Calcium in PDB 5z1q: Crystal Structures of the Trimeric N-Terminal Domain of Ciliate Euplotes Octocarinatus Centrin

The structure of Crystal Structures of the Trimeric N-Terminal Domain of Ciliate Euplotes Octocarinatus Centrin, PDB code: 5z1q was solved by W.Wang, Y.Zhao, B.Yang, H.Wang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	37.65 / 2.30
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	42.945, 43.045, 43.087, 106.88, 106.89, 106.61
R / Rfree (%)	18.4 / 22.4

The structure of Crystal Structures of the Trimeric N-Terminal Domain of Ciliate Euplotes Octocarinatus Centrin also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Calcium atom in the Crystal Structures of the Trimeric N-Terminal Domain of Ciliate Euplotes Octocarinatus Centrin (pdb code 5z1q). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 5 binding sites of Calcium where determined in the Crystal Structures of the Trimeric N-Terminal Domain of Ciliate Euplotes Octocarinatus Centrin, PDB code: 5z1q:
Jump to Calcium binding site number: 1; 2; 3; 4; 5;

Calcium binding site 1 out of 5 in the Crystal Structures of the Trimeric N-Terminal Domain of Ciliate Euplotes Octocarinatus Centrin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structures of the Trimeric N-Terminal Domain of Ciliate Euplotes Octocarinatus Centrin within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca101 b:60.9 occ:1.00 O C:ALA55 2.3 31.2 1.0 O B:ALA55 2.3 37.3 1.0 O A:ALA55 2.3 34.5 1.0 O A:HOH210 2.5 56.6 1.0 O B:HOH208 2.8 40.7 1.0 C A:ALA55 3.3 32.3 1.0 C C:ALA55 3.3 33.0 1.0 C B:ALA55 3.3 40.9 1.0 CA A:ALA55 3.8 32.4 1.0 CA B:ALA55 3.8 31.0 1.0 CA C:ALA55 3.8 28.6 1.0 CB A:ALA55 4.3 21.1 1.0 CB B:ALA55 4.4 28.1 1.0 CB C:ALA55 4.4 25.3 1.0 N A:LEU56 4.4 37.0 1.0 N C:LEU56 4.4 31.8 1.0 N B:LEU56 4.5 40.7 1.0 O B:HOH212 4.6 38.9 1.0 CA C:LEU56 4.8 30.8 1.0 CA A:LEU56 4.8 30.9 1.0 O A:ARG54 4.8 30.1 1.0 O B:ARG54 4.8 30.6 1.0 O C:ARG54 4.9 29.8 1.0 CA B:LEU56 4.9 28.2 1.0 O A:HOH214 4.9 44.8 1.0

Calcium binding site 2 out of 5 in the Crystal Structures of the Trimeric N-Terminal Domain of Ciliate Euplotes Octocarinatus Centrin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structures of the Trimeric N-Terminal Domain of Ciliate Euplotes Octocarinatus Centrin within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca102 b:83.2 occ:1.00 O A:SER43 2.7 40.8 1.0 OD1 A:ASN39 2.7 66.9 1.0 OE1 A:GLU48 3.2 37.8 1.0 OG1 A:THR41 3.4 52.6 1.0 CG A:ASN39 3.5 69.6 1.0 C A:SER43 3.6 33.6 1.0 ND2 A:ASN39 3.6 66.0 1.0 OD1 A:ASP37 3.8 70.9 1.0 OE2 A:GLU48 3.9 35.0 1.0 CD A:GLU48 3.9 44.4 1.0 OG1 A:THR38 4.0 52.5 1.0 CA A:ILE44 4.0 35.0 1.0 N A:THR38 4.1 56.5 1.0 N A:ILE44 4.2 40.2 1.0 CE1 A:TYR79 4.2 52.3 1.0 N A:ASN39 4.4 67.8 1.0 CA A:ASP37 4.4 49.5 1.0 CD1 A:TYR79 4.6 46.1 1.0 C A:ASP37 4.6 65.0 1.0 CA A:SER43 4.6 39.8 1.0 O A:PHE36 4.7 43.9 1.0 CB A:SER43 4.8 36.2 1.0 CG A:ASP37 4.8 54.5 1.0 CB A:THR41 4.8 56.8 1.0 CG2 A:ILE44 4.8 33.8 1.0 C A:ILE44 4.9 31.2 1.0 N A:SER43 4.9 27.0 1.0 N A:ASP45 4.9 33.9 1.0 CB A:ASN39 4.9 72.5 1.0 CA A:THR38 5.0 55.5 1.0

Calcium binding site 3 out of 5 in the Crystal Structures of the Trimeric N-Terminal Domain of Ciliate Euplotes Octocarinatus Centrin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structures of the Trimeric N-Terminal Domain of Ciliate Euplotes Octocarinatus Centrin within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca101 b:80.0 occ:1.00 O B:HOH204 2.6 36.1 1.0 OE1 B:GLU75 2.7 80.1 1.0 OD1 B:ASP73 2.9 39.7 1.0 O B:TYR79 3.2 33.3 1.0 N B:GLU75 3.4 46.4 1.0 N B:ARG74 3.5 40.3 1.0 CD B:GLU75 3.5 96.4 1.0 CA B:ASP73 3.7 37.1 1.0 CB B:GLU75 3.7 61.4 1.0 OD1 B:ASN77 3.8 55.0 1.0 C B:ASP73 3.8 42.1 1.0 CG B:GLU75 4.0 72.9 1.0 CG B:ASP73 4.0 29.3 1.0 O B:TYR72 4.1 36.4 1.0 CA B:GLU75 4.1 52.1 1.0 C B:ARG74 4.3 41.2 1.0 CA B:ARG74 4.4 40.3 1.0 CB B:ASP73 4.4 34.2 1.0 C B:TYR79 4.4 33.6 1.0 OE2 B:GLU75 4.4 0.1 1.0 CG B:ASN77 4.5 44.3 1.0 N B:GLY76 4.5 42.8 1.0 ND2 B:ASN77 4.6 47.3 1.0 N B:ASP73 4.7 30.1 1.0 CB B:ARG74 4.8 39.8 1.0 O B:ASP73 4.8 49.7 1.0 C B:GLU75 4.8 51.7 1.0 C B:TYR72 4.9 36.8 1.0 CA B:ILE80 5.0 32.3 1.0

Calcium binding site 4 out of 5 in the Crystal Structures of the Trimeric N-Terminal Domain of Ciliate Euplotes Octocarinatus Centrin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structures of the Trimeric N-Terminal Domain of Ciliate Euplotes Octocarinatus Centrin within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca102 b:89.5 occ:1.00 O B:SER43 2.6 47.0 1.0 OD1 B:ASN39 2.7 79.0 1.0 OG1 B:THR41 3.0 59.2 1.0 OD1 B:ASP37 3.2 75.3 1.0 OE1 B:GLU48 3.3 45.2 1.0 CG B:ASN39 3.6 78.6 1.0 C B:SER43 3.7 33.9 1.0 N B:THR38 3.8 69.7 1.0 OE2 B:GLU48 3.9 38.4 1.0 CD B:GLU48 4.0 52.4 1.0 ND2 B:ASN39 4.0 78.1 1.0 N B:ASN39 4.1 75.5 1.0 O B:HOH209 4.2 51.8 1.0 CA B:ASP37 4.3 54.5 1.0 CE1 B:TYR79 4.3 54.0 1.0 CA B:ILE44 4.3 35.2 1.0 C B:ASP37 4.3 66.0 1.0 CG B:ASP37 4.4 67.9 1.0 N B:ILE44 4.4 31.1 1.0 CB B:THR41 4.5 67.2 1.0 O B:PHE36 4.6 44.1 1.0 CA B:THR38 4.7 72.1 1.0 CB B:THR38 4.7 73.0 1.0 CA B:SER43 4.7 39.0 1.0 CD1 B:TYR79 4.7 42.6 1.0 N B:SER43 4.7 31.6 1.0 CB B:ASN39 4.9 84.5 1.0 N B:THR41 4.9 60.4 1.0 C B:THR38 4.9 86.7 1.0 CB B:ASP37 5.0 41.8 1.0 CA B:ASN39 5.0 83.6 1.0 CG2 B:ILE44 5.0 25.6 1.0

Calcium binding site 5 out of 5 in the Crystal Structures of the Trimeric N-Terminal Domain of Ciliate Euplotes Octocarinatus Centrin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Crystal Structures of the Trimeric N-Terminal Domain of Ciliate Euplotes Octocarinatus Centrin within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca101 b:86.0 occ:1.00 OD1 C:ASN39 2.6 76.0 1.0 O C:SER43 2.6 47.2 1.0 OG1 C:THR41 3.1 57.2 1.0 OE1 C:GLU48 3.4 52.8 1.0 CG C:ASN39 3.5 79.0 1.0 C C:SER43 3.7 37.6 1.0 ND2 C:ASN39 3.7 55.8 1.0 OD1 C:ASP37 3.8 63.6 1.0 N C:THR38 4.0 59.5 1.0 OE2 C:GLU48 4.1 41.0 1.0 CD C:GLU48 4.1 57.6 1.0 O C:HOH211 4.2 58.8 1.0 N C:ASN39 4.3 82.4 1.0 CA C:ILE44 4.3 29.8 1.0 N C:ILE44 4.4 39.7 1.0 CE1 C:TYR79 4.5 56.7 1.0 CB C:THR41 4.6 58.9 1.0 CA C:ASP37 4.6 47.7 1.0 CA C:SER43 4.6 50.9 1.0 C C:ASP37 4.7 63.4 1.0 O C:PHE36 4.7 49.4 1.0 CB C:THR38 4.8 77.8 1.0 N C:SER43 4.8 38.8 1.0 CB C:SER43 4.8 41.1 1.0 CB C:ASN39 4.8 94.4 1.0 CD1 C:TYR79 4.8 45.7 1.0 CA C:THR38 4.8 76.7 1.0 CG C:ASP37 4.9 56.3 1.0

W.Wang, Y.Zhao, H.Wang, B.Yang. Crystal Structure of the Trimeric N-Terminal Domain of Ciliate Euplotes Octocarinatus Centrin Binding with Calcium Ions Protein Sci. V. 27 1102 2018.
ISSN: ESSN 1469-896X
PubMed: 29607555
DOI: 10.1002/PRO.3418