Calcium in PDB 3ifk: Crystal Structure of Calcium-Saturated Calmodulin N-Terminal Domain Fragment, Residues 1-90

The structure of Crystal Structure of Calcium-Saturated Calmodulin N-Terminal Domain Fragment, Residues 1-90, PDB code: 3ifk was solved by T.J.Witt, R.A.Newman, M.A.Shea, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	67.12 / 2.03
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	55.285, 58.851, 67.115, 90.00, 90.00, 90.00
R / Rfree (%)	23.7 / 29.3

The binding sites of Calcium atom in the Crystal Structure of Calcium-Saturated Calmodulin N-Terminal Domain Fragment, Residues 1-90 (pdb code 3ifk). 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 Calcium-Saturated Calmodulin N-Terminal Domain Fragment, Residues 1-90, PDB code: 3ifk:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Crystal Structure of Calcium-Saturated Calmodulin N-Terminal Domain Fragment, Residues 1-90


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 Calcium-Saturated Calmodulin N-Terminal Domain Fragment, Residues 1-90 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca91 b:30.0 occ:1.00 OD2 A:ASP24 2.1 30.9 1.0 OD2 A:ASP20 2.2 27.0 1.0 OE2 A:GLU31 2.3 28.9 1.0 O A:THR26 2.3 25.8 1.0 OE1 A:GLU31 2.3 35.2 1.0 OD1 A:ASP22 2.4 41.4 1.0 CD A:GLU31 2.6 29.1 1.0 CG A:ASP24 3.2 35.8 1.0 CG A:ASP20 3.4 27.4 1.0 CG A:ASP22 3.4 38.3 1.0 C A:THR26 3.4 25.5 1.0 OG1 A:THR26 3.7 30.6 1.0 OD2 A:ASP22 3.7 40.9 1.0 OD1 A:ASP24 3.9 34.1 1.0 CA A:ASP20 3.9 28.9 1.0 N A:THR26 4.0 25.1 1.0 CB A:ASP20 4.0 26.9 1.0 CG A:GLU31 4.0 24.6 1.0 N A:ASP24 4.2 34.1 1.0 C A:ASP20 4.2 30.2 1.0 CB A:ASP24 4.2 33.5 1.0 CA A:THR26 4.2 26.0 1.0 OD1 A:ASP20 4.3 30.5 1.0 N A:LYS21 4.4 33.1 1.0 N A:ILE27 4.4 25.2 1.0 N A:ASP22 4.4 37.1 1.0 CA A:ILE27 4.5 23.9 1.0 CB A:THR26 4.6 26.4 1.0 O A:HOH101 4.6 36.0 1.0 CA A:ASP24 4.6 33.6 1.0 N A:GLY25 4.6 29.8 1.0 CB A:ASP22 4.7 37.7 1.0 N A:GLY23 4.7 36.6 1.0 C A:ASP24 4.8 32.8 1.0 O A:ASP20 4.8 30.2 1.0 N A:THR28 4.9 25.9 1.0 CB A:GLU31 4.9 23.9 1.0 CA A:ASP22 4.9 37.5 1.0 C A:ASP22 4.9 37.9 1.0 O A:PHE19 5.0 28.2 1.0 CB A:THR28 5.0 27.8 1.0

Calcium binding site 2 out of 4 in the Crystal Structure of Calcium-Saturated Calmodulin N-Terminal Domain Fragment, Residues 1-90


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 Calcium-Saturated Calmodulin N-Terminal Domain Fragment, Residues 1-90 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca92 b:26.9 occ:1.00 OD2 A:ASP56 2.1 34.3 1.0 O A:THR62 2.3 21.4 1.0 OE2 A:GLU67 2.3 22.1 1.0 OE1 A:GLU67 2.3 18.4 1.0 OD2 A:ASP58 2.3 30.6 1.0 OD1 A:ASN60 2.5 33.8 1.0 CD A:GLU67 2.6 19.3 1.0 CG A:ASP58 3.2 29.9 1.0 CG A:ASN60 3.3 31.2 1.0 CG A:ASP56 3.3 32.3 1.0 C A:THR62 3.5 23.7 1.0 O A:HOH96 3.5 38.0 1.0 OD1 A:ASP58 3.7 32.0 1.0 ND2 A:ASN60 3.8 31.3 1.0 OD1 A:ASP56 4.1 32.6 1.0 CG A:GLU67 4.1 18.8 1.0 N A:THR62 4.1 28.2 1.0 N A:ASN60 4.2 32.4 1.0 CA A:ASP56 4.2 29.9 1.0 CA A:ILE63 4.2 20.7 1.0 N A:ASP58 4.3 31.6 1.0 CB A:ASP56 4.3 31.4 1.0 N A:ASP64 4.3 19.6 1.0 OG1 A:THR62 4.3 30.0 1.0 N A:ILE63 4.4 21.9 1.0 CB A:ASN60 4.4 32.2 1.0 OD1 A:ASP64 4.4 27.3 1.0 CB A:ASP58 4.4 31.9 1.0 CA A:THR62 4.4 26.4 1.0 CG A:ASP64 4.5 24.2 1.0 C A:ASP56 4.5 30.7 1.0 N A:GLY59 4.6 32.6 1.0 CA A:ASN60 4.7 31.5 1.0 CA A:ASP58 4.7 32.1 1.0 N A:GLY61 4.7 30.9 1.0 OD2 A:ASP64 4.7 29.3 1.0 N A:ALA57 4.8 30.1 1.0 C A:ILE63 4.8 19.9 1.0 C A:ASP58 4.8 33.0 1.0 C A:ASN60 4.9 31.4 1.0 O A:HOH94 4.9 21.9 1.0 CB A:GLU67 4.9 15.3 1.0

Calcium binding site 3 out of 4 in the Crystal Structure of Calcium-Saturated Calmodulin N-Terminal Domain Fragment, Residues 1-90


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 Calcium-Saturated Calmodulin N-Terminal Domain Fragment, Residues 1-90 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca91 b:30.9 occ:1.00 OD2 B:ASP24 2.2 40.2 1.0 OD2 B:ASP20 2.2 24.2 1.0 O B:THR26 2.2 28.7 1.0 O B:HOH115 2.3 42.5 1.0 OE1 B:GLU31 2.4 28.8 1.0 OE2 B:GLU31 2.4 27.6 1.0 OD1 B:ASP22 2.5 42.5 1.0 CD B:GLU31 2.7 29.0 1.0 CG B:ASP24 3.2 37.4 1.0 CG B:ASP20 3.3 24.8 1.0 C B:THR26 3.4 27.5 1.0 CG B:ASP22 3.4 38.1 1.0 OD2 B:ASP22 3.6 42.2 1.0 OD1 B:ASP24 3.7 38.9 1.0 OG1 B:THR26 3.8 31.2 1.0 CA B:ASP20 3.8 28.6 1.0 CB B:ASP20 4.0 26.2 1.0 N B:THR26 4.1 27.9 1.0 N B:ASP24 4.1 34.0 1.0 CG B:GLU31 4.2 28.6 1.0 CA B:THR26 4.2 28.6 1.0 CA B:ILE27 4.3 25.9 1.0 C B:ASP20 4.3 30.4 1.0 OD1 B:ASP20 4.3 25.5 1.0 CB B:ASP24 4.3 33.2 1.0 N B:ILE27 4.3 25.4 1.0 O B:HOH111 4.5 36.6 1.0 N B:THR28 4.5 26.6 1.0 N B:ASP22 4.6 36.4 1.0 N B:LYS21 4.6 32.5 1.0 CG2 B:THR28 4.6 28.5 1.0 CA B:ASP24 4.6 33.0 1.0 CB B:THR26 4.6 28.4 1.0 CB B:ASP22 4.7 37.4 1.0 N B:GLY25 4.7 29.6 1.0 N B:GLY23 4.8 36.7 1.0 C B:ILE27 4.8 25.5 1.0 O B:ASP20 4.9 31.9 1.0 C B:ASP24 4.9 31.5 1.0 CB B:GLU31 5.0 28.8 1.0 CA B:ASP22 5.0 36.9 1.0

Calcium binding site 4 out of 4 in the Crystal Structure of Calcium-Saturated Calmodulin N-Terminal Domain Fragment, Residues 1-90


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 Calcium-Saturated Calmodulin N-Terminal Domain Fragment, Residues 1-90 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca92 b:24.0 occ:1.00 O B:THR62 2.2 24.7 1.0 OD2 B:ASP56 2.2 26.5 1.0 OE1 B:GLU67 2.4 19.4 1.0 O B:HOH103 2.4 28.9 1.0 OD1 B:ASN60 2.4 25.6 1.0 OD2 B:ASP58 2.5 33.1 1.0 OE2 B:GLU67 2.5 22.0 1.0 CD B:GLU67 2.8 16.5 1.0 CG B:ASN60 3.3 29.0 1.0 CG B:ASP56 3.4 29.2 1.0 CG B:ASP58 3.4 31.5 1.0 C B:THR62 3.4 25.1 1.0 OD1 B:ASP58 3.7 31.9 1.0 ND2 B:ASN60 3.8 27.1 1.0 N B:ASN60 4.1 30.9 1.0 CA B:ILE63 4.1 22.4 1.0 N B:THR62 4.1 27.6 1.0 CA B:ASP56 4.2 26.6 1.0 N B:ASP64 4.2 19.1 1.0 OD1 B:ASP56 4.2 30.9 1.0 CG B:GLU67 4.2 17.2 1.0 CB B:ASP56 4.3 27.0 1.0 N B:ILE63 4.3 24.2 1.0 CB B:ASN60 4.4 31.1 1.0 OG1 B:THR62 4.4 27.2 1.0 CA B:THR62 4.4 27.2 1.0 N B:ASP58 4.4 31.0 1.0 OD1 B:ASP64 4.4 34.5 1.0 CG B:ASP64 4.5 27.8 1.0 C B:ASP56 4.5 28.0 1.0 OD2 B:ASP64 4.6 31.8 1.0 CA B:ASN60 4.6 30.8 1.0 C B:ILE63 4.6 21.1 1.0 N B:ALA57 4.7 27.9 1.0 CB B:ASP58 4.7 31.8 1.0 N B:GLY61 4.7 29.0 1.0 N B:GLY59 4.8 32.9 1.0 C B:ASN60 4.8 30.7 1.0 O B:HOH94 4.8 22.7 1.0 C B:ASP58 4.9 32.7 1.0 CA B:ASP58 4.9 32.3 1.0 CB B:GLU67 5.0 14.0 1.0 CB B:ASP64 5.0 21.1 1.0

S.E.O'donnell, R.A.Newman, T.J.Witt, R.Hultman, J.R.Froehlig, A.P.Christensen, M.A.Shea. Thermodynamics and Conformational Change Governing Domain-Domain Interactions of Calmodulin. Methods Enzymol. V. 466 503 2009.
ISSN: ISSN 0076-6879
PubMed: 21609874
DOI: 10.1016/S0076-6879(09)66021-3