Calcium in PDB 6o5g: Calmodulin in Complex with Isomalbrancheamide D

The structure of Calmodulin in Complex with Isomalbrancheamide D, PDB code: 6o5g was solved by T.S.Beyett, A.E.Fraley, J.J.G.Tesmer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	37.88 / 1.89
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	50.858, 56.754, 117.168, 90.00, 90.00, 90.00
R / Rfree (%)	18.7 / 22.6

The structure of Calmodulin in Complex with Isomalbrancheamide D also contains other interesting chemical elements:

Zinc	(Zn)	1 atom
Bromine	(Br)	1 atom
Chlorine	(Cl)	1 atom

The binding sites of Calcium atom in the Calmodulin in Complex with Isomalbrancheamide D (pdb code 6o5g). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Calmodulin in Complex with Isomalbrancheamide D, PDB code: 6o5g:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Calmodulin in Complex with Isomalbrancheamide D


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Calmodulin in Complex with Isomalbrancheamide D within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca202 b:23.0 occ:1.00 OD1 A:ASP57 2.3 26.3 1.0 OD1 A:ASP59 2.3 32.0 1.0 O A:HOH309 2.4 27.8 1.0 O A:THR63 2.4 22.0 1.0 OD1 A:ASN61 2.4 24.4 1.0 OE2 A:GLU68 2.5 23.9 1.0 OE1 A:GLU68 2.6 22.5 1.0 CD A:GLU68 2.9 33.5 1.0 CG A:ASP59 3.3 38.0 1.0 CG A:ASN61 3.4 29.3 1.0 CG A:ASP57 3.5 34.2 1.0 OD2 A:ASP59 3.5 37.8 1.0 C A:THR63 3.6 23.2 1.0 O A:HOH330 3.8 62.9 1.0 ND2 A:ASN61 4.0 31.4 1.0 N A:THR63 4.2 21.7 1.0 N A:ASN61 4.2 26.2 1.0 CA A:ASP57 4.3 24.8 1.0 OD2 A:ASP57 4.3 26.3 1.0 CG A:GLU68 4.4 20.3 1.0 CB A:ASP57 4.5 24.3 1.0 N A:ASP59 4.5 26.8 1.0 N A:ILE64 4.5 19.2 1.0 N A:ASP65 4.5 23.3 1.0 CA A:ILE64 4.5 17.4 1.0 OD2 A:ASP65 4.5 41.6 1.0 CA A:THR63 4.5 24.6 1.0 N A:GLY60 4.5 32.1 1.0 CB A:ASP59 4.6 29.5 1.0 CB A:ASN61 4.6 29.5 1.0 OG1 A:THR63 4.6 30.4 1.0 N A:GLY62 4.6 28.4 1.0 C A:ASP57 4.7 26.6 1.0 CG A:ASP65 4.7 38.3 1.0 N A:ALA58 4.8 21.5 1.0 CA A:ASN61 4.8 29.1 1.0 O A:HOH327 4.8 26.3 1.0 CA A:ASP59 4.9 27.2 1.0 C A:ILE64 4.9 21.0 1.0 OD1 A:ASP65 4.9 36.3 1.0 C A:ASP59 4.9 29.9 1.0 C A:ASN61 5.0 29.9 1.0

Calcium binding site 2 out of 4 in the Calmodulin in Complex with Isomalbrancheamide D


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Calmodulin in Complex with Isomalbrancheamide D within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca203 b:23.8 occ:1.00 OD1 A:ASP21 2.3 26.0 1.0 O A:THR27 2.3 24.0 1.0 OD1 A:ASP23 2.4 28.6 1.0 OE1 A:GLU32 2.4 23.2 1.0 OD1 A:ASP25 2.4 29.6 1.0 O A:HOH321 2.5 30.1 1.0 OE2 A:GLU32 2.6 23.6 1.0 CD A:GLU32 2.8 24.9 1.0 CG A:ASP23 3.3 33.6 1.0 CG A:ASP21 3.4 29.9 1.0 CG A:ASP25 3.4 35.2 1.0 C A:THR27 3.5 22.9 1.0 OD2 A:ASP23 3.6 32.4 1.0 OD2 A:ASP25 3.9 37.1 1.0 N A:THR27 4.2 27.4 1.0 CA A:ASP21 4.2 21.8 1.0 OG1 A:THR27 4.2 46.6 1.0 OD2 A:ASP21 4.3 28.1 1.0 CB A:ASP21 4.3 24.9 1.0 CG A:GLU32 4.3 20.4 1.0 N A:ASP25 4.4 29.6 1.0 N A:ASP23 4.4 32.4 1.0 N A:ILE28 4.4 19.0 1.0 CA A:THR27 4.4 24.4 1.0 O A:HOH308 4.4 44.0 1.0 CA A:ILE28 4.4 14.7 1.0 C A:ASP21 4.5 30.6 1.0 CB A:ASP23 4.6 39.3 1.0 CB A:ASP25 4.6 29.3 1.0 N A:LYS22 4.6 31.0 1.0 N A:GLY24 4.7 27.8 1.0 CG2 A:THR29 4.7 27.3 1.0 O A:HOH319 4.7 38.7 1.0 N A:THR29 4.8 20.2 1.0 O A:HOH315 4.8 32.3 1.0 N A:GLY26 4.9 22.9 1.0 CA A:ASP23 4.9 36.3 1.0 CA A:ASP25 4.9 29.7 1.0 C A:ASP23 5.0 32.0 1.0

Calcium binding site 3 out of 4 in the Calmodulin in Complex with Isomalbrancheamide D


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Calmodulin in Complex with Isomalbrancheamide D within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca204 b:22.6 occ:1.00 O A:TYR100 2.3 33.6 1.0 OD1 A:ASP96 2.3 30.6 1.0 OD1 A:ASP94 2.3 22.3 1.0 O A:HOH377 2.4 36.1 1.0 OD1 A:ASN98 2.5 30.4 1.0 OE1 A:GLU105 2.5 24.5 1.0 OE2 A:GLU105 2.5 21.8 1.0 CD A:GLU105 2.8 27.1 1.0 CG A:ASP96 3.3 33.0 1.0 CG A:ASN98 3.4 33.5 1.0 C A:TYR100 3.5 33.8 1.0 CG A:ASP94 3.5 23.3 1.0 OD2 A:ASP96 3.7 34.3 1.0 ND2 A:ASN98 4.0 31.5 1.0 N A:ASN98 4.2 26.5 1.0 N A:TYR100 4.2 24.0 1.0 N A:ASP96 4.3 18.7 1.0 CA A:ASP94 4.3 20.1 1.0 CG A:GLU105 4.3 24.7 1.0 OD2 A:ASP94 4.3 25.2 1.0 CA A:TYR100 4.4 27.1 1.0 N A:ILE101 4.4 27.1 1.0 N A:GLY97 4.4 27.2 1.0 CB A:ASP94 4.4 22.4 1.0 CA A:ILE101 4.4 26.3 1.0 CB A:ASP96 4.4 26.3 1.0 CB A:ASN98 4.5 31.8 1.0 C A:ASP94 4.5 25.4 1.0 N A:SER102 4.6 24.5 1.0 N A:LYS95 4.7 19.9 1.0 CA A:ASP96 4.7 22.3 1.0 CA A:ASN98 4.7 31.0 1.0 CB A:TYR100 4.7 28.3 1.0 C A:ASP96 4.8 28.9 1.0 N A:GLY99 4.8 26.7 1.0 O A:ASP94 4.9 23.4 1.0 C A:ILE101 5.0 26.7 1.0

Calcium binding site 4 out of 4 in the Calmodulin in Complex with Isomalbrancheamide D


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Calmodulin in Complex with Isomalbrancheamide D within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca205 b:36.0 occ:1.00 O A:GLN136 2.4 33.6 1.0 OD1 A:ASP132 2.4 56.6 1.0 OD1 A:ASP134 2.4 45.2 1.0 OD1 A:ASP130 2.4 41.8 1.0 O A:HOH320 2.4 36.6 1.0 OE1 A:GLU141 2.4 34.2 1.0 OE2 A:GLU141 2.6 39.0 1.0 CD A:GLU141 2.9 41.9 1.0 CG A:ASP134 3.2 50.1 1.0 CG A:ASP132 3.3 58.4 1.0 CG A:ASP130 3.5 43.8 1.0 OD2 A:ASP134 3.5 53.5 1.0 C A:GLN136 3.5 34.4 1.0 OD2 A:ASP132 3.6 62.6 1.0 CA A:ASP130 4.2 44.1 1.0 N A:GLN136 4.3 32.3 1.0 N A:ASP132 4.3 42.0 1.0 N A:ASP134 4.3 43.5 1.0 CB A:ASP130 4.3 39.6 1.0 OD2 A:ASP130 4.3 45.0 1.0 N A:ASN138 4.4 28.4 1.0 CG A:GLU141 4.4 38.8 1.0 N A:VAL137 4.4 25.9 1.0 CA A:VAL137 4.4 25.8 1.0 CB A:ASP134 4.4 51.8 1.0 CA A:GLN136 4.5 33.0 1.0 N A:ILE131 4.5 40.3 1.0 CB A:ASP132 4.5 50.6 1.0 N A:GLY133 4.6 45.4 1.0 C A:ASP130 4.6 47.5 1.0 CA A:ASP132 4.8 46.4 1.0 CA A:ASP134 4.8 44.4 1.0 C A:VAL137 4.8 32.0 1.0 CG A:ASN138 4.9 39.0 1.0 O A:HOH341 4.9 37.9 1.0 N A:GLY135 4.9 37.2 1.0 ND2 A:ASN138 4.9 38.9 1.0 C A:ASP132 4.9 48.1 1.0

T.S.Beyett, A.E.Fraley, E.Labudde, D.Patra, R.C.Coleman, A.Eguchi, A.Glukhova, Q.Chen, R.M.Williams, W.J.Koch, D.H.Sherman, J.J.G.Tesmer. Perturbation of the Interactions of Calmodulin with GRK5 Using A Natural Product Chemical Probe. Proc.Natl.Acad.Sci.Usa V. 116 15895 2019.
ISSN: ESSN 1091-6490
PubMed: 31337679
DOI: 10.1073/PNAS.1818547116