Calcium in PDB 1y6w: Trapped Intermediate of Calmodulin

The structure of Trapped Intermediate of Calmodulin, PDB code: 1y6w was solved by Z.Grabarek, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.88 / 2.40
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	109.875, 109.875, 42.640, 90.00, 90.00, 90.00
R / Rfree (%)	22 / 23.8

The binding sites of Calcium atom in the Trapped Intermediate of Calmodulin (pdb code 1y6w). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Trapped Intermediate of Calmodulin, PDB code: 1y6w:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Trapped Intermediate of Calmodulin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Trapped Intermediate of Calmodulin within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca149 b:42.4 occ:1.00 O A:THR26 2.3 30.4 1.0 OD1 A:ASP20 2.3 35.4 1.0 OD2 A:ASP24 2.4 38.9 1.0 OD1 A:ASP22 2.4 55.4 1.0 O A:HOH602 2.6 40.9 1.0 O A:HOH606 2.8 57.0 1.0 OD2 A:ASP22 3.0 54.9 1.0 CG A:ASP22 3.0 49.4 1.0 CG A:ASP24 3.4 38.0 1.0 CG A:ASP20 3.5 36.6 1.0 C A:THR26 3.5 30.0 1.0 O A:HOH639 3.6 59.8 1.0 OD1 A:ASP24 3.9 40.7 1.0 OG1 A:THR26 4.0 35.8 1.0 CA A:ASP20 4.0 38.3 1.0 N A:THR26 4.1 28.4 1.0 CB A:ASP20 4.2 36.5 1.0 N A:ASP24 4.3 33.5 1.0 CA A:THR26 4.4 29.5 1.0 OD2 A:ASP20 4.4 35.6 1.0 N A:ILE27 4.5 30.7 1.0 CB A:ASP24 4.5 33.6 1.0 C A:ASP20 4.5 40.8 1.0 CB A:ASP22 4.5 47.0 1.0 CA A:ILE27 4.6 31.7 1.0 N A:ASP22 4.7 44.2 1.0 N A:GLY23 4.7 38.4 1.0 CA A:ASP24 4.8 33.0 1.0 N A:GLY25 4.8 27.7 1.0 CB A:THR26 4.8 31.1 1.0 N A:LYS21 4.9 43.4 1.0 O A:ASP20 5.0 41.8 1.0 C A:ASP24 5.0 31.0 1.0

Calcium binding site 2 out of 4 in the Trapped Intermediate of Calmodulin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Trapped Intermediate of Calmodulin within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca150 b:43.8 occ:1.00 OD2 A:ASP56 2.2 39.5 1.0 O4 A:MPD400 2.4 41.6 1.0 OD1 A:ASN60 2.4 49.5 1.0 OD2 A:ASP58 2.5 53.6 1.0 O A:THR62 2.5 33.5 1.0 O2 A:MPD400 2.5 37.3 1.0 OD1 A:ASP56 2.6 44.6 1.0 OD1 A:ASP58 2.7 54.4 1.0 CG A:ASP56 2.7 46.9 1.0 CG A:ASP58 2.9 54.3 1.0 CG A:ASN60 3.4 48.9 1.0 C4 A:MPD400 3.5 41.0 1.0 C2 A:MPD400 3.6 41.6 1.0 C A:THR62 3.6 34.1 1.0 C3 A:MPD400 3.9 37.7 1.0 ND2 A:ASN60 3.9 46.0 1.0 O A:HOH660 4.1 53.3 1.0 OG1 A:THR62 4.1 36.2 1.0 C1 A:MPD400 4.2 37.3 1.0 CB A:ASP56 4.3 48.1 1.0 N A:THR62 4.3 38.2 1.0 OE2 A:GLU67 4.4 33.2 1.0 OE1 A:GLU67 4.4 42.3 1.0 C5 A:MPD400 4.4 38.4 1.0 N A:ASN60 4.5 50.0 1.0 CB A:ASP58 4.5 53.9 1.0 CA A:THR62 4.5 34.9 1.0 N A:ILE63 4.6 34.4 1.0 CA A:ILE63 4.6 32.4 1.0 CB A:ASN60 4.7 48.0 1.0 CM A:MPD400 4.8 39.2 1.0 O A:HOH641 4.8 56.4 1.0 CD A:GLU67 4.8 35.1 1.0 CA A:ASP56 4.9 52.1 1.0 CA A:ASN60 4.9 46.9 1.0 CB A:THR62 4.9 32.8 1.0

Calcium binding site 3 out of 4 in the Trapped Intermediate of Calmodulin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Trapped Intermediate of Calmodulin within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca151 b:48.6 occ:1.00 O A:TYR99 2.3 43.1 1.0 OD1 A:ASP93 2.3 58.8 1.0 OD2 A:ASP95 2.3 58.7 1.0 OD1 A:ASN97 2.4 43.9 1.0 OE2 A:GLU104 2.5 43.7 1.0 OE1 A:GLU104 2.6 44.8 1.0 O A:HOH611 2.7 37.3 1.0 CD A:GLU104 2.9 44.4 1.0 CG A:ASP95 3.3 59.0 1.0 CG A:ASN97 3.5 45.8 1.0 C A:TYR99 3.5 45.1 1.0 CG A:ASP93 3.5 58.5 1.0 OD1 A:ASP95 3.6 62.0 1.0 N A:TYR99 4.2 45.8 1.0 CA A:ASP93 4.2 57.3 1.0 N A:ASN97 4.2 49.5 1.0 ND2 A:ASN97 4.3 43.5 1.0 CA A:TYR99 4.4 45.1 1.0 N A:ASP95 4.4 58.2 1.0 CB A:ASP93 4.4 58.2 1.0 CG A:GLU104 4.4 47.0 1.0 C A:ASP93 4.4 57.5 1.0 OD2 A:ASP93 4.4 61.1 1.0 N A:ILE100 4.4 44.1 1.0 O A:HOH648 4.5 45.5 1.0 CB A:ASN97 4.5 46.7 1.0 CA A:ILE100 4.5 45.1 1.0 CB A:ASP95 4.6 57.2 1.0 O A:HOH631 4.6 43.3 1.0 N A:GLY96 4.6 54.8 1.0 N A:SER101 4.7 46.4 1.0 N A:LYS94 4.7 58.9 1.0 O A:ASP93 4.7 55.1 1.0 O A:HOH666 4.8 53.2 1.0 CB A:TYR99 4.8 45.4 1.0 CA A:ASN97 4.8 46.9 1.0 CA A:ASP95 4.8 57.7 1.0 N A:GLY98 4.9 44.8 1.0 C A:ASP95 4.9 56.2 1.0

Calcium binding site 4 out of 4 in the Trapped Intermediate of Calmodulin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Trapped Intermediate of Calmodulin within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca152 b:49.4 occ:1.00 OD1 A:ASP131 2.2 55.3 1.0 O A:GLN135 2.4 40.1 1.0 O A:HOH604 2.5 48.2 1.0 OD1 A:ASP129 2.5 68.4 1.0 OD1 A:ASP133 2.5 45.6 1.0 OE1 A:GLU140 2.6 59.1 1.0 OE2 A:GLU140 2.7 55.9 1.0 CD A:GLU140 3.0 58.5 1.0 CG A:ASP131 3.2 56.5 1.0 CG A:ASP133 3.3 46.8 1.0 C A:GLN135 3.4 42.4 1.0 OD2 A:ASP131 3.5 56.2 1.0 CG A:ASP129 3.6 69.1 1.0 OD2 A:ASP133 3.8 43.7 1.0 N A:ASP133 4.1 53.5 1.0 N A:GLN135 4.1 46.1 1.0 CA A:ASP129 4.2 72.5 1.0 N A:ASP131 4.2 62.0 1.0 N A:ILE130 4.3 70.3 1.0 N A:VAL136 4.3 41.0 1.0 CB A:ASP129 4.3 70.4 1.0 CB A:ASP133 4.3 48.4 1.0 CA A:GLN135 4.3 45.0 1.0 CA A:VAL136 4.4 41.6 1.0 N A:ASN137 4.4 43.4 1.0 CG A:GLU140 4.5 60.7 1.0 N A:GLY132 4.5 57.9 1.0 CB A:ASP131 4.5 57.3 1.0 OD2 A:ASP129 4.5 68.0 1.0 C A:ASP129 4.6 71.7 1.0 ND2 A:ASN137 4.6 46.4 1.0 CA A:ASP131 4.7 59.8 1.0 C A:ASP131 4.7 59.0 1.0 CA A:ASP133 4.7 50.8 1.0 N A:GLY134 4.8 49.0 1.0 CB A:GLN135 4.9 46.0 1.0 C A:VAL136 4.9 41.2 1.0 CG A:ASN137 4.9 48.1 1.0

Z.Grabarek, Z.Grabarek. N/A N/A.
ISSN: ISSN 0022-2836
PubMed: 15713486
DOI: 10.1016/J.JMB.2005.01.004