Calcium in PDB 5e1k: Selenomethionine CA2+-Calmodulin From Paramecium Tetraurelia Sad Data

The structure of Selenomethionine CA2+-Calmodulin From Paramecium Tetraurelia Sad Data, PDB code: 5e1k was solved by J.Lin, H.Van Den Bedem, A.T.Brunger, M.A.Wilson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	25.00 / 1.00
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	25.036, 29.410, 52.794, 89.45, 86.29, 82.39
R / Rfree (%)	14.3 / 16.5

The binding sites of Calcium atom in the Selenomethionine CA2+-Calmodulin From Paramecium Tetraurelia Sad Data (pdb code 5e1k). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 5 binding sites of Calcium where determined in the Selenomethionine CA2+-Calmodulin From Paramecium Tetraurelia Sad Data, PDB code: 5e1k:
Jump to Calcium binding site number: 1; 2; 3; 4; 5;

Calcium binding site 1 out of 5 in the Selenomethionine CA2+-Calmodulin From Paramecium Tetraurelia Sad Data


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Selenomethionine CA2+-Calmodulin From Paramecium Tetraurelia Sad Data within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca201 b:8.5 occ:1.00 OD1 A:ASP20 2.3 9.0 1.0 OD1 A:ASP24 2.3 9.0 1.0 O A:HOH420 2.3 12.5 1.0 O A:THR26 2.3 9.0 1.0 OD1 A:ASP22 2.4 10.5 1.0 OE1 A:GLU31 2.5 10.1 1.0 OE2 A:GLU31 2.5 11.8 1.0 CD A:GLU31 2.8 10.1 1.0 CG A:ASP24 3.3 9.0 1.0 CG A:ASP20 3.4 8.5 1.0 C A:THR26 3.5 7.9 1.0 CG A:ASP22 3.5 11.4 1.0 OG1 A:THR26 3.9 11.5 1.0 OD2 A:ASP24 4.0 10.6 1.0 CA A:ASP20 4.1 8.8 1.0 OD2 A:ASP22 4.1 16.1 1.0 N A:ASP24 4.1 9.3 1.0 N A:THR26 4.2 7.8 1.0 CB A:ASP20 4.2 9.4 1.0 OD2 A:ASP20 4.3 10.1 1.0 CB A:ASP24 4.3 9.3 1.0 CG A:GLU31 4.3 10.6 1.0 N A:ASP22 4.3 11.3 1.0 CA A:THR26 4.3 8.4 1.0 C A:ASP20 4.4 9.7 1.0 N A:ILE27 4.5 8.1 1.0 O A:HOH378 4.5 12.6 0.6 N A:LYS21 4.5 11.1 0.6 N A:GLY23 4.6 9.9 1.0 CA A:ILE27 4.6 8.3 1.0 CA A:ASP24 4.6 9.1 1.0 CB A:ASP22 4.6 12.5 1.0 N A:LYS21 4.7 10.9 0.4 CB A:THR26 4.7 9.3 1.0 CA A:ASP22 4.8 11.2 1.0 O A:HOH374 4.8 32.2 1.0 C A:ASP22 4.8 11.0 1.0 N A:GLY25 4.9 8.6 1.0 O A:ASP20 4.9 12.2 1.0 C A:ASP24 4.9 8.7 1.0 N A:THR28 5.0 9.0 1.0

Calcium binding site 2 out of 5 in the Selenomethionine CA2+-Calmodulin From Paramecium Tetraurelia Sad Data


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Selenomethionine CA2+-Calmodulin From Paramecium Tetraurelia Sad Data within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca202 b:10.3 occ:1.00 OD1 A:ASP56 2.3 13.6 0.5 OD1 A:ASP56 2.4 10.1 0.5 O A:THR62 2.4 9.6 1.0 O A:HOH339 2.4 11.0 1.0 OD1 A:ASN60 2.4 10.6 1.0 OD1 A:ASP58 2.4 10.5 1.0 OE1 A:GLU67 2.5 9.8 1.0 OE2 A:GLU67 2.6 10.7 1.0 O A:HOH344 2.8 14.3 1.0 CD A:GLU67 2.9 9.7 1.0 CG A:ASN60 3.3 10.0 1.0 CG A:ASP56 3.4 11.0 0.5 CG A:ASP58 3.4 11.0 1.0 CG A:ASP56 3.5 13.7 0.5 C A:THR62 3.6 8.9 1.0 ND2 A:ASN60 3.8 11.7 1.0 OD2 A:ASP58 3.9 11.7 1.0 OD2 A:ASP56 4.2 11.5 0.5 CB A:ASP56 4.2 12.7 0.5 CA A:ASP56 4.3 12.0 0.5 OD2 A:ASP56 4.3 15.4 0.5 N A:THR62 4.3 10.1 1.0 N A:ASN60 4.4 13.6 1.0 CA A:ILE63 4.4 8.1 0.4 CA A:ILE63 4.4 8.3 0.6 N A:ASP58 4.4 13.3 1.0 N A:ILE63 4.4 7.1 0.4 N A:ILE63 4.4 9.3 0.6 CG A:GLU67 4.4 10.3 1.0 CB A:ASP56 4.4 15.5 0.5 N A:ASP64 4.5 8.4 1.0 OG1 A:THR62 4.5 9.7 1.0 CA A:ASP56 4.5 14.8 0.5 CB A:ASN60 4.5 16.1 1.0 CA A:THR62 4.5 9.2 1.0 C A:ASP56 4.6 13.4 0.5 CB A:ASP58 4.7 13.5 1.0 C A:ASP56 4.7 12.2 0.5 OD2 A:ASP64 4.7 13.6 1.0 N A:ALA57 4.7 12.9 1.0 N A:GLY59 4.7 14.6 1.0 CG A:ASP64 4.8 11.2 1.0 C A:ILE63 4.8 7.8 0.6 O A:HOH371 4.8 16.0 1.0 CA A:ASN60 4.8 14.9 1.0 CA A:ASP58 4.9 13.7 1.0 C A:ILE63 4.9 8.8 0.4 CD1 A:ILE63 4.9 10.9 0.4 N A:GLY61 4.9 11.4 1.0 C A:ASP58 5.0 14.6 1.0

Calcium binding site 3 out of 5 in the Selenomethionine CA2+-Calmodulin From Paramecium Tetraurelia Sad Data


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Selenomethionine CA2+-Calmodulin From Paramecium Tetraurelia Sad Data within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca203 b:12.6 occ:1.00 OD1 A:ASP129 2.3 13.3 1.0 OD1 A:ASP131 2.3 14.8 1.0 O A:HIS135 2.3 12.6 1.0 OD1 A:ASP133 2.4 14.8 1.0 O A:HOH358 2.4 16.0 1.0 OE1 A:GLU140 2.4 12.9 1.0 OE2 A:GLU140 2.5 13.1 1.0 CD A:GLU140 2.9 12.4 1.0 CG A:ASP131 3.2 16.0 1.0 CG A:ASP133 3.3 15.8 1.0 CG A:ASP129 3.4 13.5 1.0 C A:HIS135 3.5 11.5 1.0 OD2 A:ASP131 3.5 19.5 1.0 OD2 A:ASP133 3.8 17.5 1.0 N A:HIS135 4.1 12.2 1.0 N A:ASP133 4.2 16.7 1.0 OD2 A:ASP129 4.2 15.2 1.0 N A:ASP131 4.3 15.0 1.0 N A:ILE136 4.3 11.2 0.5 CG A:GLU140 4.3 12.5 1.0 CA A:ILE136 4.4 10.7 0.5 N A:ILE136 4.4 11.1 0.5 CA A:HIS135 4.4 12.2 1.0 CA A:ILE136 4.4 11.6 0.5 CB A:ASP133 4.4 18.0 1.0 CB A:ASP129 4.4 13.6 1.0 CA A:ASP129 4.4 12.7 1.0 N A:GLY132 4.4 16.1 1.0 N A:ASN137 4.4 11.9 1.0 CB A:ASP131 4.5 17.0 1.0 N A:ILE130 4.5 13.7 1.0 CA A:ASP133 4.7 17.1 1.0 N A:GLY134 4.7 14.5 1.0 CA A:ASP131 4.7 16.8 1.0 CB A:HIS135 4.7 13.0 1.0 C A:ASP131 4.8 17.2 1.0 C A:ILE136 4.8 11.5 0.5 C A:ASP133 4.9 15.8 1.0 C A:ILE136 4.9 10.7 0.5 CD1 A:ILE136 4.9 11.5 0.5 C A:ASP129 4.9 14.3 1.0

Calcium binding site 4 out of 5 in the Selenomethionine CA2+-Calmodulin From Paramecium Tetraurelia Sad Data


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Selenomethionine CA2+-Calmodulin From Paramecium Tetraurelia Sad Data within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca204 b:12.2 occ:1.00 O A:HOH392 2.4 12.1 1.0 O A:HOH433 2.4 14.3 1.0 O A:HOH410 2.4 15.0 1.0 O A:HOH414 2.4 16.5 1.0 OE2 A:GLU47 2.4 17.9 1.0 OE1 A:GLU47 2.5 11.3 1.0 CD A:GLU47 2.8 11.6 1.0 CG A:GLU47 4.3 11.7 1.0 CA A:PRO43 4.4 10.1 0.4 CA A:PRO43 4.5 9.2 0.6 O A:HOH313 4.6 42.1 1.0 N A:THR44 4.7 10.5 1.0 O A:ASN42 4.7 9.8 1.0 O A:HOH440 4.8 59.1 1.0 CG2 A:THR44 4.8 14.7 1.0 O A:HOH375 4.9 16.2 1.0

Calcium binding site 5 out of 5 in the Selenomethionine CA2+-Calmodulin From Paramecium Tetraurelia Sad Data


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Selenomethionine CA2+-Calmodulin From Paramecium Tetraurelia Sad Data within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca205 b:13.9 occ:1.00 OD1 A:ASP93 2.3 16.1 1.0 O A:LEU99 2.3 17.9 1.0 OD1 A:ASP95 2.3 18.7 1.0 O A:HOH422 2.3 21.4 1.0 OD1 A:ASN97 2.4 17.6 1.0 OE1 A:GLU104 2.5 12.5 1.0 OE2 A:GLU104 2.5 13.9 1.0 CD A:GLU104 2.8 12.1 1.0 CG A:ASP95 3.3 18.7 1.0 CG A:ASN97 3.4 20.2 1.0 CG A:ASP93 3.5 15.2 1.0 C A:LEU99 3.5 13.6 1.0 OD2 A:ASP95 3.7 27.4 1.0 ND2 A:ASN97 4.1 27.8 1.0 N A:ASN97 4.2 21.5 1.0 N A:LEU99 4.2 15.7 1.0 N A:ASP95 4.2 16.1 1.0 OD2 A:ASP93 4.3 15.9 1.0 CA A:ASP93 4.3 13.0 1.0 CA A:LEU99 4.3 14.1 1.0 CG A:GLU104 4.3 11.7 1.0 N A:ILE100 4.4 11.0 1.0 C A:ASP93 4.4 13.8 1.0 CB A:ASN97 4.4 24.3 1.0 CB A:ASP93 4.4 13.7 1.0 CA A:ILE100 4.5 10.6 1.0 CB A:ASP95 4.5 19.6 1.0 N A:SER101 4.5 10.5 1.0 N A:ARG94 4.5 14.7 0.4 N A:ARG94 4.5 12.7 0.6 N A:GLY96 4.6 19.3 1.0 O A:HOH421 4.6 33.4 1.0 CB A:LEU99 4.7 15.6 1.0 CA A:ASP95 4.7 18.1 1.0 CA A:ASN97 4.7 22.6 1.0 C A:ASP95 4.8 19.8 1.0 N A:GLY98 4.8 18.8 1.0 C A:ILE100 4.9 10.5 1.0 O A:ASP93 4.9 16.4 1.0 C A:ASN97 5.0 21.4 1.0

J.Lin, H.Van Den Bedem, A.T.Brunger, M.A.Wilson. Atomic Resolution Experimental Phase Information Reveals Extensive Disorder and Bound 2-Methyl-2,4-Pentanediol in Ca(2+)-Calmodulin. Acta Crystallogr D Struct V. 72 83 2016BIOL.
ISSN: ISSN 2059-7983
PubMed: 26894537
DOI: 10.1107/S2059798315021609