Calcium in PDB 5h4z: Crystal Structure of S202G Mutant of Human Syt-5 C2A Domain

The structure of Crystal Structure of S202G Mutant of Human Syt-5 C2A Domain, PDB code: 5h4z was solved by X.Qiu, J.Ge, X.Yan, 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)	50.00 / 3.01
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	76.005, 118.656, 109.464, 90.00, 90.00, 90.00
R / Rfree (%)	20 / 25.7

The structure of Crystal Structure of S202G Mutant of Human Syt-5 C2A Domain also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Calcium atom in the Crystal Structure of S202G Mutant of Human Syt-5 C2A Domain (pdb code 5h4z). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the Crystal Structure of S202G Mutant of Human Syt-5 C2A Domain, PDB code: 5h4z:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in the Crystal Structure of S202G Mutant of Human Syt-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 S202G Mutant of Human Syt-5 C2A Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca301 b:10.6 occ:1.00 OD2 A:ASP145 2.2 13.8 1.0 OD1 A:ASP197 2.3 15.8 1.0 O A:HOH404 2.4 17.4 1.0 OD1 A:ASP199 2.4 18.2 1.0 O A:PHE198 2.5 16.9 1.0 OD1 A:ASP139 2.6 16.4 1.0 OD2 A:ASP139 2.7 17.5 1.0 CG A:ASP139 3.0 17.7 1.0 CG A:ASP197 3.0 15.7 1.0 OD2 A:ASP197 3.0 15.4 1.0 CG A:ASP145 3.3 14.2 1.0 C A:PHE198 3.3 17.0 1.0 CG A:ASP199 3.5 17.8 1.0 CA A:CA302 3.6 21.6 1.0 CA A:ASP199 3.8 18.9 1.0 N A:ASP199 3.8 18.1 1.0 CB A:ASP145 3.9 13.2 1.0 N A:ASP145 4.3 13.4 1.0 CB A:ASP199 4.3 18.7 1.0 OD1 A:ASP145 4.3 15.8 1.0 C A:ASP197 4.4 15.5 1.0 N A:PHE198 4.4 16.0 1.0 CA A:PHE198 4.4 16.4 1.0 CB A:ASP197 4.5 15.7 1.0 O A:ASP197 4.5 15.0 1.0 OD2 A:ASP199 4.5 14.4 1.0 CB A:ASP139 4.5 17.9 1.0 CA A:ASP145 4.7 13.1 1.0 CA A:ASP197 4.9 15.5 1.0

Calcium binding site 2 out of 6 in the Crystal Structure of S202G Mutant of Human Syt-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 S202G Mutant of Human Syt-5 C2A Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca302 b:21.6 occ:1.00 OD2 A:ASP197 2.2 15.4 1.0 OD1 A:ASP199 2.3 18.2 1.0 OD1 A:ASP139 2.3 16.4 1.0 OD2 A:ASP205 2.3 20.2 1.0 O A:LEU138 2.4 17.3 1.0 OD2 A:ASP199 2.6 14.4 1.0 CG A:ASP199 2.8 17.8 1.0 C A:LEU138 3.3 17.3 1.0 CG A:ASP197 3.4 15.7 1.0 CG A:ASP139 3.5 17.7 1.0 CG A:ASP205 3.5 20.9 1.0 CA A:CA301 3.6 10.6 1.0 N A:ASP139 3.9 17.6 1.0 CA A:ASP139 4.0 18.1 1.0 OD1 A:ASP197 4.1 15.8 1.0 CB A:ASP199 4.3 18.7 1.0 OD1 A:ASP205 4.3 19.7 1.0 CB A:ASP139 4.3 17.9 1.0 CB A:LEU138 4.3 16.6 1.0 OD2 A:ASP139 4.4 17.5 1.0 CA A:CA303 4.4 24.7 1.0 CA A:LEU138 4.4 16.9 1.0 CB A:ASP205 4.5 21.2 1.0 CB A:ASP197 4.6 15.7 1.0 O A:HOH404 4.6 17.4 1.0 O A:ASP197 4.9 15.0 1.0

Calcium binding site 3 out of 6 in the Crystal Structure of S202G Mutant of Human Syt-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 S202G Mutant of Human Syt-5 C2A Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca303 b:24.7 occ:1.00 OD2 A:ASP199 2.3 14.4 1.0 O A:HOH416 2.3 25.4 1.0 OD1 A:ASP205 2.4 19.7 1.0 O A:ARG203 2.4 23.3 1.0 O A:HOH417 2.6 35.7 1.0 CG A:ASP205 3.2 20.9 1.0 OD2 A:ASP205 3.3 20.2 1.0 CG A:ASP199 3.4 17.8 1.0 C A:ARG203 3.6 23.4 1.0 CB A:ASP199 3.8 18.7 1.0 N A:ARG203 4.2 24.3 1.0 O A:HOH408 4.4 16.2 1.0 CA A:CA302 4.4 21.6 1.0 CA A:ARG203 4.4 24.0 1.0 OD1 A:ASP199 4.4 18.2 1.0 C A:GLY202 4.5 24.7 1.0 N A:ASN204 4.6 22.7 1.0 O A:HOH421 4.6 32.0 1.0 CB A:ASP205 4.6 21.2 1.0 N A:ASP205 4.6 21.3 1.0 C A:ASN204 4.7 21.5 1.0 CA A:ASN204 4.7 21.8 1.0 CB A:ARG203 4.7 24.4 1.0 O A:GLY202 4.8 24.8 1.0 CA A:GLY202 5.0 24.7 1.0

Calcium binding site 4 out of 6 in the Crystal Structure of S202G Mutant of Human Syt-5 C2A Domain


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 S202G Mutant of Human Syt-5 C2A Domain within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca301 b:35.1 occ:1.00 OD2 B:ASP145 2.3 25.1 1.0 OD1 B:ASP199 2.3 39.7 1.0 OD2 B:ASP139 2.3 28.9 1.0 O B:PHE198 2.3 38.5 1.0 OD1 B:ASP139 2.4 28.2 1.0 OD1 B:ASP197 2.5 31.5 1.0 CG B:ASP139 2.7 29.6 1.0 OD2 B:ASP197 3.2 31.9 1.0 CG B:ASP197 3.2 32.3 1.0 CG B:ASP145 3.4 26.9 1.0 C B:PHE198 3.5 38.7 1.0 CG B:ASP199 3.5 40.5 1.0 CA B:CA302 3.8 37.8 1.0 CB B:ASP145 3.9 26.9 1.0 CA B:ASP199 4.1 41.0 1.0 N B:ASP199 4.2 40.0 1.0 CB B:ASP139 4.2 30.0 1.0 N B:ASP145 4.3 27.5 1.0 OD2 B:ASP199 4.3 39.4 1.0 CB B:ASP199 4.4 41.0 1.0 N B:PHE198 4.4 36.4 1.0 OD1 B:ASP145 4.4 27.5 1.0 CA B:PHE198 4.5 37.8 1.0 C B:ASP197 4.5 34.6 1.0 NE2 B:GLN167 4.6 37.6 1.0 CB B:ASP197 4.6 33.0 1.0 CA B:ASP145 4.8 26.8 1.0 O B:ASP197 4.8 34.8 1.0 C B:SER144 4.9 28.5 1.0

Calcium binding site 5 out of 6 in the Crystal Structure of S202G Mutant of Human Syt-5 C2A Domain


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Crystal Structure of S202G Mutant of Human Syt-5 C2A Domain within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca302 b:37.8 occ:1.00 OD2 B:ASP205 2.2 37.2 1.0 O B:LEU138 2.2 28.5 1.0 OD1 B:ASP139 2.3 28.2 1.0 OD2 B:ASP197 2.3 31.9 1.0 OD2 B:ASP199 2.4 39.4 1.0 O B:HOH405 2.7 33.5 1.0 OD1 B:ASP199 2.8 39.7 1.0 CG B:ASP199 3.0 40.5 1.0 C B:LEU138 3.3 28.8 1.0 CG B:ASP205 3.4 36.7 1.0 CG B:ASP139 3.5 29.6 1.0 CG B:ASP197 3.6 32.3 1.0 CA B:CA301 3.8 35.1 1.0 CA B:ASP139 3.9 29.9 1.0 CA B:CA303 3.9 55.0 1.0 N B:ASP139 4.0 29.3 1.0 OD1 B:ASP197 4.2 31.5 1.0 OD1 B:ASP205 4.2 37.1 1.0 CB B:ASP139 4.3 30.0 1.0 CB B:ASP205 4.4 36.2 1.0 OD2 B:ASP139 4.4 28.9 1.0 CB B:ASP199 4.5 41.0 1.0 CB B:LEU138 4.5 28.4 1.0 CA B:LEU138 4.5 28.3 1.0 CB B:ASP197 4.7 33.0 1.0

Calcium binding site 6 out of 6 in the Crystal Structure of S202G Mutant of Human Syt-5 C2A Domain


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Crystal Structure of S202G Mutant of Human Syt-5 C2A Domain within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca303 b:55.0 occ:1.00 OD2 B:ASP199 2.3 39.4 1.0 O B:HOH405 2.6 33.5 1.0 O B:ARG203 2.6 43.4 1.0 O B:HOH403 2.7 54.7 1.0 OD1 B:ASP205 2.8 37.1 1.0 OD2 B:ASP205 3.1 37.2 1.0 CG B:ASP205 3.3 36.7 1.0 CG B:ASP199 3.4 40.5 1.0 C B:ARG203 3.8 43.4 1.0 CA B:CA302 3.9 37.8 1.0 CB B:ASP199 3.9 41.0 1.0 N B:ARG203 4.2 45.2 1.0 CA B:GLY202 4.3 46.5 1.0 C B:GLY202 4.3 46.0 1.0 OD1 B:ASP199 4.5 39.7 1.0 CA B:ARG203 4.6 44.5 1.0 N B:ASN204 4.7 42.0 1.0 CB B:ASP205 4.8 36.2 1.0 N B:ASP205 4.8 37.6 1.0 CA B:ASN204 4.8 40.6 1.0 C B:ASN204 4.9 39.2 1.0 O B:GLY202 4.9 45.9 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