Calcium in PDB 7pu9: Crystal Structure of Cam in Complex with Cdz (Form 2)

The structure of Crystal Structure of Cam in Complex with Cdz (Form 2), PDB code: 7pu9 was solved by A.E.Mechaly, C.Leger, A.Haouz, A.Chenal, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	56.15 / 2.28
Space group	P 61 2 2
Cell size a, b, c (Å), α, β, γ (°)	39.351, 39.351, 336.92, 90, 90, 120
R / Rfree (%)	23.4 / 26.6

The structure of Crystal Structure of Cam in Complex with Cdz (Form 2) also contains other interesting chemical elements:

Chlorine

(Cl)

12 atoms

The binding sites of Calcium atom in the Crystal Structure of Cam in Complex with Cdz (Form 2) (pdb code 7pu9). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Crystal Structure of Cam in Complex with Cdz (Form 2), PDB code: 7pu9:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Crystal Structure of Cam in Complex with Cdz (Form 2)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of Cam in Complex with Cdz (Form 2) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca203 b:46.1 occ:1.00 OD1 A:ASP131 2.4 53.0 1.0 O A:HOH312 2.4 40.7 1.0 O A:GLN135 2.4 45.0 1.0 OD1 A:ASP133 2.5 48.0 1.0 OD1 A:ASP129 2.5 51.8 1.0 OE1 A:GLU140 2.6 45.3 1.0 OE2 A:GLU140 2.7 44.7 1.0 CD A:GLU140 3.0 45.0 1.0 CG A:ASP133 3.2 48.8 1.0 CG A:ASP131 3.2 52.3 1.0 C A:GLN135 3.5 44.6 1.0 OD2 A:ASP131 3.5 55.2 1.0 OD2 A:ASP133 3.6 51.7 1.0 CG A:ASP129 3.6 51.2 1.0 N A:ASP133 4.1 45.6 1.0 N A:GLN135 4.1 45.2 1.0 N A:ASP131 4.3 45.6 1.0 CB A:ASP133 4.3 46.1 1.0 N A:VAL136 4.4 43.9 1.0 CA A:GLN135 4.4 44.3 1.0 N A:GLY132 4.4 45.1 1.0 OD2 A:ASP129 4.4 52.3 1.0 CA A:ASP129 4.4 46.4 1.0 CB A:ASP129 4.4 47.4 1.0 CA A:VAL136 4.4 43.2 1.0 N A:ILE130 4.4 46.2 1.0 N A:ASN137 4.5 43.8 1.0 CG A:GLU140 4.5 44.0 1.0 CB A:ASP131 4.5 46.5 1.0 CA A:ASP133 4.6 45.7 1.0 N A:GLY134 4.7 46.3 1.0 CA A:ASP131 4.7 45.1 1.0 C A:ASP133 4.8 46.3 1.0 CB A:GLN135 4.9 45.1 1.0 C A:ASP129 4.9 46.3 1.0 C A:ASP131 4.9 45.4 1.0 C A:VAL136 4.9 43.6 1.0 ND2 A:ASN137 5.0 45.3 1.0

Calcium binding site 2 out of 4 in the Crystal Structure of Cam in Complex with Cdz (Form 2)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of Cam in Complex with Cdz (Form 2) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca204 b:53.6 occ:1.00 OD1 A:ASP93 2.2 54.8 1.0 O A:TYR99 2.2 47.7 1.0 OD1 A:ASP95 2.3 64.4 1.0 OD1 A:ASN97 2.4 46.7 1.0 OE2 A:GLU104 2.5 60.3 1.0 OE1 A:GLU104 2.5 59.5 1.0 CD A:GLU104 2.8 58.0 1.0 O A:HOH338 3.3 64.0 1.0 CG A:ASN97 3.4 47.7 1.0 C A:TYR99 3.4 46.7 1.0 CG A:ASP95 3.4 62.8 1.0 CG A:ASP93 3.4 54.2 1.0 OD2 A:ASP95 3.9 64.5 1.0 ND2 A:ASN97 4.0 47.8 1.0 N A:TYR99 4.1 45.5 1.0 CA A:ASP93 4.2 53.2 1.0 N A:ASN97 4.2 49.2 1.0 OD2 A:ASP93 4.2 54.3 1.0 CA A:TYR99 4.3 45.7 1.0 CG A:GLU104 4.3 55.4 1.0 N A:ASP95 4.3 57.0 1.0 CB A:ASP93 4.4 52.6 1.0 N A:ILE100 4.4 46.4 1.0 C A:ASP93 4.4 55.2 1.0 CA A:ILE100 4.5 46.8 1.0 CB A:ASN97 4.5 47.4 1.0 N A:GLY96 4.6 53.2 1.0 CB A:ASP95 4.6 57.7 1.0 N A:LYS94 4.6 56.7 1.0 CB A:TYR99 4.7 45.6 1.0 N A:SER101 4.7 46.9 1.0 CA A:ASN97 4.8 48.0 1.0 CA A:ASP95 4.8 56.2 1.0 C A:ASP95 4.9 55.2 1.0 N A:GLY98 4.9 46.5 1.0 O A:ASP93 4.9 55.2 1.0

Calcium binding site 3 out of 4 in the Crystal Structure of Cam in Complex with Cdz (Form 2)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of Cam in Complex with Cdz (Form 2) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca205 b:55.0 occ:1.00 OD1 A:ASP56 2.2 62.6 1.0 OD1 A:ASN60 2.4 65.8 1.0 OE1 A:GLU67 2.4 52.9 1.0 OD1 A:ASP58 2.4 71.3 1.0 O A:THR62 2.4 53.7 1.0 OE2 A:GLU67 2.4 51.0 1.0 CD A:GLU67 2.7 52.2 1.0 CG A:ASN60 3.2 65.6 1.0 CG A:ASP56 3.3 63.4 1.0 CG A:ASP58 3.5 72.0 1.0 ND2 A:ASN60 3.5 65.9 1.0 C A:THR62 3.6 53.9 1.0 OD2 A:ASP58 3.9 74.3 1.0 OD2 A:ASP56 4.0 64.9 1.0 CG A:GLU67 4.3 50.2 1.0 CB A:ASP56 4.3 63.5 1.0 N A:THR62 4.3 56.5 1.0 CA A:ASP56 4.4 64.2 1.0 CA A:ILE63 4.4 51.8 1.0 CB A:ASN60 4.5 64.5 1.0 N A:ILE63 4.5 52.6 1.0 N A:ASP64 4.5 53.1 1.0 CA A:THR62 4.6 55.0 1.0 OG1 A:THR62 4.6 58.2 1.0 N A:ASP58 4.6 68.1 1.0 O A:ASP58 4.6 70.7 1.0 OD2 A:ASP64 4.7 65.4 1.0 N A:ASN60 4.7 65.8 1.0 C A:ASP56 4.8 65.6 1.0 CB A:ASP58 4.8 69.8 1.0 CG A:ASP64 4.8 61.9 1.0 N A:ALA57 4.9 66.3 1.0 C A:ILE63 4.9 52.5 1.0 C A:ASP58 4.9 70.0 1.0 OD1 A:ASP64 4.9 62.6 1.0 CA A:ASN60 5.0 64.1 1.0 N A:GLY61 5.0 60.5 1.0 CA A:ASP58 5.0 69.0 1.0

Calcium binding site 4 out of 4 in the Crystal Structure of Cam in Complex with Cdz (Form 2)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of Cam in Complex with Cdz (Form 2) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca206 b:52.5 occ:1.00 OD1 A:ASP20 2.2 55.4 1.0 OE2 A:GLU31 2.3 51.6 1.0 OD1 A:ASP22 2.4 59.1 1.0 OD1 A:ASP24 2.4 63.3 1.0 O A:THR26 2.4 52.6 1.0 OE1 A:GLU31 2.5 53.4 1.0 CD A:GLU31 2.7 51.4 1.0 CG A:ASP22 3.3 60.5 1.0 CG A:ASP24 3.3 62.6 1.0 CG A:ASP20 3.4 55.5 1.0 OD2 A:ASP22 3.6 64.0 1.0 C A:THR26 3.6 51.9 1.0 OD2 A:ASP24 3.8 65.1 1.0 N A:ASP24 4.1 58.3 1.0 CA A:ASP20 4.1 51.8 1.0 CG A:GLU31 4.2 48.0 1.0 OD2 A:ASP20 4.2 56.4 1.0 CB A:ASP20 4.3 52.3 1.0 N A:ASP22 4.3 57.9 1.0 N A:THR26 4.3 54.1 1.0 CB A:ASP24 4.4 58.4 1.0 OG1 A:THR26 4.4 58.7 1.0 C A:ASP20 4.4 53.7 1.0 N A:ILE27 4.5 50.1 1.0 CB A:ASP22 4.5 58.5 1.0 CA A:THR26 4.5 53.7 1.0 N A:GLY23 4.5 58.2 1.0 N A:LYS21 4.6 55.3 1.0 CA A:ILE27 4.6 48.8 1.0 CA A:ASP24 4.7 57.8 1.0 CG2 A:THR28 4.7 49.0 1.0 CA A:ASP22 4.8 57.8 1.0 N A:GLY25 4.8 56.1 1.0 C A:ASP22 4.9 58.3 1.0 O A:HOH306 4.9 50.9 1.0 N A:THR28 4.9 48.7 1.0 O A:ASP20 4.9 53.6 1.0

C.Leger, I.Pitard, M.Sadi, N.Carvalho, S.Brier, A.Mechaly, D.Raoux-Barbot, M.Davi, S.Hoos, P.Weber, P.Vachette, D.Durand, A.Haouz, J.I.Guijarro, D.Ladant, A.Chenal. Dynamics and Structural Changes of Calmodulin Upon Interaction with the Antagonist Calmidazolium. Bmc Biol. V. 20 176 2022.
ISSN: ESSN 1741-7007
PubMed: 35945584
DOI: 10.1186/S12915-022-01381-5