Calcium in PDB 7tx9: Human Synaptotagmin-1 C2B Y312F CA2+ Bound

The structure of Human Synaptotagmin-1 C2B Y312F CA2+ Bound, PDB code: 7tx9 was solved by M.J.Dominguez, S.Karmakar, K.L.Fuson, R.B.Sutton, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	34.61 / 1.34
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	54.29, 54.29, 102.3, 90, 90, 120
R / Rfree (%)	16.9 / 18.8

The structure of Human Synaptotagmin-1 C2B Y312F CA2+ Bound also contains other interesting chemical elements:

Chlorine

(Cl)

4 atoms

The binding sites of Calcium atom in the Human Synaptotagmin-1 C2B Y312F CA2+ Bound (pdb code 7tx9). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Human Synaptotagmin-1 C2B Y312F CA2+ Bound, PDB code: 7tx9:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Human Synaptotagmin-1 C2B Y312F CA2+ Bound


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Human Synaptotagmin-1 C2B Y312F CA2+ Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca501 b:23.2 occ:0.56 OD1 A:ASP304 2.4 42.5 1.0 O A:HOH603 2.5 56.6 1.0 O A:TYR365 2.5 18.2 1.0 OD1 A:ASP366 2.5 30.9 1.0 OD2 A:ASP310 2.6 27.9 1.0 OD1 A:ASP364 2.7 20.7 1.0 OD2 A:ASP364 2.7 25.8 1.0 CG A:ASP364 3.0 20.7 1.0 CG A:ASP304 3.2 38.7 1.0 HB2 A:ASP310 3.2 25.1 1.0 OD2 A:ASP304 3.3 37.2 1.0 C A:TYR365 3.5 16.7 1.0 H A:ASP310 3.6 22.2 1.0 CA A:CA502 3.6 59.2 0.6 CG A:ASP310 3.6 23.4 1.0 CG A:ASP366 3.6 28.4 1.0 HA A:ASP366 3.7 25.6 1.0 CB A:ASP310 3.9 20.9 1.0 N A:ASP310 4.1 18.5 1.0 N A:ASP366 4.2 18.3 1.0 CA A:ASP366 4.3 21.4 1.0 N A:TYR365 4.3 16.2 1.0 H A:TYR365 4.3 19.4 1.0 HA A:SER309 4.3 26.3 1.0 OD2 A:ASP366 4.4 31.9 1.0 CB A:ASP364 4.4 17.0 1.0 CA A:TYR365 4.5 15.9 1.0 C A:ASP364 4.5 15.8 1.0 CB A:ASP366 4.6 23.2 1.0 CA A:ASP310 4.6 18.6 1.0 HB3 A:ASP310 4.6 25.1 1.0 CB A:ASP304 4.7 36.3 1.0 OD1 A:ASP310 4.7 23.9 1.0 O A:HOH673 4.8 45.6 1.0 HB3 A:ASP364 4.8 20.4 1.0 C A:SER309 4.9 20.1 1.0 HB3 A:TYR365 4.9 19.9 1.0 HB2 A:MET303 4.9 32.5 1.0 HA A:ASP304 4.9 43.0 1.0 HA A:ASP364 4.9 18.1 1.0 H A:ASP366 4.9 22.0 1.0 CA A:ASP364 4.9 15.1 1.0 O A:ASP364 4.9 18.5 1.0 HB2 A:ASP364 5.0 20.4 1.0

Calcium binding site 2 out of 3 in the Human Synaptotagmin-1 C2B Y312F CA2+ Bound


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Human Synaptotagmin-1 C2B Y312F CA2+ Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca502 b:59.2 occ:0.60 CA A:CA502 0.0 59.2 0.6 OD2 A:ASP364 2.5 25.8 1.0 CA A:CA502 2.9 51.3 0.4 OD1 A:ASP304 2.9 42.5 1.0 O A:MET303 2.9 36.0 1.0 OD2 A:ASP366 3.0 31.9 1.0 OD1 A:ASP366 3.0 30.9 1.0 HA A:ASP304 3.3 43.0 1.0 CG A:ASP366 3.4 28.4 1.0 CA A:CA501 3.6 23.2 0.6 C A:MET303 3.6 32.3 1.0 HB3 A:MET303 3.7 32.5 1.0 CG A:ASP364 3.7 20.7 1.0 O A:HOH656 3.8 24.2 1.0 O A:HOH669 3.8 42.7 1.0 CG A:ASP304 4.1 38.7 1.0 CA A:ASP304 4.1 35.8 1.0 O A:HOH603 4.1 56.6 1.0 N A:ASP304 4.1 34.1 1.0 HB2 A:MET303 4.2 32.5 1.0 CB A:MET303 4.3 27.1 1.0 OD1 A:ASP364 4.4 20.7 1.0 HB3 A:ASP364 4.5 20.4 1.0 CA A:MET303 4.6 27.3 1.0 CB A:ASP304 4.7 36.3 1.0 CB A:ASP364 4.7 17.0 1.0 H A:ASP304 4.8 40.9 1.0 CB A:ASP366 4.9 23.2 1.0 H A:VAL305 5.0 54.7 1.0 HE3 A:MET303 5.0 34.4 1.0 HA A:MET303 5.0 32.7 1.0

Calcium binding site 3 out of 3 in the Human Synaptotagmin-1 C2B Y312F CA2+ Bound


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Human Synaptotagmin-1 C2B Y312F CA2+ Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca502 b:51.3 occ:0.40 CA A:CA502 0.0 51.3 0.4 O A:HOH656 2.6 24.2 1.0 CA A:CA502 2.9 59.2 0.6 OD2 A:ASP372 2.9 35.7 1.0 HB2 A:ASP372 2.9 28.7 1.0 HE3 A:MET303 2.9 34.4 1.0 HB3 A:MET303 3.2 32.5 1.0 OD2 A:ASP364 3.4 25.8 1.0 HB3 A:ASP364 3.6 20.4 1.0 CG A:ASP372 3.7 29.9 1.0 OD2 A:ASP366 3.7 31.9 1.0 CB A:ASP372 3.7 23.9 1.0 H A:ASP372 3.8 23.0 1.0 O A:MET303 3.8 36.0 1.0 CE A:MET303 3.9 28.7 1.0 CB A:MET303 4.2 27.1 1.0 HE1 A:MET303 4.2 34.4 1.0 HB3 A:ASP372 4.2 28.7 1.0 HE2 A:MET303 4.3 34.4 1.0 CG A:ASP364 4.3 20.7 1.0 CB A:ASP364 4.4 17.0 1.0 N A:ASP372 4.5 19.1 1.0 HB2 A:MET303 4.6 32.5 1.0 CG A:ASP366 4.6 28.4 1.0 C A:MET303 4.6 32.3 1.0 CA A:ASP372 4.7 19.9 1.0 HB2 A:ASP364 4.7 20.4 1.0 OD1 A:ASP372 4.8 33.4 1.0 HA A:MET303 4.8 32.7 1.0 CA A:MET303 4.9 27.3 1.0 OD1 A:ASP366 4.9 30.9 1.0 CG A:MET303 5.0 26.2 1.0 SD A:MET303 5.0 27.6 1.0 HG3 A:MET303 5.0 31.5 1.0

M.J.Dominguez, S.Karmakar, K.L.Fuson, R.B.Sutton. Human Synaptotagmin-1 C2B Y312F CA2+ Bound To Be Published.