Calcium in PDB 1yr5: 1.7-A Structure of Calmodulin Bound to A Peptide From Dap Kinase

All present enzymatic activity of 1.7-A Structure of Calmodulin Bound to A Peptide From Dap Kinase:
2.7.1.37;

The structure of 1.7-A Structure of Calmodulin Bound to A Peptide From Dap Kinase, PDB code: 1yr5 was solved by P.Kursula, J.Vahokoski, M.Wilmanns, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 1.70
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	66.070, 33.710, 75.890, 90.00, 111.16, 90.00
R / Rfree (%)	20 / 25.7

The binding sites of Calcium atom in the 1.7-A Structure of Calmodulin Bound to A Peptide From Dap Kinase (pdb code 1yr5). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the 1.7-A Structure of Calmodulin Bound to A Peptide From Dap Kinase, PDB code: 1yr5:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the 1.7-A Structure of Calmodulin Bound to A Peptide From Dap Kinase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of 1.7-A Structure of Calmodulin Bound to A Peptide From Dap Kinase within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca151 b:7.9 occ:1.00 OD1 A:ASP24 2.3 10.9 1.0 O A:HOH5011 2.3 9.9 1.0 O A:THR26 2.3 7.6 1.0 OD2 A:ASP20 2.4 5.0 1.0 OE1 A:GLU31 2.4 5.6 1.0 OE2 A:GLU31 2.5 4.1 1.0 OD2 A:ASP22 2.5 8.0 1.0 CD A:GLU31 2.8 3.2 1.0 CG A:ASP24 3.3 11.8 1.0 CG A:ASP22 3.4 11.4 1.0 CG A:ASP20 3.5 5.3 1.0 C A:THR26 3.6 8.1 1.0 OD1 A:ASP22 3.7 14.1 1.0 OD2 A:ASP24 3.9 14.3 1.0 CA A:ASP20 4.1 5.1 1.0 O A:HOH5048 4.2 12.2 1.0 CB A:ASP20 4.2 3.5 1.0 N A:THR26 4.3 7.2 1.0 CG A:GLU31 4.3 3.7 1.0 N A:ASP24 4.3 11.4 1.0 OG1 A:THR26 4.3 16.4 1.0 OD1 A:ASP20 4.4 4.7 1.0 CB A:ASP24 4.5 12.5 1.0 CA A:THR26 4.5 8.2 1.0 N A:ASP22 4.5 10.3 1.0 C A:ASP20 4.5 5.4 1.0 N A:ILE27 4.5 6.8 1.0 CA A:ILE27 4.6 3.0 1.0 CB A:ASP22 4.7 11.2 1.0 O A:HOH5033 4.7 2.0 1.0 N A:GLY23 4.7 8.9 1.0 CG2 A:THR28 4.7 7.8 1.0 N A:LYS21 4.8 8.3 1.0 CA A:ASP24 4.8 12.1 1.0 N A:THR28 4.8 5.5 1.0 CA A:ASP22 4.9 10.0 1.0 N A:GLY25 5.0 9.4 1.0 C A:ASP22 5.0 10.2 1.0 O A:ASP20 5.0 7.5 1.0

Calcium binding site 2 out of 4 in the 1.7-A Structure of Calmodulin Bound to A Peptide From Dap Kinase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of 1.7-A Structure of Calmodulin Bound to A Peptide From Dap Kinase within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca152 b:7.2 occ:1.00 O A:HOH5012 2.3 5.9 1.0 OE2 A:GLU67 2.3 7.4 1.0 OD1 A:ASN60 2.3 9.1 1.0 OD1 A:ASP56 2.4 10.7 1.0 O A:THR62 2.4 6.3 1.0 OD1 A:ASP58 2.6 9.4 1.0 OE1 A:GLU67 2.6 5.1 1.0 CD A:GLU67 2.8 3.9 1.0 CG A:ASN60 3.4 13.3 1.0 CG A:ASP58 3.5 12.7 1.0 C A:THR62 3.5 7.1 1.0 CG A:ASP56 3.5 9.0 1.0 OD2 A:ASP58 3.9 6.6 1.0 ND2 A:ASN60 4.0 7.5 1.0 N A:ASN60 4.2 10.9 1.0 N A:THR62 4.3 6.6 1.0 CG A:GLU67 4.3 5.1 1.0 N A:ASP64 4.3 8.7 1.0 OD2 A:ASP56 4.3 12.6 1.0 CA A:ILE63 4.4 8.3 1.0 N A:ILE63 4.4 7.3 1.0 O A:HOH5057 4.4 11.4 1.0 CA A:ASP56 4.4 5.6 1.0 CB A:ASP56 4.5 5.0 1.0 CB A:ASN60 4.5 13.0 1.0 N A:ASP58 4.5 14.3 1.0 CA A:THR62 4.5 6.3 1.0 OG1 A:THR62 4.6 9.6 1.0 C A:ASP56 4.6 9.1 1.0 N A:GLY61 4.7 11.7 1.0 CA A:ASN60 4.7 11.1 1.0 CB A:ASP58 4.7 11.7 1.0 C A:ILE63 4.7 8.7 1.0 CG A:ASP64 4.8 7.6 1.0 N A:GLY59 4.8 13.6 1.0 OD1 A:ASP64 4.8 11.3 1.0 N A:ALA57 4.9 9.2 1.0 OD2 A:ASP64 4.9 10.0 1.0 CA A:ASP58 4.9 13.5 1.0 C A:ASN60 4.9 11.9 1.0 C A:ASP58 4.9 13.1 1.0 O A:HOH5034 5.0 7.5 1.0

Calcium binding site 3 out of 4 in the 1.7-A Structure of Calmodulin Bound to A Peptide From Dap Kinase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of 1.7-A Structure of Calmodulin Bound to A Peptide From Dap Kinase within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca153 b:6.5 occ:1.00 OD2 A:ASP93 2.3 11.1 1.0 O A:TYR99 2.3 7.7 0.5 O A:TYR99 2.3 7.7 0.5 OD1 A:ASN97 2.3 7.6 1.0 O A:HOH5013 2.3 7.0 1.0 OD1 A:ASP95 2.3 6.7 1.0 OE1 A:GLU104 2.5 6.8 1.0 OE2 A:GLU104 2.5 5.8 1.0 CD A:GLU104 2.8 5.3 1.0 CG A:ASN97 3.3 4.4 1.0 CG A:ASP95 3.4 8.9 1.0 C A:TYR99 3.4 7.5 0.5 C A:TYR99 3.4 7.4 0.5 CG A:ASP93 3.4 10.8 1.0 OD2 A:ASP95 4.0 10.2 1.0 ND2 A:ASN97 4.1 7.1 1.0 N A:TYR99 4.1 7.5 0.5 N A:TYR99 4.2 7.4 0.5 N A:ASN97 4.2 6.4 1.0 OD1 A:ASP93 4.2 7.3 1.0 CA A:ASP93 4.2 8.4 1.0 CG A:GLU104 4.3 2.5 1.0 N A:ASP95 4.3 7.0 1.0 CB A:ASN97 4.3 5.9 1.0 CA A:TYR99 4.3 7.6 0.5 CA A:TYR99 4.3 7.5 0.5 N A:ILE100 4.3 6.9 1.0 CB A:ASP93 4.3 9.1 1.0 C A:ASP93 4.4 8.5 1.0 CA A:ILE100 4.4 6.3 1.0 CB A:ASP95 4.5 6.5 1.0 N A:LYS94 4.6 9.4 1.0 N A:GLY96 4.6 5.7 1.0 CA A:ASN97 4.6 5.9 1.0 N A:SER101 4.6 6.7 1.0 CA A:ASP95 4.7 7.1 1.0 CB A:TYR99 4.7 7.8 0.5 N A:GLY98 4.8 6.1 1.0 CB A:TYR99 4.8 7.6 0.5 O A:ASP93 4.8 8.7 1.0 C A:ASP95 4.8 6.4 1.0 C A:ASN97 5.0 5.9 1.0 C A:ILE100 5.0 6.5 1.0

Calcium binding site 4 out of 4 in the 1.7-A Structure of Calmodulin Bound to A Peptide From Dap Kinase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of 1.7-A Structure of Calmodulin Bound to A Peptide From Dap Kinase within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca154 b:8.1 occ:1.00 OD1 A:ASP129 2.3 9.1 1.0 OD2 A:ASP131 2.3 5.8 1.0 OD2 A:ASP133 2.3 9.6 1.0 O A:HOH5014 2.3 8.8 1.0 O A:GLN135 2.3 9.4 1.0 OE2 A:GLU140 2.5 13.4 1.0 OE1 A:GLU140 2.7 10.1 1.0 CD A:GLU140 3.0 9.6 1.0 CG A:ASP131 3.2 5.6 1.0 CG A:ASP133 3.3 6.3 1.0 CG A:ASP129 3.4 9.7 1.0 C A:GLN135 3.5 10.5 1.0 OD1 A:ASP131 3.5 7.8 1.0 OD1 A:ASP133 3.7 5.4 1.0 N A:GLN135 4.2 8.8 1.0 CA A:ASP129 4.2 9.0 1.0 CB A:ASP129 4.2 7.8 1.0 OD2 A:ASP129 4.2 6.8 1.0 N A:ASP133 4.2 3.4 1.0 N A:VAL136 4.3 10.2 1.0 N A:ASP131 4.3 3.4 1.0 CA A:VAL136 4.3 8.8 1.0 CA A:GLN135 4.4 10.2 1.0 N A:GLY132 4.4 3.2 1.0 N A:ASN137 4.4 6.5 1.0 CB A:ASP131 4.4 3.1 1.0 CG A:GLU140 4.5 8.7 1.0 CB A:ASP133 4.5 4.8 1.0 C A:ASP129 4.6 8.8 1.0 N A:ILE130 4.6 7.9 1.0 CA A:ASP131 4.7 3.4 1.0 N A:GLY134 4.7 5.3 1.0 CA A:ASP133 4.7 4.6 1.0 C A:ASP131 4.8 3.4 1.0 C A:VAL136 4.9 7.3 1.0 CB A:GLN135 4.9 11.4 1.0 C A:ASP133 5.0 5.0 1.0

P.Kursula, J.Vahokoski, M.Wilmanns. Recognition of Human Death-Associated Protein Kinases By Calmodulin To Be Published.