Calcium in PDB 5dsu: Crystal Structure of Double Mutant of N-Domain of Human Calmodulin

The structure of Crystal Structure of Double Mutant of N-Domain of Human Calmodulin, PDB code: 5dsu was solved by A.Ababou, M.Zaleska, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.99 / 1.93
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	38.400, 38.400, 81.200, 90.00, 90.00, 120.00
R / Rfree (%)	22.9 / 26.4

The binding sites of Calcium atom in the Crystal Structure of Double Mutant of N-Domain of Human Calmodulin (pdb code 5dsu). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Crystal Structure of Double Mutant of N-Domain of Human Calmodulin, PDB code: 5dsu:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Crystal Structure of Double Mutant of N-Domain of Human Calmodulin


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 Double Mutant of N-Domain of Human Calmodulin within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca101 b:32.6 occ:1.00 OD1 A:ASP20 2.2 30.0 1.0 O A:HOH211 2.3 33.0 1.0 OD1 A:ASP24 2.3 31.5 1.0 O A:THR26 2.3 28.7 1.0 OD1 A:ASP22 2.5 34.3 1.0 OE2 A:GLU31 2.7 26.0 1.0 OE1 A:GLU31 2.8 30.7 1.0 CD A:GLU31 3.1 30.1 1.0 CG A:ASP20 3.3 31.6 1.0 CG A:ASP22 3.4 33.1 1.0 CG A:ASP24 3.4 35.8 1.0 C A:THR26 3.5 28.5 1.0 OD2 A:ASP22 3.6 33.4 1.0 OD2 A:ASP20 4.0 32.1 1.0 N A:THR26 4.1 30.2 1.0 OD2 A:ASP24 4.1 34.1 1.0 N A:ASP24 4.1 36.1 1.0 O A:HOH216 4.3 35.2 1.0 CB A:ASP20 4.4 30.7 1.0 CA A:THR26 4.4 31.1 1.0 CA A:ASP20 4.4 29.4 1.0 CB A:ASP24 4.5 32.9 1.0 N A:ILE27 4.5 28.2 1.0 CA A:ILE27 4.6 26.1 1.0 OG1 A:THR26 4.6 35.5 1.0 N A:GLY25 4.6 31.7 1.0 CA A:ASP24 4.6 31.7 1.0 CG A:GLU31 4.6 26.6 1.0 N A:ASP22 4.7 37.2 1.0 N A:GLY23 4.7 36.0 1.0 CB A:ASP22 4.7 32.3 1.0 C A:ASP24 4.8 32.5 1.0 C A:ASP20 4.8 33.8 1.0 N A:LYS21 4.8 33.4 1.0 N A:THR28 4.9 23.5 1.0

Calcium binding site 2 out of 2 in the Crystal Structure of Double Mutant of N-Domain of Human Calmodulin


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 Double Mutant of N-Domain of Human Calmodulin within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca102 b:25.4 occ:1.00 OD1 A:ASP56 2.3 26.9 1.0 OD1 A:ASN60 2.3 27.6 1.0 O A:THR62 2.4 26.1 1.0 OD1 A:ASP58 2.5 28.0 1.0 OE1 A:GLU67 2.6 24.8 1.0 OE2 A:GLU67 2.6 23.3 1.0 O A:HOH237 2.7 31.6 1.0 CD A:GLU67 3.0 28.4 1.0 CG A:ASN60 3.3 28.6 1.0 CG A:ASP58 3.4 28.4 1.0 CG A:ASP56 3.5 28.2 1.0 C A:THR62 3.6 25.7 1.0 OD2 A:ASP58 3.8 29.4 1.0 ND2 A:ASN60 3.9 30.8 1.0 N A:ASN60 4.2 24.1 1.0 N A:THR62 4.2 26.8 1.0 OD2 A:ASP56 4.3 26.9 1.0 CA A:ASP56 4.4 26.9 1.0 CB A:ASN60 4.4 26.6 1.0 CB A:ASP56 4.4 25.4 1.0 N A:ASP58 4.4 25.6 1.0 N A:ASP64 4.4 26.7 1.0 CA A:ILE63 4.5 22.9 1.0 N A:ILE63 4.5 24.4 1.0 CG A:GLU67 4.5 24.3 1.0 CA A:THR62 4.5 25.2 1.0 C A:ASP56 4.6 29.6 1.0 N A:GLY61 4.6 25.6 1.0 CA A:ASN60 4.6 25.5 1.0 N A:ALA57 4.7 25.3 1.0 CB A:ASP58 4.7 28.2 1.0 N A:GLY59 4.7 25.7 1.0 O A:HOH250 4.7 34.2 1.0 OD2 A:ASP64 4.7 31.6 1.0 CG A:ASP64 4.7 29.2 1.0 C A:ILE63 4.9 27.6 1.0 C A:ASN60 4.9 28.1 1.0 CA A:ASP58 4.9 27.2 1.0 OD1 A:ASP64 4.9 30.3 1.0 OG1 A:THR62 4.9 29.1 1.0

A.Ababou, M.Zaleska, M.Pfuhl. On the Ca(2+) Binding and Conformational Change in Ef-Hand Domains: Experimental Evidence of Ca(2+)-Saturated Intermediates of N-Domain of Calmodulin. Biochim. Biophys. Acta V.1865 640 2017.
ISSN: ISSN 0006-3002
PubMed: 28288938
DOI: 10.1016/J.BBAPAP.2017.03.003