Calcium in PDB 1w15: Rat Synaptotagmin 4 C2B Domain in the Presence of Calcium

The structure of Rat Synaptotagmin 4 C2B Domain in the Presence of Calcium, PDB code: 1w15 was solved by H.Dai, O.-H.Shin, M.Machius, D.R.Tomchick, T.C.Sudhof, J.Rizo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 1.93
Space group	P 63 2 2
Cell size a, b, c (Å), α, β, γ (°)	91.490, 91.490, 122.142, 90.00, 90.00, 120.00
R / Rfree (%)	20.4 / 23.3

The structure of Rat Synaptotagmin 4 C2B Domain in the Presence of Calcium also contains other interesting chemical elements:

Chlorine	(Cl)	9 atoms
Sodium	(Na)	2 atoms

The binding sites of Calcium atom in the Rat Synaptotagmin 4 C2B Domain in the Presence of Calcium (pdb code 1w15). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Rat Synaptotagmin 4 C2B Domain in the Presence of Calcium, PDB code: 1w15:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Rat Synaptotagmin 4 C2B Domain in the Presence of Calcium


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Rat Synaptotagmin 4 C2B Domain in the Presence of Calcium within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1001 b:70.7 occ:1.00 OD2 A:ASP324 2.5 45.7 1.0 OE1 A:GLU380 2.6 54.7 1.0 O A:SER379 2.7 38.1 1.0 OD1 A:ASP378 2.7 38.5 1.0 O A:HOH2049 2.7 73.3 1.0 OD2 A:ASP378 3.2 42.8 1.0 CG A:ASP378 3.3 38.6 1.0 CG A:ASP324 3.4 43.5 1.0 C A:SER379 3.7 37.9 1.0 CD A:GLU380 3.7 49.5 1.0 CB A:ASP324 3.8 39.9 1.0 N A:ASP324 4.0 43.5 1.0 CA A:GLU380 4.1 37.8 1.0 CB A:GLU380 4.1 38.6 1.0 N A:GLU380 4.4 37.6 1.0 OD1 A:ASP324 4.4 43.8 1.0 OE2 A:GLU380 4.5 54.0 1.0 N A:SER379 4.5 37.4 1.0 CG A:GLU380 4.5 42.2 1.0 CA A:ASP324 4.6 41.0 1.0 O A:HOH2051 4.6 61.9 1.0 C A:SER323 4.6 46.3 1.0 O A:LEU322 4.7 52.5 1.0 CA A:SER323 4.7 48.4 1.0 CB A:ASP378 4.7 36.1 1.0 C A:ASP378 4.7 37.9 1.0 CA A:SER379 4.7 38.1 1.0

Calcium binding site 2 out of 3 in the Rat Synaptotagmin 4 C2B Domain in the Presence of Calcium


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Rat Synaptotagmin 4 C2B Domain in the Presence of Calcium within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1002 b:48.5 occ:1.00 O A:HOH2042 2.1 56.1 1.0 O A:HOH2010 2.3 57.1 1.0 O A:GLU365 2.5 42.5 1.0 C A:GLU365 3.7 43.5 1.0 CB A:GLU365 4.4 44.8 1.0 CA A:GLU365 4.5 43.7 1.0 OH A:TYR297 4.5 32.6 1.0 O A:SER299 4.5 42.8 1.0 OE1 A:GLU365 4.7 56.2 1.0 N A:SER366 4.7 42.3 1.0 CA A:SER366 4.8 42.8 1.0 CB A:SER366 4.9 43.5 1.0

Calcium binding site 3 out of 3 in the Rat Synaptotagmin 4 C2B Domain in the Presence of Calcium


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Rat Synaptotagmin 4 C2B Domain in the Presence of Calcium within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1003 b:95.8 occ:1.00 OXT A:GLY425 2.4 60.7 1.0 OD1 A:ASP424 2.5 66.0 1.0 O A:HOH2062 2.9 65.7 1.0 CG A:ASP424 3.3 63.0 1.0 OD2 A:ASP424 3.3 68.3 1.0 C A:GLY425 3.5 60.1 1.0 O A:HOH2091 3.6 66.1 1.0 N A:GLY425 4.0 58.2 1.0 O A:HOH2092 4.2 30.9 1.0 CA A:GLY425 4.3 59.2 1.0 O A:GLY425 4.3 60.8 1.0 CB A:ASP424 4.7 58.0 1.0 C A:ASP424 4.8 57.4 1.0 O A:HOH2089 4.9 70.5 1.0 CA A:ASP424 5.0 56.6 1.0

H.Dai, O.-H.Shin, M.Machius, D.R.Tomchick, T.C.Sudhof, J.Rizo. Structural Basis For the Evolutionary Inactivation of CA2+ Binding to Synaptotagmin 4 Nat.Struct.Mol.Biol. V. 11 844 2004.
ISSN: ISSN 1545-9993
PubMed: 15311271
DOI: 10.1038/NSMB817