Calcium in PDB 1iq5: Calmodulin/Nematode CA2+/Calmodulin Dependent Kinase Kinase Fragment

The structure of Calmodulin/Nematode CA2+/Calmodulin Dependent Kinase Kinase Fragment, PDB code: 1iq5 was solved by H.Kurokawa, M.Osawa, H.Kurihara, N.Katayama, H.Tokumitsu, M.B.Swindells, M.Kainosho, M.Ikura, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	100.00 / 1.80
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	77.090, 84.400, 59.250, 90.00, 90.00, 90.00
R / Rfree (%)	21.7 / 24.8

The binding sites of Calcium atom in the Calmodulin/Nematode CA2+/Calmodulin Dependent Kinase Kinase Fragment (pdb code 1iq5). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Calmodulin/Nematode CA2+/Calmodulin Dependent Kinase Kinase Fragment, PDB code: 1iq5:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Calmodulin/Nematode CA2+/Calmodulin Dependent Kinase Kinase Fragment


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Calmodulin/Nematode CA2+/Calmodulin Dependent Kinase Kinase Fragment within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca361 b:6.8 occ:1.00 O A:THR26 2.4 17.0 1.0 OD1 A:ASP20 2.4 17.5 1.0 OD1 A:ASP22 2.5 17.4 1.0 OE2 A:GLU31 2.5 18.7 1.0 O A:HOH467 2.5 20.0 1.0 OD1 A:ASP24 2.5 20.3 1.0 OE1 A:GLU31 2.7 16.3 1.0 CD A:GLU31 2.9 17.1 1.0 CG A:ASP24 3.4 18.3 1.0 CG A:ASP22 3.5 19.5 1.0 C A:THR26 3.6 15.7 1.0 CG A:ASP20 3.6 18.2 1.0 OD2 A:ASP24 3.9 19.7 1.0 OG1 A:THR26 4.0 17.1 1.0 OD2 A:ASP22 4.1 20.0 1.0 N A:ASP24 4.1 17.8 1.0 CA A:ASP20 4.1 18.7 1.0 N A:THR26 4.2 14.7 1.0 N A:ASP22 4.3 20.5 1.0 CB A:ASP24 4.4 16.5 1.0 C A:ASP20 4.4 19.2 1.0 CG A:GLU31 4.4 16.2 1.0 CB A:ASP20 4.4 18.2 1.0 CA A:THR26 4.4 15.7 1.0 OD2 A:ASP20 4.5 16.3 1.0 N A:LYS21 4.5 20.9 1.0 N A:ILE27 4.5 14.5 1.0 CA A:ILE27 4.6 14.5 1.0 N A:GLY23 4.6 19.3 1.0 CA A:ASP24 4.7 17.5 1.0 CB A:ASP22 4.7 20.2 1.0 CG2 A:THR28 4.7 15.2 1.0 O A:HOH461 4.8 28.8 1.0 N A:GLY25 4.8 15.7 1.0 CB A:THR26 4.9 16.3 1.0 CA A:ASP22 4.9 20.5 1.0 N A:THR28 4.9 16.0 1.0 O A:HOH469 4.9 24.4 1.0 C A:ASP24 4.9 16.1 1.0 C A:ASP22 5.0 18.9 1.0 O A:ASP20 5.0 19.8 1.0

Calcium binding site 2 out of 4 in the Calmodulin/Nematode CA2+/Calmodulin Dependent Kinase Kinase Fragment


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Calmodulin/Nematode CA2+/Calmodulin Dependent Kinase Kinase Fragment within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca362 b:15.7 occ:1.00 OD1 A:ASP56 2.4 18.8 1.0 O A:THR62 2.5 14.8 1.0 OD1 A:ASN60 2.5 13.4 1.0 OD2 A:ASP58 2.5 17.1 1.0 O A:HOH492 2.5 19.6 1.0 OE2 A:GLU67 2.6 14.1 1.0 OE1 A:GLU67 2.6 15.5 1.0 CD A:GLU67 2.9 15.9 1.0 CG A:ASP58 3.3 17.6 1.0 CG A:ASN60 3.4 15.8 1.0 CG A:ASP56 3.5 18.7 1.0 OD1 A:ASP58 3.7 19.0 1.0 C A:THR62 3.7 16.5 1.0 O A:HOH502 3.9 24.0 1.0 ND2 A:ASN60 4.0 16.1 1.0 N A:ASN60 4.2 16.8 1.0 OD2 A:ASP56 4.2 18.1 1.0 N A:THR62 4.3 15.3 1.0 CA A:ASP56 4.4 18.2 1.0 CG A:GLU67 4.4 14.0 1.0 CB A:ASP56 4.4 18.4 1.0 N A:ASP58 4.4 16.6 1.0 CA A:ILE63 4.4 13.0 1.0 CB A:ASN60 4.5 15.8 1.0 N A:ILE63 4.5 14.0 1.0 CB A:ASP58 4.6 15.9 1.0 C A:ASP56 4.6 18.1 1.0 N A:ASP64 4.6 15.8 1.0 CA A:THR62 4.6 14.6 1.0 N A:GLY59 4.6 15.7 1.0 OG1 A:THR62 4.7 16.8 1.0 CA A:ASN60 4.8 14.9 1.0 N A:GLY61 4.8 13.9 1.0 OD2 A:ASP64 4.8 18.7 1.0 O A:HOH468 4.8 27.5 1.0 CA A:ASP58 4.8 16.2 1.0 N A:ALA57 4.9 17.5 1.0 C A:ASP58 4.9 16.9 1.0 CG A:ASP64 4.9 17.4 1.0 C A:ILE63 5.0 14.8 1.0

Calcium binding site 3 out of 4 in the Calmodulin/Nematode CA2+/Calmodulin Dependent Kinase Kinase Fragment


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Calmodulin/Nematode CA2+/Calmodulin Dependent Kinase Kinase Fragment within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca363 b:33.8 occ:1.00 O A:TYR99 2.4 31.7 1.0 OD1 A:ASP93 2.6 39.1 1.0 OE2 A:GLU104 2.6 35.7 1.0 OE1 A:GLU104 2.7 35.0 1.0 OD1 A:ASP95 2.7 47.2 1.0 OD1 A:ASN97 2.8 48.6 1.0 CD A:GLU104 3.0 34.5 1.0 CG A:ASP95 3.4 46.6 1.0 OD2 A:ASP95 3.5 46.8 1.0 CG A:ASN97 3.5 47.3 1.0 C A:TYR99 3.6 32.2 1.0 CG A:ASP93 3.7 39.8 1.0 N A:ASN97 4.1 43.0 1.0 ND2 A:ASN97 4.1 48.6 1.0 N A:TYR99 4.2 34.3 1.0 CA A:ASP93 4.3 39.2 1.0 CB A:ASN97 4.4 44.2 1.0 N A:GLY96 4.4 44.9 1.0 CA A:TYR99 4.5 33.7 1.0 CG A:GLU104 4.5 31.7 1.0 OD2 A:ASP93 4.5 39.9 1.0 CB A:ASP93 4.6 39.4 1.0 N A:ASP95 4.6 46.3 1.0 N A:ILE100 4.6 29.2 1.0 CA A:ILE100 4.7 25.2 1.0 CB A:ASP95 4.7 46.1 1.0 C A:ASP93 4.7 41.4 1.0 CA A:ASN97 4.7 42.3 1.0 N A:LYS94 4.7 43.1 1.0 N A:GLY98 4.8 36.8 1.0 N A:SER101 4.9 23.6 1.0 CB A:TYR99 5.0 37.2 1.0 CA A:ASP95 5.0 45.8 1.0

Calcium binding site 4 out of 4 in the Calmodulin/Nematode CA2+/Calmodulin Dependent Kinase Kinase Fragment


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Calmodulin/Nematode CA2+/Calmodulin Dependent Kinase Kinase Fragment within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca364 b:30.9 occ:1.00 O A:GLN135 2.5 33.4 1.0 OD1 A:ASP129 2.6 36.9 1.0 OD2 A:ASP133 2.6 42.3 1.0 OE2 A:GLU140 2.6 40.2 1.0 OD1 A:ASP131 2.6 41.3 1.0 OE1 A:GLU140 2.6 40.1 1.0 CD A:GLU140 3.0 40.0 1.0 CG A:ASP133 3.2 41.1 1.0 CG A:ASP131 3.3 40.1 1.0 OD1 A:ASP133 3.5 42.5 1.0 C A:GLN135 3.5 33.1 1.0 OD2 A:ASP131 3.5 39.5 1.0 CG A:ASP129 3.6 35.5 1.0 N A:GLN135 4.1 32.7 1.0 OD2 A:ASP129 4.2 35.3 1.0 CB A:ASP133 4.2 38.6 1.0 N A:VAL136 4.3 31.7 1.0 N A:ASP133 4.3 38.0 1.0 CA A:GLN135 4.3 33.9 1.0 CA A:VAL136 4.3 31.7 1.0 N A:ASP131 4.4 39.4 1.0 CA A:ASP129 4.4 34.2 1.0 CG A:GLU140 4.5 39.0 1.0 N A:ASN137 4.5 33.8 1.0 CB A:ASP129 4.5 34.4 1.0 CB A:ASP131 4.6 38.9 1.0 N A:ILE130 4.6 36.6 1.0 CB A:GLN135 4.7 36.2 1.0 CA A:ASP133 4.7 36.5 1.0 CA A:ASP131 4.8 39.9 1.0 C A:ASP129 4.8 35.4 1.0 N A:GLY134 4.9 33.6 1.0 C A:ASP131 4.9 40.5 1.0 OD1 A:ASN137 4.9 39.4 1.0 C A:VAL136 4.9 32.2 1.0 N A:GLY132 4.9 40.3 1.0 CG A:ASN137 4.9 36.9 1.0

H.Kurokawa, M.Osawa, H.Kurihara, N.Katayama, H.Tokumitsu, M.B.Swindells, M.Kainosho, M.Ikura. Target-Induced Conformational Adaptation of Calmodulin Revealed By the Crystal Structure of A Complex with Nematode Ca(2+)/Calmodulin-Dependent Kinase Kinase Peptide J.Mol.Biol. V. 312 59 2001.
ISSN: ISSN 0022-2836
PubMed: 11545585
DOI: 10.1006/JMBI.2001.4822