Calcium in PDB 5h4y: Crystal Structure of Human Synaptotagmin 5 C2A Domain

The structure of Crystal Structure of Human Synaptotagmin 5 C2A Domain, PDB code: 5h4y was solved by X.Qiu, Y.Gao, M.Teng, L.Niu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.76 / 1.90
Space group	P 65
Cell size a, b, c (Å), α, β, γ (°)	93.966, 93.966, 28.052, 90.00, 90.00, 120.00
R / Rfree (%)	17.1 / 21.2

The binding sites of Calcium atom in the Crystal Structure of Human Synaptotagmin 5 C2A Domain (pdb code 5h4y). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Crystal Structure of Human Synaptotagmin 5 C2A Domain, PDB code: 5h4y:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Crystal Structure of Human Synaptotagmin 5 C2A Domain


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 Human Synaptotagmin 5 C2A Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca301 b:15.6 occ:1.00 O A:PHE198 2.4 16.6 1.0 OD2 A:ASP145 2.4 16.0 1.0 OD1 A:ASP197 2.4 13.0 1.0 O A:HOH448 2.4 16.2 1.0 OD1 A:ASP199 2.4 15.6 1.0 OD2 A:ASP139 2.5 17.0 1.0 OD1 A:ASP139 2.5 12.8 1.0 CG A:ASP139 2.9 15.3 1.0 CG A:ASP197 3.2 16.1 1.0 OD2 A:ASP197 3.3 14.2 1.0 C A:PHE198 3.5 16.6 1.0 CG A:ASP145 3.5 15.6 1.0 CG A:ASP199 3.7 15.4 1.0 CA A:CA302 3.8 16.4 1.0 N A:ASP145 4.0 14.0 1.0 CB A:ASP145 4.0 13.7 1.0 CA A:ASP199 4.0 16.1 1.0 N A:ASP199 4.1 16.4 1.0 NE2 A:GLN167 4.4 13.7 1.0 CB A:ASP139 4.4 15.1 1.0 CB A:ASP199 4.5 15.3 1.0 N A:PHE198 4.5 15.4 1.0 O A:HOH506 4.5 31.0 1.0 OD2 A:ASP199 4.5 15.7 1.0 C A:ASP197 4.6 15.4 1.0 OD1 A:ASP145 4.6 15.5 1.0 C A:SER144 4.6 14.1 1.0 CA A:PHE198 4.6 16.7 1.0 CB A:ASP197 4.6 15.2 1.0 CA A:ASP145 4.6 14.0 1.0 O A:HOH466 4.7 29.5 1.0 CA A:SER144 4.7 14.1 1.0 OXT A:ACT304 4.7 18.8 1.0 O A:ASP197 4.8 15.2 1.0 CH3 A:ACT304 4.8 19.4 1.0 C A:ACT304 4.9 19.2 1.0

Calcium binding site 2 out of 3 in the Crystal Structure of Human Synaptotagmin 5 C2A Domain


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 Human Synaptotagmin 5 C2A Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca302 b:16.4 occ:1.00 OD2 A:ASP197 2.3 14.2 1.0 OD1 A:ASP139 2.3 12.8 1.0 OD2 A:ASP205 2.4 18.8 1.0 O A:LEU138 2.4 15.8 1.0 O A:HOH504 2.5 16.4 1.0 OD2 A:ASP199 2.5 15.7 1.0 OD1 A:ASP199 2.5 15.6 1.0 CG A:ASP199 2.9 15.4 1.0 C A:LEU138 3.3 15.4 1.0 CG A:ASP197 3.4 16.1 1.0 CG A:ASP205 3.5 18.3 1.0 CG A:ASP139 3.6 15.3 1.0 CA A:CA301 3.8 15.6 1.0 N A:ASP139 3.9 15.6 1.0 CA A:ASP139 3.9 15.2 1.0 O A:HOH495 3.9 17.1 1.0 CA A:CA303 4.0 16.4 1.0 OD1 A:ASP197 4.0 13.0 1.0 O A:HOH474 4.1 36.2 1.0 CB A:LEU138 4.2 16.1 1.0 CB A:ASP205 4.2 16.3 1.0 CB A:ASP139 4.3 15.1 1.0 CA A:LEU138 4.4 15.7 1.0 CB A:ASP199 4.4 15.3 1.0 OD1 A:ASP205 4.4 17.6 1.0 OD2 A:ASP139 4.5 17.0 1.0 CB A:ASP197 4.6 15.2 1.0 O A:HOH481 4.7 16.1 1.0 O A:ASP197 4.9 15.2 1.0

Calcium binding site 3 out of 3 in the Crystal Structure of Human Synaptotagmin 5 C2A Domain


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 Human Synaptotagmin 5 C2A Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca303 b:16.4 occ:1.00 O A:HOH495 2.2 17.1 1.0 OD2 A:ASP199 2.3 15.7 1.0 O A:ARG203 2.4 16.1 1.0 OG A:SER202 2.4 17.0 1.0 O A:HOH505 2.4 19.4 1.0 OD1 A:ASP205 2.5 17.6 1.0 OD2 A:ASP205 2.9 18.8 1.0 CG A:ASP205 3.0 18.3 1.0 CG A:ASP199 3.5 15.4 1.0 CB A:SER202 3.5 17.5 1.0 C A:ARG203 3.6 17.2 1.0 N A:ARG203 4.0 17.2 1.0 C A:SER202 4.0 17.2 1.0 CB A:ASP199 4.0 15.3 1.0 CA A:CA302 4.0 16.4 1.0 O A:HOH504 4.2 16.4 1.0 O A:HOH415 4.2 20.0 1.0 O A:SER202 4.3 16.4 1.0 CA A:SER202 4.3 16.9 1.0 CA A:ARG203 4.4 18.2 1.0 CB A:ASP205 4.4 16.3 1.0 OD1 A:ASP199 4.5 15.6 1.0 C A:ASN204 4.5 17.1 1.0 N A:ASP205 4.5 16.6 1.0 N A:ASN204 4.5 17.1 1.0 CA A:ASN204 4.6 17.2 1.0 O A:HOH447 4.7 35.2 1.0 CA A:ASP205 4.9 16.8 1.0 O A:ASN204 4.9 16.5 1.0 CB A:ARG203 4.9 19.3 1.0 O A:HOH474 5.0 36.2 1.0

X.Qiu, J.Ge, Y.Gao, M.Teng, L.Niu. Structural Analysis of Ca(2+)-Binding Pocket of Synaptotagmin 5 C2A Domain Int. J. Biol. Macromol. V. 95 946 2017.
ISSN: ISSN 1879-0003
PubMed: 27793683
DOI: 10.1016/J.IJBIOMAC.2016.10.083