Calcium in PDB 5cfr: Crystal Structure of Anemone Sting (Nematostella Vectensis) in Apo 'Unrotated' Closed Conformation

The structure of Crystal Structure of Anemone Sting (Nematostella Vectensis) in Apo 'Unrotated' Closed Conformation, PDB code: 5cfr was solved by P.J.Kranzusch, S.C.Wilson, A.S.Y.Lee, J.M.Berger, J.A.Doudna, R.E.Vance, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	41.74 / 2.85
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	43.043, 43.037, 170.942, 90.00, 90.00, 90.00
R / Rfree (%)	25.7 / 27.8

The binding sites of Calcium atom in the Crystal Structure of Anemone Sting (Nematostella Vectensis) in Apo 'Unrotated' Closed Conformation (pdb code 5cfr). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Crystal Structure of Anemone Sting (Nematostella Vectensis) in Apo 'Unrotated' Closed Conformation, PDB code: 5cfr:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Crystal Structure of Anemone Sting (Nematostella Vectensis) in Apo 'Unrotated' Closed Conformation


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of Anemone Sting (Nematostella Vectensis) in Apo 'Unrotated' Closed Conformation within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca401 b:85.6 occ:1.00 O A:SER226 2.5 0.9 1.0 CB A:SER226 3.1 0.2 1.0 C A:SER226 3.4 0.9 1.0 CA A:SER226 3.6 0.9 1.0 OG A:SER226 4.0 0.3 1.0 N A:LYS227 4.7 99.1 1.0

Calcium binding site 2 out of 4 in the Crystal Structure of Anemone Sting (Nematostella Vectensis) in Apo 'Unrotated' Closed Conformation


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of Anemone Sting (Nematostella Vectensis) in Apo 'Unrotated' Closed Conformation within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca402 b:66.4 occ:1.00 O A:ILE259 2.5 48.6 1.0 OD1 A:ASN257 2.5 70.3 1.0 OD2 A:ASP254 2.7 54.4 1.0 C A:ILE259 3.6 46.2 1.0 CG A:ASN257 3.7 71.4 1.0 CG A:ASP254 3.9 56.0 1.0 O A:HOH501 4.1 12.8 1.0 CB A:ASP254 4.4 61.2 1.0 O B:GLY274 4.4 53.1 1.0 N A:THR260 4.4 46.4 1.0 CA A:THR260 4.4 49.3 1.0 ND2 A:ASN257 4.5 70.4 1.0 CA A:ILE259 4.5 46.0 1.0 OG1 A:THR260 4.5 55.8 1.0 N A:ILE259 4.6 49.5 1.0 CA A:ASN257 4.7 73.6 1.0 CB A:ILE259 4.7 42.1 1.0 CB A:ASN257 4.8 73.6 1.0 OD1 A:ASP254 4.9 53.9 1.0

Calcium binding site 3 out of 4 in the Crystal Structure of Anemone Sting (Nematostella Vectensis) in Apo 'Unrotated' Closed Conformation


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of Anemone Sting (Nematostella Vectensis) in Apo 'Unrotated' Closed Conformation within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca401 b:66.7 occ:1.00 OD1 B:ASN257 2.5 68.7 1.0 O B:ILE259 2.5 50.5 1.0 OD2 B:ASP254 2.9 49.8 1.0 C B:ILE259 3.6 48.5 1.0 CG B:ASN257 3.7 68.7 1.0 O B:HOH501 4.0 10.2 1.0 CG B:ASP254 4.0 51.1 1.0 O A:GLY274 4.2 57.3 1.0 CA B:THR260 4.4 51.5 1.0 N B:THR260 4.4 48.9 1.0 ND2 B:ASN257 4.4 68.0 1.0 OG1 B:THR260 4.4 57.4 1.0 CB B:ASP254 4.5 56.8 1.0 CA B:ILE259 4.6 48.1 1.0 CA B:ASN257 4.7 68.6 1.0 N B:ILE259 4.7 52.5 1.0 CB B:ASN257 4.7 69.0 1.0 CB B:ILE259 4.8 42.7 1.0 CB B:THR260 5.0 54.9 1.0

Calcium binding site 4 out of 4 in the Crystal Structure of Anemone Sting (Nematostella Vectensis) in Apo 'Unrotated' Closed Conformation


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of Anemone Sting (Nematostella Vectensis) in Apo 'Unrotated' Closed Conformation within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca402 b:87.4 occ:1.00 O B:SER226 2.6 94.8 1.0 CB B:SER226 3.1 0.5 1.0 C B:SER226 3.5 93.1 1.0 CA B:SER226 3.6 96.8 1.0 OG B:SER226 4.3 0.8 1.0 N B:LYS227 4.7 88.9 1.0

P.J.Kranzusch, S.C.Wilson, A.S.Lee, J.M.Berger, J.A.Doudna, R.E.Vance. Ancient Origin of Cgas-Sting Reveals Mechanism of Universal 2',3' Cgamp Signaling. Mol.Cell V. 59 891 2015.
ISSN: ISSN 1097-2765
PubMed: 26300263
DOI: 10.1016/J.MOLCEL.2015.07.022