Calcium in PDB 1cdm: Modulation of Calmodulin Plasticity in Molecular Recognition on the Basis of X-Ray Structures

The structure of Modulation of Calmodulin Plasticity in Molecular Recognition on the Basis of X-Ray Structures, PDB code: 1cdm was solved by W.E.Meador, F.A.Quiocho, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	10.00 / 2.00
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	39.000, 75.200, 120.150, 90.00, 90.00, 90.00
R / Rfree (%)	20.8 / n/a

The binding sites of Calcium atom in the Modulation of Calmodulin Plasticity in Molecular Recognition on the Basis of X-Ray Structures (pdb code 1cdm). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Modulation of Calmodulin Plasticity in Molecular Recognition on the Basis of X-Ray Structures, PDB code: 1cdm:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Modulation of Calmodulin Plasticity in Molecular Recognition on the Basis of X-Ray Structures


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Modulation of Calmodulin Plasticity in Molecular Recognition on the Basis of X-Ray Structures within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1 b:23.9 occ:1.00 O A:THR26 1.9 26.9 1.0 OD2 A:ASP22 2.2 36.8 1.0 OE1 A:GLU31 2.3 21.7 1.0 OD1 A:ASP24 2.4 45.8 1.0 O A:HOH186 2.4 34.5 1.0 OD2 A:ASP20 2.4 26.7 1.0 OE2 A:GLU31 2.7 25.3 1.0 CD A:GLU31 2.8 23.5 1.0 CG A:ASP22 3.1 39.3 1.0 C A:THR26 3.1 26.4 1.0 CG A:ASP24 3.3 37.1 1.0 OD1 A:ASP22 3.4 42.3 1.0 CG A:ASP20 3.6 27.4 1.0 OG1 A:THR26 3.7 32.6 1.0 OD2 A:ASP24 3.8 38.4 1.0 CA A:THR26 4.1 27.2 1.0 N A:THR26 4.1 29.4 1.0 N A:ILE27 4.1 24.1 1.0 N A:ASP24 4.3 43.8 1.0 CG A:GLU31 4.3 21.5 1.0 CA A:ASP20 4.3 21.0 1.0 CA A:ILE27 4.3 24.1 1.0 N A:ASP22 4.4 34.6 1.0 OD1 A:ASP20 4.4 25.8 1.0 CB A:THR26 4.4 30.7 1.0 CB A:ASP24 4.5 40.3 1.0 CB A:ASP22 4.5 37.9 1.0 CB A:ASP20 4.5 22.5 1.0 C A:ASP20 4.5 23.6 1.0 N A:GLY23 4.6 38.7 1.0 N A:THR28 4.7 24.6 1.0 CG2 A:THR28 4.8 17.5 1.0 O A:ASP20 4.8 26.2 1.0 N A:LYS21 4.8 26.4 1.0 O A:HOH170 4.8 36.7 1.0 CA A:ASP22 4.8 38.4 1.0 CA A:ASP24 4.8 40.0 1.0 C A:ILE27 5.0 23.0 1.0

Calcium binding site 2 out of 4 in the Modulation of Calmodulin Plasticity in Molecular Recognition on the Basis of X-Ray Structures


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Modulation of Calmodulin Plasticity in Molecular Recognition on the Basis of X-Ray Structures within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca2 b:32.0 occ:1.00 O A:HOH189 1.7 40.2 1.0 OD1 A:ASN60 1.7 37.4 1.0 OD1 A:ASP56 2.3 35.2 1.0 O A:THR62 2.3 28.6 1.0 OE1 A:GLU67 2.4 37.2 1.0 OD1 A:ASP58 2.5 42.8 1.0 OE2 A:GLU67 2.5 36.3 1.0 CG A:ASN60 2.8 40.4 1.0 CD A:GLU67 2.8 35.2 1.0 ND2 A:ASN60 3.4 38.6 1.0 CG A:ASP56 3.5 42.0 1.0 C A:THR62 3.5 28.6 1.0 CG A:ASP58 3.5 40.2 1.0 OD2 A:ASP58 3.9 40.2 1.0 CB A:ASN60 4.0 39.4 1.0 N A:ASN60 4.2 41.5 1.0 OD2 A:ASP56 4.2 40.8 1.0 N A:THR62 4.2 35.0 1.0 CG A:GLU67 4.3 34.1 1.0 OG1 A:THR62 4.4 33.7 1.0 N A:ILE63 4.4 28.4 1.0 CA A:ILE63 4.4 28.8 1.0 CA A:THR62 4.5 28.9 1.0 OD2 A:ASP64 4.5 39.0 1.0 CA A:ASN60 4.6 37.8 1.0 CB A:ASP56 4.6 42.6 1.0 N A:ASP64 4.6 25.6 1.0 O A:HOH152 4.6 40.1 1.0 CA A:ASP56 4.7 45.0 1.0 N A:ASP58 4.7 39.8 1.0 N A:GLY61 4.8 35.8 1.0 CB A:ASP58 4.8 38.9 1.0 CG A:ASP64 4.8 26.8 1.0 C A:ASN60 4.9 36.2 1.0 C A:ILE63 4.9 29.1 1.0 N A:GLY59 5.0 41.5 1.0

Calcium binding site 3 out of 4 in the Modulation of Calmodulin Plasticity in Molecular Recognition on the Basis of X-Ray Structures


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Modulation of Calmodulin Plasticity in Molecular Recognition on the Basis of X-Ray Structures within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca3 b:21.0 occ:1.00 OE1 A:GLU104 2.2 19.6 1.0 OD1 A:ASN97 2.3 20.8 1.0 OD2 A:ASP93 2.3 18.7 1.0 O A:TYR99 2.3 21.4 1.0 OE2 A:GLU104 2.4 21.6 1.0 OD1 A:ASP95 2.4 27.5 1.0 O A:HOH158 2.5 21.6 1.0 CD A:GLU104 2.6 19.8 1.0 CG A:ASP95 3.3 24.9 1.0 CG A:ASN97 3.4 22.0 1.0 CG A:ASP93 3.5 18.7 1.0 C A:TYR99 3.6 16.3 1.0 OD2 A:ASP95 3.7 28.9 1.0 ND2 A:ASN97 4.0 24.5 1.0 CG A:GLU104 4.1 16.1 1.0 CA A:ASP93 4.2 16.5 1.0 N A:ASN97 4.3 21.8 1.0 N A:ASP95 4.3 25.4 1.0 N A:TYR99 4.3 12.2 1.0 OD1 A:ASP93 4.4 19.9 1.0 O A:HOH159 4.4 16.9 1.0 CB A:ASP93 4.4 12.8 1.0 CB A:ASN97 4.5 22.5 1.0 N A:ILE100 4.5 16.7 1.0 CA A:TYR99 4.5 12.9 1.0 CA A:ILE100 4.5 16.6 1.0 C A:ASP93 4.5 16.7 1.0 CB A:ASP95 4.5 23.2 1.0 N A:GLY96 4.6 18.4 1.0 N A:LYS94 4.7 19.8 1.0 CA A:ASP95 4.7 23.5 1.0 O A:HOH191 4.8 48.3 1.0 CA A:ASN97 4.8 18.8 1.0 N A:SER101 4.8 23.5 1.0 C A:ASP95 4.8 23.9 1.0 O A:ASP93 4.9 15.0 1.0 CB A:TYR99 4.9 12.1 1.0 OG A:SER101 5.0 20.6 1.0 CB A:GLU104 5.0 19.6 1.0

Calcium binding site 4 out of 4 in the Modulation of Calmodulin Plasticity in Molecular Recognition on the Basis of X-Ray Structures


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Modulation of Calmodulin Plasticity in Molecular Recognition on the Basis of X-Ray Structures within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca148 b:21.9 occ:1.00 O A:GLN135 2.1 14.3 1.0 OD2 A:ASP133 2.3 19.5 1.0 O A:HOH179 2.4 41.4 1.0 OE2 A:GLU140 2.4 19.8 1.0 OD1 A:ASP129 2.5 18.1 1.0 OD2 A:ASP131 2.6 23.3 1.0 OE1 A:GLU140 2.8 19.6 1.0 CD A:GLU140 3.0 18.0 1.0 CG A:ASP133 3.2 15.4 1.0 C A:GLN135 3.3 15.4 1.0 CG A:ASP129 3.5 15.8 1.0 CG A:ASP131 3.6 19.4 1.0 OD1 A:ASP133 3.6 19.6 1.0 OD1 A:ASP131 4.0 25.4 1.0 N A:GLN135 4.1 12.8 1.0 N A:ASP133 4.1 18.8 1.0 N A:VAL136 4.2 20.6 1.0 CA A:VAL136 4.3 21.0 1.0 CA A:ASP129 4.3 16.6 1.0 OD2 A:ASP129 4.3 14.6 1.0 CA A:GLN135 4.3 15.8 1.0 CB A:ASP129 4.3 16.9 1.0 CB A:ASP133 4.3 18.3 1.0 N A:ASP131 4.5 23.0 1.0 CG A:GLU140 4.5 17.3 1.0 N A:ASN137 4.5 20.1 1.0 N A:GLY132 4.5 17.0 1.0 N A:ILE130 4.5 17.0 1.0 N A:GLY134 4.6 14.7 1.0 CA A:ASP133 4.7 14.4 1.0 C A:ASP129 4.8 18.8 1.0 CB A:ASP131 4.8 21.9 1.0 C A:VAL136 4.9 18.9 1.0 CB A:GLN135 4.9 20.4 1.0 CA A:ASP131 5.0 19.8 1.0 C A:ASP133 5.0 16.7 1.0

W.E.Meador, A.R.Means, F.A.Quiocho. Modulation of Calmodulin Plasticity in Molecular Recognition on the Basis of X-Ray Structures. Science V. 262 1718 1993.
ISSN: ISSN 0036-8075
PubMed: 8259515