Zinc 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:

Calcium

(Ca)

4 atoms

The binding sites of Zinc atom in the A Novel Conformation of Calmodulin (pdb code 4hex). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the A Novel Conformation of Calmodulin, PDB code: 4hex:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in the A Novel Conformation of Calmodulin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of A Novel Conformation of Calmodulin within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn201 b:53.9 occ:1.00 OD1 A:ASP57 2.0 39.5 1.0 OD1 A:ASN61 2.3 34.8 1.0 O A:THR63 2.4 34.1 1.0 OD1 A:ASP59 2.5 36.7 1.0 OE1 A:GLU68 2.6 33.3 1.0 OE2 A:GLU68 2.6 33.3 1.0 CD A:GLU68 3.0 33.2 1.0 CG A:ASP57 3.2 37.7 1.0 CG A:ASN61 3.3 38.3 1.0 CG A:ASP59 3.4 39.4 1.0 C A:THR63 3.6 37.4 1.0 OD2 A:ASP59 3.8 36.4 1.0 OD2 A:ASP57 4.0 40.0 1.0 ND2 A:ASN61 4.0 40.2 1.0 N A:THR63 4.0 40.9 1.0 N A:ASN61 4.1 41.3 1.0 CB A:ASP57 4.2 38.1 1.0 CA A:ASP57 4.3 35.0 1.0 CA A:THR63 4.4 42.1 1.0 CB A:ASN61 4.4 38.5 1.0 CG A:GLU68 4.5 32.9 1.0 N A:ILE64 4.5 35.1 1.0 C A:ASP57 4.5 36.6 1.0 N A:ASP59 4.5 36.1 1.0 CG2 A:THR63 4.5 41.3 1.0 CA A:ASN61 4.6 37.9 1.0 CA A:ILE64 4.6 36.3 1.0 N A:GLY62 4.6 42.3 1.0 N A:ASP65 4.6 35.3 1.0 N A:GLY60 4.7 37.0 1.0 CB A:ASP59 4.7 39.1 1.0 N A:ALA58 4.7 37.6 1.0 C A:ASN61 4.7 38.2 1.0 OD2 A:ASP65 4.8 35.3 1.0 O A:ASP57 4.9 35.1 1.0 O A:HOH328 4.9 74.1 1.0 C A:ASP59 4.9 40.1 1.0 CB A:THR63 4.9 41.9 1.0 CA A:ASP59 4.9 41.2 1.0 CG A:ASP65 4.9 37.8 1.0

Zinc binding site 2 out of 6 in the A Novel Conformation of Calmodulin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of A Novel Conformation of Calmodulin within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn203 b:47.7 occ:1.00 OD1 A:ASP94 2.2 34.1 1.0 O A:TYR100 2.3 34.0 1.0 OE1 A:GLU105 2.4 33.1 1.0 OE2 A:GLU105 2.5 34.9 1.0 OD1 A:ASP96 2.6 37.5 1.0 OD1 A:ASN98 2.6 35.5 1.0 CD A:GLU105 2.8 33.0 1.0 CG A:ASP96 3.3 36.6 1.0 CG A:ASP94 3.4 34.0 1.0 CG A:ASN98 3.5 36.3 1.0 C A:TYR100 3.5 34.2 1.0 OD2 A:ASP96 3.6 35.2 1.0 ND2 A:ASN98 4.0 36.2 1.0 CA A:ASP94 4.1 32.9 1.0 N A:TYR100 4.2 35.3 1.0 N A:ASN98 4.2 37.9 1.0 OD2 A:ASP94 4.3 34.6 1.0 CB A:ASP94 4.3 33.3 1.0 CG A:GLU105 4.3 32.7 1.0 N A:ASP96 4.3 34.6 1.0 C A:ASP94 4.3 33.2 1.0 CA A:TYR100 4.4 35.0 1.0 CA A:ILE101 4.4 33.2 1.0 N A:ILE101 4.4 33.8 1.0 N A:GLY97 4.5 37.1 1.0 N A:SER102 4.5 33.2 1.0 CB A:ASP96 4.5 38.2 1.0 N A:LYS95 4.6 33.0 1.0 CB A:ASN98 4.6 37.0 1.0 O A:HOH303 4.8 33.0 1.0 O A:ASP94 4.8 33.6 1.0 CA A:ASP96 4.8 37.3 1.0 CA A:ASN98 4.8 37.0 1.0 C A:ASP96 4.8 39.0 1.0 CB A:TYR100 4.8 37.2 1.0 C A:ILE101 4.9 33.3 1.0 N A:GLY99 4.9 37.7 1.0

Zinc binding site 3 out of 6 in the A Novel Conformation of Calmodulin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of A Novel Conformation of Calmodulin within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn205 b:29.0 occ:1.00 OE2 A:GLU85 1.6 32.4 1.0 OD2 A:ASP81 1.8 33.0 1.0 NE2 B:HIS108 2.0 32.1 1.0 CE B:LYS95 2.4 34.7 1.0 CG A:ASP81 2.6 33.4 1.0 CD A:GLU85 2.7 32.3 1.0 OD1 A:ASP81 2.8 33.5 1.0 NZ B:LYS95 3.0 42.5 1.0 CE1 B:HIS108 3.0 32.2 1.0 CD2 B:HIS108 3.0 31.8 1.0 OE1 A:GLU85 3.2 32.2 1.0 CD B:LYS95 3.6 32.5 1.0 OG1 A:THR71 3.6 33.5 1.0 ND2 B:ASN112 4.0 35.3 1.0 CB A:ASP81 4.0 34.1 1.0 O A:HOH308 4.0 29.4 1.0 CG A:GLU85 4.1 32.3 1.0 ND1 B:HIS108 4.1 32.0 1.0 CG B:HIS108 4.2 31.8 1.0 O A:HOH304 4.3 26.6 1.0 O A:PRO67 4.4 32.8 1.0 CG B:LYS95 4.5 34.1 1.0 O A:ASP81 4.7 36.7 1.0 C A:ASP81 4.8 36.8 1.0 CA A:ASP81 4.9 35.4 1.0

Zinc binding site 4 out of 6 in the A Novel Conformation of Calmodulin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of A Novel Conformation of Calmodulin within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn201 b:59.9 occ:1.00 O B:HOH322 2.1 30.1 1.0 OD1 B:ASP130 2.2 48.4 1.0 OD1 B:ASP134 2.3 57.1 1.0 O B:GLN136 2.3 43.1 1.0 OE1 B:GLU141 2.4 57.9 1.0 OE2 B:GLU141 2.5 54.7 1.0 OD1 B:ASP132 2.6 48.3 1.0 CD B:GLU141 2.8 53.0 1.0 CG B:ASP134 3.2 55.8 1.0 CG B:ASP132 3.3 48.6 1.0 CG B:ASP130 3.3 46.9 1.0 OD2 B:ASP132 3.4 47.8 1.0 C B:GLN136 3.5 40.6 1.0 OD2 B:ASP134 3.6 54.4 1.0 OD2 B:ASP130 4.1 46.5 1.0 N B:GLN136 4.2 43.7 1.0 N B:ASP134 4.2 51.5 1.0 CA B:ASP130 4.3 52.8 1.0 CB B:ASP130 4.3 49.8 1.0 N B:ASN138 4.3 37.5 1.0 CB B:ASP134 4.3 52.9 1.0 CG B:GLU141 4.4 50.0 1.0 N B:ASP132 4.4 54.5 1.0 CA B:GLN136 4.4 41.0 1.0 CA B:VAL137 4.4 35.8 1.0 N B:VAL137 4.4 37.2 1.0 CB B:ASP132 4.5 50.2 1.0 N B:ILE131 4.6 65.8 1.0 C B:ASP130 4.6 60.0 1.0 CA B:ASP134 4.7 50.3 1.0 N B:GLY133 4.7 55.6 1.0 CA B:ASP132 4.8 53.6 1.0 C B:VAL137 4.9 34.7 1.0 CB B:GLN136 4.9 44.7 1.0 N B:GLY135 4.9 47.7 1.0 C B:ASP132 4.9 53.8 1.0 C B:ASP134 5.0 50.3 1.0

Zinc binding site 5 out of 6 in the A Novel Conformation of Calmodulin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of A Novel Conformation of Calmodulin within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn204 b:67.8 occ:1.00 OD1 B:ASP23 2.2 50.0 1.0 O B:THR27 2.4 44.8 1.0 OD1 B:ASP21 2.4 37.6 1.0 O B:HOH307 2.4 37.0 1.0 OE2 B:GLU32 2.6 36.7 1.0 CB B:ASP25 2.7 44.1 1.0 OE1 B:GLU32 2.9 36.0 1.0 OD2 B:ASP25 2.9 53.8 1.0 CG B:ASP25 3.0 46.8 1.0 CD B:GLU32 3.0 41.5 1.0 CG B:ASP23 3.2 48.1 1.0 CG B:ASP21 3.5 43.4 1.0 C B:THR27 3.6 42.5 1.0 OD2 B:ASP23 3.6 43.4 1.0 OD1 B:ASP25 4.0 48.8 1.0 CA B:ASP25 4.1 41.5 1.0 OD2 B:ASP21 4.3 47.7 1.0 N B:THR27 4.3 42.2 1.0 N B:ASP25 4.3 44.7 1.0 CA B:ASP21 4.4 45.6 1.0 CB B:ASP21 4.4 44.4 1.0 CG B:GLU32 4.5 41.7 1.0 N B:ASP23 4.5 56.8 1.0 CA B:THR27 4.5 41.6 1.0 CB B:ASP23 4.5 49.0 1.0 N B:ILE28 4.5 36.9 1.0 C B:ASP21 4.6 50.1 1.0 CA B:ILE28 4.6 40.4 1.0 O B:HOH335 4.7 50.8 1.0 N B:GLY24 4.8 51.5 1.0 CA B:ASP23 4.8 51.4 1.0 OG1 B:THR27 4.9 50.1 1.0 C B:ASP25 4.9 37.8 1.0 C B:ASP23 4.9 54.6 1.0 N B:LYS22 4.9 49.7 1.0 N B:GLY26 4.9 40.4 1.0 O B:ASP21 5.0 52.2 1.0

Zinc binding site 6 out of 6 in the A Novel Conformation of Calmodulin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of A Novel Conformation of Calmodulin within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn205 b:30.3 occ:1.00 OE2 B:GLU85 1.7 31.9 1.0 OD2 B:ASP81 1.8 32.4 1.0 NE2 A:HIS108 2.1 33.6 1.0 CE A:LYS95 2.2 33.9 1.0 CG B:ASP81 2.6 36.8 1.0 CD B:GLU85 2.7 31.9 1.0 OD1 B:ASP81 2.8 33.5 1.0 CD2 A:HIS108 2.9 33.1 1.0 NZ A:LYS95 3.0 38.1 1.0 OE1 B:GLU85 3.1 31.9 1.0 CE1 A:HIS108 3.2 34.4 1.0 CD A:LYS95 3.4 33.5 1.0 OG1 B:THR71 3.7 37.4 1.0 ND2 A:ASN112 3.8 34.1 1.0 CB B:ASP81 4.0 41.7 1.0 CG B:GLU85 4.1 31.9 1.0 CG A:HIS108 4.1 33.0 1.0 ND1 A:HIS108 4.2 33.4 1.0 O B:PRO67 4.3 32.1 1.0 CG A:LYS95 4.5 33.6 1.0 C B:ASP81 4.8 40.3 1.0 O B:ASP81 4.8 39.7 1.0 CA B:ASP81 5.0 43.0 1.0 C B:PRO67 5.0 32.0 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