Calcium in PDB 6eeb: Calmodulin in Complex with Malbrancheamide

The structure of Calmodulin in Complex with Malbrancheamide, PDB code: 6eeb 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)	37.17 / 1.96
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	49.113, 56.880, 116.781, 90.00, 90.00, 90.00
R / Rfree (%)	21.5 / 26.3

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

Chlorine	(Cl)	2 atoms
Zinc	(Zn)	1 atom

The binding sites of Calcium atom in the Calmodulin in Complex with Malbrancheamide (pdb code 6eeb). 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 Malbrancheamide, PDB code: 6eeb:
Jump to Calcium binding site number: 1; 2; 3; 4;

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


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 Malbrancheamide within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca202 b:34.5 occ:1.00 OE1 A:GLU68 2.3 34.5 1.0 OD1 A:ASP59 2.3 45.6 1.0 OD1 A:ASP57 2.4 39.2 1.0 O A:THR63 2.4 35.1 1.0 O A:HOH320 2.4 42.1 1.0 OD1 A:ASN61 2.5 42.9 1.0 OE2 A:GLU68 2.6 27.5 1.0 CD A:GLU68 2.8 34.1 1.0 CG A:ASP59 3.2 51.2 1.0 CG A:ASN61 3.5 41.7 1.0 C A:THR63 3.6 32.3 1.0 CG A:ASP57 3.6 46.7 1.0 OD2 A:ASP59 3.6 53.8 1.0 O A:HOH319 3.8 44.8 1.0 ND2 A:ASN61 4.0 47.6 1.0 N A:THR63 4.3 33.0 1.0 CG A:GLU68 4.3 28.4 1.0 N A:ASN61 4.3 38.8 1.0 OD2 A:ASP57 4.4 44.9 1.0 CA A:ASP57 4.4 40.0 1.0 N A:ASP59 4.5 37.7 1.0 N A:ASP65 4.5 36.4 1.0 N A:ILE64 4.5 29.8 1.0 CA A:ILE64 4.5 31.6 1.0 OG1 A:THR63 4.5 42.4 1.0 CB A:ASP59 4.5 45.9 1.0 CA A:THR63 4.5 32.3 1.0 CB A:ASP57 4.5 42.1 1.0 OD2 A:ASP65 4.5 49.0 1.0 CB A:ASN61 4.6 35.0 1.0 C A:ASP57 4.7 33.5 1.0 N A:GLY60 4.7 41.2 1.0 CG A:ASP65 4.7 45.1 1.0 O A:HOH315 4.7 37.7 1.0 N A:ALA58 4.8 33.4 1.0 N A:GLY62 4.8 40.1 1.0 C A:ILE64 4.8 32.9 1.0 CA A:ASN61 4.9 41.1 1.0 CA A:ASP59 4.9 38.3 1.0 OD1 A:ASP65 4.9 43.9 1.0 CB A:GLU68 5.0 29.4 1.0

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


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 Malbrancheamide within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca203 b:35.9 occ:1.00 O A:THR27 2.3 36.8 1.0 OD1 A:ASP21 2.3 37.4 1.0 O A:HOH342 2.3 37.7 1.0 OD1 A:ASP25 2.3 40.9 1.0 OD1 A:ASP23 2.4 56.4 1.0 OE2 A:GLU32 2.5 38.7 1.0 OE1 A:GLU32 2.6 35.9 1.0 CD A:GLU32 2.9 46.0 1.0 CG A:ASP25 3.4 45.5 1.0 CG A:ASP23 3.4 56.6 1.0 CG A:ASP21 3.4 42.6 1.0 C A:THR27 3.5 38.7 1.0 OD2 A:ASP23 3.8 52.8 1.0 OG1 A:THR27 3.8 50.4 1.0 OD2 A:ASP25 3.9 51.2 1.0 N A:THR27 4.2 38.3 1.0 CA A:ASP21 4.2 36.9 1.0 CB A:ASP21 4.2 38.4 1.0 OD2 A:ASP21 4.2 39.9 1.0 N A:ASP25 4.2 42.5 1.0 CA A:THR27 4.3 38.2 1.0 CG A:GLU32 4.4 40.6 1.0 N A:ILE28 4.4 30.1 1.0 N A:ASP23 4.4 47.9 1.0 CA A:ILE28 4.5 25.9 1.0 C A:ASP21 4.5 44.8 1.0 CB A:ASP25 4.5 41.0 1.0 N A:LYS22 4.6 43.7 1.0 N A:GLY24 4.6 37.2 1.0 CB A:ASP23 4.7 51.8 1.0 CB A:THR27 4.7 41.5 1.0 O A:HOH307 4.7 40.6 1.0 O A:HOH322 4.8 49.5 1.0 CA A:ASP25 4.8 38.3 1.0 N A:THR29 4.9 33.6 1.0 CA A:ASP23 4.9 49.2 1.0 CG2 A:THR29 4.9 47.2 1.0 C A:ASP23 4.9 44.0 1.0 N A:GLY26 4.9 33.5 1.0

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


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 Malbrancheamide within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca204 b:37.6 occ:1.00 O A:TYR100 2.2 43.7 1.0 OD1 A:ASP94 2.3 42.0 1.0 OE1 A:GLU105 2.3 33.2 1.0 OD1 A:ASP96 2.4 49.9 1.0 OD1 A:ASN98 2.4 38.8 1.0 O A:HOH339 2.5 41.1 1.0 OE2 A:GLU105 2.5 32.6 1.0 CD A:GLU105 2.7 33.2 1.0 CG A:ASP96 3.2 42.8 1.0 CG A:ASN98 3.4 43.6 1.0 C A:TYR100 3.5 44.7 1.0 CG A:ASP94 3.5 38.8 1.0 OD2 A:ASP96 3.6 51.8 1.0 ND2 A:ASN98 3.8 46.1 1.0 N A:TYR100 4.1 34.5 1.0 N A:ASN98 4.2 40.5 1.0 CG A:GLU105 4.3 30.9 1.0 CA A:ASP94 4.3 30.8 1.0 OD2 A:ASP94 4.3 34.5 1.0 CA A:TYR100 4.3 46.6 1.0 N A:ASP96 4.4 28.8 1.0 N A:GLY97 4.4 39.4 1.0 N A:ILE101 4.4 43.4 1.0 CB A:ASP94 4.4 37.0 1.0 CB A:ASP96 4.5 33.7 1.0 C A:ASP94 4.5 30.6 1.0 CA A:ILE101 4.5 40.0 1.0 CB A:ASN98 4.5 47.5 1.0 N A:SER102 4.5 39.0 1.0 OE1 A:GLN136 4.7 67.1 1.0 N A:LYS95 4.7 32.5 1.0 CA A:ASP96 4.8 34.9 1.0 CA A:ASN98 4.8 43.9 1.0 N A:GLY99 4.8 41.4 1.0 CB A:TYR100 4.8 49.5 1.0 C A:ASP96 4.9 42.0 1.0 O A:ASP94 5.0 31.2 1.0

Calcium binding site 4 out of 4 in the Calmodulin in Complex with Malbrancheamide


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 Malbrancheamide within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca205 b:59.5 occ:1.00 O A:GLN136 2.3 48.5 1.0 OE1 A:GLU141 2.3 62.9 1.0 OD1 A:ASP130 2.4 54.9 1.0 O A:HOH324 2.5 42.4 1.0 OD1 A:ASP134 2.6 61.0 1.0 OE2 A:GLU141 2.7 54.5 1.0 OD1 A:ASP132 2.7 71.9 1.0 CD A:GLU141 2.9 63.9 1.0 CG A:ASP132 3.3 74.0 1.0 C A:GLN136 3.5 53.3 1.0 OD2 A:ASP132 3.5 76.1 1.0 CG A:ASP134 3.5 64.5 1.0 CG A:ASP130 3.6 60.6 1.0 OD2 A:ASP134 4.0 66.1 1.0 CA A:ASP130 4.1 55.6 1.0 N A:GLN136 4.3 49.8 1.0 N A:ASP132 4.3 66.3 1.0 N A:ILE131 4.3 63.2 1.0 CA A:VAL137 4.3 48.8 1.0 N A:ASN138 4.3 46.9 1.0 CB A:ASP130 4.3 55.6 1.0 N A:VAL137 4.3 46.5 1.0 N A:ASP134 4.4 66.0 1.0 CG A:GLU141 4.4 55.7 1.0 OD2 A:ASP130 4.4 58.3 1.0 CA A:GLN136 4.5 47.0 1.0 C A:ASP130 4.5 64.9 1.0 N A:GLY133 4.5 63.6 1.0 CB A:ASP134 4.6 67.1 1.0 CB A:ASP132 4.6 73.1 1.0 C A:VAL137 4.8 47.8 1.0 CA A:ASP132 4.8 70.7 1.0 ND2 A:ASN138 4.8 48.5 1.0 CG A:ASN138 4.8 46.1 1.0 N A:GLY135 4.9 59.0 1.0 C A:ASP132 4.9 62.2 1.0 CA A:ASP134 4.9 64.8 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