson, B.Rupp, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	15.00 / 1.90
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	59.696, 53.073, 24.572, 93.22, 96.86, 89.19
R / Rfree (%)	20.6 / 25.9

The binding sites of Calcium atom in the Chicken Calmodulin (pdb code 1up5). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 8 binding sites of Calcium where determined in the Chicken Calmodulin, PDB code: 1up5:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in the Chicken Calmodulin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Chicken Calmodulin within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca601 b:12.9 occ:1.00 OD1 A:ASP20 2.3 13.4 1.0 O A:THR26 2.3 10.4 1.0 OD1 A:ASP24 2.4 9.3 1.0 OE1 A:GLU31 2.5 11.1 1.0 OD1 A:ASP22 2.5 12.9 1.0 OE2 A:GLU31 2.5 9.5 1.0 CD A:GLU31 2.9 19.1 1.0 CG A:ASP24 3.3 8.2 1.0 CG A:ASP20 3.5 9.2 1.0 C A:THR26 3.5 11.6 1.0 CG A:ASP22 3.7 13.6 1.0 OD2 A:ASP24 3.9 14.8 1.0 CA A:ASP20 4.1 14.7 1.0 OG1 A:THR26 4.1 6.7 1.0 N A:THR26 4.2 12.7 1.0 N A:ASP24 4.3 14.3 1.0 OD2 A:ASP20 4.3 13.9 1.0 OD2 A:ASP22 4.3 19.5 1.0 CB A:ASP20 4.3 11.2 1.0 N A:ASP22 4.3 14.0 1.0 CA A:THR26 4.3 10.6 1.0 C A:ASP20 4.3 14.1 1.0 CB A:ASP24 4.3 18.5 1.0 N A:ILE27 4.4 16.3 1.0 CG A:GLU31 4.5 9.2 1.0 N A:LYS21 4.5 16.0 1.0 CA A:ILE27 4.5 16.3 1.0 O A:HOH2042 4.6 15.0 1.0 N A:GLY23 4.7 14.2 1.0 CB A:ASP22 4.8 21.5 1.0 CA A:ASP24 4.8 15.7 1.0 CA A:ASP22 4.8 16.2 1.0 CB A:THR26 4.9 9.7 1.0 N A:THR28 4.9 16.3 1.0 C A:ASP22 4.9 14.9 1.0 O A:ASP20 4.9 11.3 1.0 N A:GLY25 5.0 13.9 1.0 CG2 A:THR28 5.0 15.8 1.0

Calcium binding site 2 out of 8 in the Chicken Calmodulin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Chicken Calmodulin within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca602 b:12.9 occ:1.00 OD1 A:ASP56 2.2 14.8 1.0 OD1 A:ASP58 2.3 13.3 1.0 O A:THR62 2.3 8.6 1.0 OD1 A:ASN60 2.3 15.0 1.0 O A:HOH2073 2.3 10.5 1.0 OE1 A:GLU67 2.4 19.9 1.0 OE2 A:GLU67 2.6 10.4 1.0 CD A:GLU67 2.9 15.6 1.0 CG A:ASP58 3.2 15.0 1.0 CG A:ASN60 3.3 14.0 1.0 CG A:ASP56 3.5 13.8 1.0 OD2 A:ASP58 3.5 19.6 1.0 C A:THR62 3.6 12.2 1.0 O A:HOH2075 3.8 24.9 1.0 ND2 A:ASN60 3.9 16.3 1.0 N A:ASN60 4.1 13.1 1.0 OD2 A:ASP56 4.2 12.0 1.0 CA A:ILE63 4.3 14.4 1.0 CA A:ASP56 4.3 15.0 1.0 CB A:ASP56 4.3 13.2 1.0 N A:ASP58 4.3 18.9 1.0 N A:THR62 4.3 13.5 1.0 CG A:GLU67 4.4 16.0 1.0 N A:ILE63 4.4 8.0 1.0 CB A:ASN60 4.4 16.1 1.0 CB A:ASP58 4.4 18.6 1.0 C A:ASP56 4.5 14.2 1.0 CA A:THR62 4.6 12.8 1.0 N A:GLY59 4.6 18.0 1.0 N A:ASP64 4.6 11.5 1.0 N A:GLY61 4.7 12.4 1.0 CA A:ASN60 4.7 13.8 1.0 CA A:ASP58 4.7 19.4 1.0 OG1 A:THR62 4.7 12.1 1.0 N A:ALA57 4.7 19.7 1.0 C A:ASP58 4.9 20.7 1.0 C A:ASN60 4.9 12.8 1.0 C A:ILE63 5.0 15.7 1.0 O A:ASP56 5.0 14.1 1.0

Calcium binding site 3 out of 8 in the Chicken Calmodulin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Chicken Calmodulin within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca603 b:25.3 occ:1.00 OD1 A:ASP129 2.3 34.1 1.0 OD2 A:ASP131 2.3 32.2 1.0 OE1 A:GLU140 2.3 23.7 1.0 OD1 A:ASP133 2.3 22.7 1.0 OE2 A:GLU140 2.4 26.9 1.0 O A:GLN135 2.6 30.0 1.0 O A:HOH2121 2.6 29.3 1.0 CD A:GLU140 2.7 21.7 1.0 CG A:ASP133 3.1 29.9 1.0 CG A:ASP131 3.3 40.5 1.0 OD2 A:ASP133 3.5 32.9 1.0 CG A:ASP129 3.5 29.9 1.0 C A:GLN135 3.7 28.9 1.0 OD1 A:ASP131 3.8 41.4 1.0 CA A:ASP129 4.1 22.8 1.0 N A:ASP133 4.2 32.1 1.0 CG A:GLU140 4.2 24.6 1.0 OD2 A:ASP129 4.3 27.1 1.0 CB A:ASP133 4.3 35.7 1.0 N A:ASN137 4.3 22.3 1.0 CB A:ASP129 4.4 21.6 1.0 N A:ASP131 4.4 33.1 1.0 N A:GLN135 4.4 31.9 1.0 CA A:VAL136 4.4 24.8 1.0 C A:ASP129 4.5 22.9 1.0 N A:VAL136 4.5 24.1 1.0 CB A:ASP131 4.5 35.0 1.0 N A:GLY132 4.6 33.7 1.0 N A:ILE130 4.6 28.1 1.0 CA A:GLN135 4.6 30.2 1.0 CA A:ASP133 4.7 35.3 1.0 CG A:ASN137 4.7 28.5 1.0 CA A:ASP131 4.8 35.1 1.0 ND2 A:ASN137 4.8 37.9 1.0 C A:ASP131 4.8 33.9 1.0 C A:VAL136 4.9 25.9 1.0 CB A:ASN137 5.0 26.7 1.0

Calcium binding site 4 out of 8 in the Chicken Calmodulin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Chicken Calmodulin within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca604 b:30.2 occ:1.00 O A:HOH2102 2.0 35.5 1.0 OD1 A:ASP93 2.3 25.4 1.0 O A:TYR99 2.3 28.4 1.0 OE1 A:GLU104 2.4 20.0 1.0 OD1 A:ASN97 2.4 37.2 1.0 OE2 A:GLU104 2.6 23.8 1.0 OD1 A:ASP95 2.6 32.8 1.0 CD A:GLU104 2.8 24.4 1.0 CG A:ASN97 3.4 30.2 1.0 CG A:ASP93 3.4 33.0 1.0 CG A:ASP95 3.5 36.9 1.0 C A:TYR99 3.5 28.3 1.0 OD2 A:ASP95 3.7 44.2 1.0 ND2 A:ASN97 3.9 29.4 1.0 N A:TYR99 4.2 26.1 1.0 CB A:ASP93 4.2 31.6 1.0 CA A:ASP93 4.2 29.1 1.0 OD2 A:ASP93 4.2 31.1 1.0 CG A:GLU104 4.3 21.1 1.0 N A:ASN97 4.3 33.5 1.0 CA A:TYR99 4.3 27.8 1.0 C A:ASP93 4.4 30.2 1.0 N A:GLY96 4.4 36.9 1.0 N A:ASP95 4.4 31.2 1.0 N A:ILE100 4.5 24.2 1.0 CB A:ASN97 4.5 31.7 1.0 CA A:ILE100 4.5 18.1 1.0 N A:LYS94 4.6 27.7 1.0 N A:SER101 4.6 21.5 1.0 CB A:ASP95 4.7 32.4 1.0 CB A:TYR99 4.7 25.2 1.0 OE1 A:GLN135 4.8 52.5 1.0 O A:ASP93 4.8 29.6 1.0 CA A:ASN97 4.8 32.1 1.0 C A:ASP95 4.9 33.3 1.0 CA A:ASP95 4.9 33.5 1.0 C A:ILE100 5.0 18.8 1.0

Calcium binding site 5 out of 8 in the Chicken Calmodulin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Chicken Calmodulin within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca605 b:28.1 occ:1.00 O B:HOH2080 2.2 33.1 1.0 OD1 B:ASP93 2.3 26.4 1.0 O B:TYR99 2.4 31.5 1.0 ND2 B:ASN97 2.4 33.1 1.0 OD1 B:ASP95 2.5 36.4 1.0 OE2 B:GLU104 2.6 29.2 1.0 OE1 B:GLU104 2.6 23.1 1.0 CD B:GLU104 3.0 26.8 1.0 CG B:ASP95 3.2 35.3 1.0 OD2 B:ASP95 3.4 44.4 1.0 CG B:ASP93 3.5 32.2 1.0 CG B:ASN97 3.5 42.1 1.0 C B:TYR99 3.5 27.9 1.0 OD1 B:ASN97 4.0 47.1 1.0 OD2 B:ASP93 4.2 40.5 1.0 N B:TYR99 4.4 28.3 1.0 N B:ASN97 4.4 40.6 1.0 CA B:ILE100 4.4 23.4 1.0 N B:ILE100 4.4 26.6 1.0 N B:SER101 4.4 22.6 1.0 CG B:GLU104 4.4 21.2 1.0 CA B:TYR99 4.4 27.8 1.0 CB B:ASP93 4.5 31.4 1.0 CA B:ASP93 4.5 31.2 1.0 CB B:ASP95 4.6 38.5 1.0 OE1 B:GLN135 4.6 51.0 1.0 N B:ASP95 4.6 33.4 1.0 CB B:ASN97 4.6 37.5 1.0 C B:ASP93 4.7 32.9 1.0 N B:LYS94 4.8 35.6 1.0 C B:ILE100 4.8 26.3 1.0 CB B:TYR99 4.8 26.7 1.0 N B:GLY96 4.8 37.9 1.0 CA B:ASN97 4.9 38.3 1.0 CA B:ASP95 4.9 36.8 1.0 C B:ASP95 5.0 38.7 1.0

Calcium binding site 6 out of 8 in the Chicken Calmodulin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Chicken Calmodulin within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca606 b:38.7 occ:1.00 OD1 B:ASP133 2.3 48.0 1.0 OE2 B:GLU140 2.3 32.0 1.0 OD1 B:ASP129 2.3 34.9 1.0 OD1 B:ASP131 2.3 42.3 1.0 OE1 B:GLU140 2.4 19.9 1.0 O B:GLN135 2.5 30.9 1.0 CD B:GLU140 2.7 24.4 1.0 CG B:ASP131 3.1 39.4 1.0 OD2 B:ASP131 3.3 50.5 1.0 CG B:ASP129 3.4 35.2 1.0 CG B:ASP133 3.4 48.9 1.0 C B:GLN135 3.6 30.7 1.0 N B:ASP133 4.0 46.8 1.0 CB B:ASP133 4.1 48.5 1.0 CA B:ASP129 4.1 29.4 1.0 OD2 B:ASP129 4.2 36.7 1.0 CG B:GLU140 4.2 24.1 1.0 N B:GLN135 4.2 35.8 1.0 CB B:ASP129 4.2 30.1 1.0 OD2 B:ASP133 4.4 49.5 1.0 N B:ASP131 4.4 38.8 1.0 CB B:ASP131 4.5 43.4 1.0 CA B:ASP133 4.5 47.6 1.0 CA B:GLN135 4.5 35.5 1.0 N B:VAL136 4.5 25.8 1.0 C B:ASP129 4.5 32.8 1.0 CA B:VAL136 4.5 23.3 1.0 N B:GLY132 4.6 47.9 1.0 N B:ASN137 4.6 25.9 1.0 C B:ASP131 4.6 46.8 1.0 ND2 B:ASN137 4.7 45.7 1.0 CA B:ASP131 4.7 42.3 1.0 C B:ASP133 4.7 47.8 1.0 N B:ILE130 4.8 32.5 1.0 N B:GLY134 4.8 45.0 1.0 CG B:ASN137 5.0 35.2 1.0 CB B:GLN135 5.0 39.1 1.0

Calcium binding site 7 out of 8 in the Chicken Calmodulin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Chicken Calmodulin within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca607 b:14.7 occ:1.00 OD1 B:ASP56 2.3 14.6 1.0 O B:THR62 2.3 11.8 1.0 OD1 B:ASN60 2.3 12.4 1.0 O B:HOH2067 2.4 10.2 1.0 OE1 B:GLU67 2.4 17.8 1.0 OD1 B:ASP58 2.5 16.2 1.0 OE2 B:GLU67 2.6 15.7 1.0 CD B:GLU67 2.8 14.8 1.0 CG B:ASN60 3.4 18.0 1.0 CG B:ASP56 3.4 14.0 1.0 CG B:ASP58 3.5 14.9 1.0 C B:THR62 3.6 12.1 1.0 OD2 B:ASP58 3.7 16.5 1.0 N B:ASN60 4.1 16.3 1.0 ND2 B:ASN60 4.2 13.6 1.0 OD2 B:ASP56 4.2 12.9 1.0 N B:THR62 4.2 14.4 1.0 O B:HOH2066 4.2 15.8 1.0 CA B:ILE63 4.3 17.7 1.0 CA B:ASP56 4.3 17.6 1.0 CG B:GLU67 4.3 13.4 1.0 CB B:ASP56 4.4 17.5 1.0 N B:ASP58 4.4 22.1 1.0 N B:ILE63 4.4 8.5 1.0 CB B:ASN60 4.4 17.0 1.0 N B:GLY59 4.5 21.4 1.0 CA B:THR62 4.5 15.2 1.0 C B:ASP56 4.5 16.7 1.0 N B:GLY61 4.6 10.9 1.0 OD2 B:ASP64 4.6 10.2 1.0 CA B:ASN60 4.6 14.8 1.0 CB B:ASP58 4.7 20.0 1.0 OG1 B:THR62 4.7 17.7 1.0 N B:ASP64 4.7 14.4 1.0 N B:ALA57 4.8 18.4 1.0 CA B:ASP58 4.9 22.4 1.0 O B:HOH2070 4.9 22.7 1.0 C B:ASN60 4.9 13.7 1.0 C B:ASP58 4.9 22.0 1.0 O B:ASP56 5.0 17.8 1.0

Calcium binding site 8 out of 8 in the Chicken Calmodulin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Chicken Calmodulin within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca608 b:12.9 occ:1.00 OE1 B:GLU31 2.3 10.5 1.0 OD1 B:ASP20 2.3 11.3 1.0 O B:THR26 2.4 10.3 1.0 OE2 B:GLU31 2.4 13.1 1.0 OD1 B:ASP22 2.5 11.0 1.0 OD1 B:ASP24 2.6 11.6 1.0 CD B:GLU31 2.7 12.2 1.0 CG B:ASP20 3.5 7.9 1.0 CG B:ASP24 3.5 13.0 1.0 C B:THR26 3.5 10.2 1.0 CG B:ASP22 3.6 18.5 1.0 CA B:ASP20 4.1 11.7 1.0 OD2 B:ASP24 4.1 17.6 1.0 OG1 B:THR26 4.2 12.5 1.0 N B:ASP24 4.2 14.4 1.0 OD2 B:ASP22 4.2 24.2 1.0 N B:ASP22 4.3 13.9 1.0 OD2 B:ASP20 4.3 10.2 1.0 CG B:GLU31 4.3 9.1 1.0 N B:THR26 4.3 10.5 1.0 CB B:ASP20 4.3 12.2 1.0 C B:ASP20 4.3 12.4 1.0 N B:LYS21 4.4 15.2 1.0 N B:ILE27 4.5 9.9 1.0 CA B:THR26 4.5 12.1 1.0 CB B:ASP24 4.5 15.4 1.0 CA B:ILE27 4.5 10.4 1.0 N B:GLY23 4.6 12.3 1.0 CB B:ASP22 4.6 14.4 1.0 CA B:ASP22 4.7 13.9 1.0 CA B:ASP24 4.8 16.2 1.0 O B:HOH2035 4.8 14.5 1.0 C B:ASP22 4.8 14.3 1.0 O B:ASP20 4.9 13.0 1.0 N B:GLY25 4.9 15.5 1.0 CG2 B:THR28 5.0 16.9 1.0 N B:THR28 5.0 13.8 1.0 CB B:THR26 5.0 12.4 1.0

B.Rupp, D.Marshak, S.Parkin. Crystallization and Preliminary X-Ray Analysis of Two New Crystal Forms of Calmodulin Acta Crystallogr.,Sect.D V. 52 411 1996.
ISSN: ISSN 0907-4449
PubMed: 15299715
DOI: 10.1107/S0907444995011826