Calcium in PDB 4hex: A Novel Conformation of Calmodulin

The structure of A Novel Conformation of Calmodulin, PDB code: 4hex was solved by V.Kumar, V.P.R.Chichili, J.Sivaraman, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	28.58 / 2.00
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	38.827, 116.397, 38.797, 90.00, 94.83, 90.00
R / Rfree (%)	21 / 23.7

The structure of A Novel Conformation of Calmodulin also contains other interesting chemical elements:

Zinc

(Zn)

6 atoms

The binding sites of Calcium atom in the A Novel Conformation of Calmodulin (pdb code 4hex). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the A Novel Conformation of Calmodulin, PDB code: 4hex:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the A Novel Conformation of Calmodulin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of A Novel Conformation of Calmodulin within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca202 b:42.6 occ:1.00 O A:THR27 2.3 47.8 1.0 OD1 A:ASP23 2.3 56.8 1.0 OD1 A:ASP25 2.4 36.7 1.0 OD1 A:ASP21 2.4 37.3 1.0 OE2 A:GLU32 2.6 44.5 1.0 OE1 A:GLU32 2.7 41.2 1.0 CD A:GLU32 3.0 41.3 1.0 CG A:ASP25 3.3 42.0 1.0 CG A:ASP23 3.3 52.8 1.0 C A:THR27 3.5 40.2 1.0 CG A:ASP21 3.6 36.0 1.0 OD2 A:ASP23 3.7 51.8 1.0 OD2 A:ASP25 3.8 49.9 1.0 N A:THR27 4.2 47.1 1.0 OD2 A:ASP21 4.3 40.2 1.0 O A:HOH340 4.3 42.0 1.0 N A:ASP25 4.3 43.8 1.0 CA A:ASP21 4.3 36.5 1.0 N A:ILE28 4.4 37.7 1.0 CA A:THR27 4.4 45.3 1.0 CB A:ASP25 4.4 43.8 1.0 CB A:ASP21 4.4 36.8 1.0 CA A:ILE28 4.5 37.3 1.0 CG A:GLU32 4.5 40.9 1.0 C A:ASP21 4.5 42.6 1.0 N A:ASP23 4.5 52.1 1.0 CB A:ASP23 4.6 52.7 1.0 N A:LYS22 4.8 43.8 1.0 CA A:ASP25 4.8 41.9 1.0 O A:ASP21 4.9 38.8 1.0 N A:GLY24 4.9 40.8 1.0 N A:THR29 4.9 39.4 1.0 CG2 A:THR29 4.9 37.8 1.0 CA A:ASP23 4.9 49.6 1.0 OG1 A:THR27 4.9 56.8 1.0 N A:GLY26 5.0 45.4 1.0

Calcium binding site 2 out of 4 in the A Novel Conformation of Calmodulin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of A Novel Conformation of Calmodulin within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca204 b:46.0 occ:1.00 OD2 A:ASP132 2.0 86.1 1.0 OD1 A:ASP132 2.0 73.1 1.0 OD1 A:ASP130 2.2 41.4 1.0 CG A:ASP132 2.2 78.5 1.0 OD1 A:ASP134 2.3 48.8 1.0 O A:GLN136 2.3 40.5 1.0 OE1 A:GLU141 2.4 51.2 1.0 OE2 A:GLU141 2.6 46.3 1.0 CD A:GLU141 2.9 52.1 1.0 CG A:ASP130 3.3 41.1 1.0 CG A:ASP134 3.3 49.9 1.0 C A:GLN136 3.5 40.9 1.0 CB A:ASP132 3.6 70.7 1.0 OD2 A:ASP134 3.9 51.8 1.0 OD2 A:ASP130 3.9 38.4 1.0 N A:ASP134 4.0 51.0 1.0 N A:ASP132 4.1 64.2 1.0 N A:GLN136 4.1 43.9 1.0 CA A:ASP132 4.2 67.8 1.0 CB A:ASP130 4.3 40.7 1.0 N A:ASN138 4.3 36.1 1.0 CA A:ASP130 4.3 43.7 1.0 CA A:GLN136 4.3 43.7 1.0 N A:VAL137 4.4 35.5 1.0 CB A:ASP134 4.4 49.8 1.0 CA A:VAL137 4.4 35.0 1.0 CG A:GLU141 4.4 49.2 1.0 N A:GLY133 4.4 60.5 1.0 C A:ASP132 4.5 64.5 1.0 CA A:ASP134 4.6 49.3 1.0 N A:ILE131 4.6 53.6 1.0 C A:ASP130 4.6 46.1 1.0 N A:GLY135 4.7 41.0 1.0 CB A:GLN136 4.8 46.7 1.0 C A:VAL137 4.8 36.4 1.0 C A:ASP134 4.9 46.5 1.0 CG A:ASN138 5.0 43.5 1.0

Calcium binding site 3 out of 4 in the A Novel Conformation of Calmodulin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of A Novel Conformation of Calmodulin within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca202 b:33.8 occ:1.00 O B:HOH305 2.2 29.5 1.0 OD1 B:ASP94 2.3 33.4 1.0 O B:TYR100 2.3 33.5 1.0 OD1 B:ASP96 2.5 34.4 1.0 OE1 B:GLU105 2.5 32.6 1.0 OD1 B:ASN98 2.6 37.0 1.0 OE2 B:GLU105 2.6 32.7 1.0 CD B:GLU105 2.9 32.7 1.0 CG B:ASP96 3.2 34.2 1.0 OD2 B:ASP96 3.4 34.1 1.0 CG B:ASP94 3.4 33.4 1.0 CG B:ASN98 3.5 36.0 1.0 C B:TYR100 3.5 36.1 1.0 ND2 B:ASN98 3.9 35.3 1.0 N B:TYR100 4.1 39.5 1.0 N B:ASN98 4.2 40.2 1.0 CA B:ASP94 4.2 32.4 1.0 OD2 B:ASP94 4.3 33.8 1.0 CB B:ASP94 4.3 32.8 1.0 CA B:TYR100 4.3 36.8 1.0 N B:ASP96 4.3 33.2 1.0 C B:ASP94 4.4 32.5 1.0 CB B:ASP96 4.4 34.5 1.0 N B:GLY97 4.4 39.0 1.0 CG B:GLU105 4.5 32.1 1.0 N B:ILE101 4.5 33.4 1.0 N B:SER102 4.6 32.9 1.0 CB B:ASN98 4.6 37.6 1.0 CA B:ILE101 4.6 32.9 1.0 N B:LYS95 4.7 32.3 1.0 CA B:ASP96 4.7 35.3 1.0 CB B:TYR100 4.7 37.1 1.0 C B:ASP96 4.8 38.2 1.0 CA B:ASN98 4.8 38.6 1.0 O B:ASP94 4.8 32.8 1.0 N B:GLY99 4.9 39.2 1.0

Calcium binding site 4 out of 4 in the A Novel Conformation of Calmodulin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of A Novel Conformation of Calmodulin within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca203 b:35.8 occ:1.00 OD1 B:ASP57 2.0 38.3 1.0 O B:HOH332 2.1 29.9 1.0 O B:THR63 2.3 37.7 1.0 OE1 B:GLU68 2.4 33.0 1.0 OD1 B:ASN61 2.5 38.9 1.0 OE2 B:GLU68 2.6 33.6 1.0 OD1 B:ASP59 2.6 48.5 1.0 CD B:GLU68 2.8 32.5 1.0 CG B:ASP57 3.3 44.6 1.0 CG B:ASP59 3.5 48.9 1.0 CG B:ASN61 3.5 41.9 1.0 C B:THR63 3.6 39.3 1.0 OD2 B:ASP59 3.8 44.5 1.0 OD2 B:ASP57 4.1 42.9 1.0 ND2 B:ASN61 4.1 43.5 1.0 CA B:ASP57 4.2 42.6 1.0 N B:THR63 4.2 36.9 1.0 CB B:ASP57 4.2 41.5 1.0 CG B:GLU68 4.3 32.4 1.0 N B:ASN61 4.4 44.9 1.0 N B:ASP65 4.4 37.0 1.0 OG1 B:THR63 4.4 40.6 1.0 CA B:ILE64 4.4 34.9 1.0 N B:ILE64 4.4 36.2 1.0 N B:ASP59 4.5 43.3 1.0 CA B:THR63 4.5 38.4 1.0 OD2 B:ASP65 4.6 43.2 1.0 N B:ALA58 4.7 38.5 1.0 CB B:ASN61 4.7 44.5 1.0 CB B:ASP59 4.7 49.4 1.0 C B:ASP57 4.7 44.1 1.0 CG B:ASP65 4.7 39.7 1.0 N B:GLY60 4.7 48.5 1.0 O B:HOH301 4.8 25.0 1.0 N B:GLY62 4.8 42.8 1.0 C B:ILE64 4.9 36.4 1.0 CA B:ASN61 4.9 43.4 1.0 CA B:ASP59 4.9 46.1 1.0 C B:ASP59 5.0 48.2 1.0

V.Kumar, V.P.R.Chichili, X.Tang, J.Sivaraman. A Novel Trans Conformation of Ligand-Free Calmodulin Plos One V. 8 54834 2013.
ISSN: ESSN 1932-6203
PubMed: 23382982
DOI: 10.1371/JOURNAL.PONE.0054834