Sodium 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
Calcium	(Ca)	3 atoms

The binding sites of Sodium 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 Sodium atom.
In total 2 binding sites of Sodium where determined in the Rat Synaptotagmin 4 C2B Domain in the Presence of Calcium, PDB code: 1w15:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Rat Synaptotagmin 4 C2B Domain in the Presence of Calcium


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na 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:Na2001 b:46.7 occ:1.00 OG A:SER339 3.2 39.6 1.0 N A:ASP361 3.3 37.6 1.0 O A:HOH2041 3.3 48.9 1.0 CB A:SER339 3.7 37.9 1.0 CA A:PHE360 3.7 37.5 1.0 CD1 A:PHE360 3.9 40.0 1.0 C A:PHE360 4.0 37.1 1.0 CB A:ASP361 4.1 40.0 1.0 O A:VAL359 4.1 34.9 1.0 CA A:ASP361 4.3 39.1 1.0 OD2 A:ASP361 4.3 51.1 1.0 O A:HOH2040 4.3 67.2 1.0 CB A:PHE360 4.3 36.4 1.0 CG A:ASP361 4.4 44.1 1.0 NZ A:LYS341 4.5 44.5 1.0 O A:ASP361 4.5 40.6 1.0 CG A:PHE360 4.6 37.7 1.0 CE A:LYS341 4.6 41.4 1.0 CE1 A:PHE360 4.8 39.2 1.0 N A:PHE360 4.8 36.6 1.0 C A:ASP361 4.9 38.8 1.0 C A:VAL359 4.9 36.3 1.0

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


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na 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:Na2002 b:42.5 occ:1.00 O A:GLU380 2.3 36.7 1.0 O A:SER383 2.3 33.3 1.0 OD1 A:ASN385 2.4 31.1 1.0 O A:HOH2050 2.4 61.7 1.0 O A:HOH2059 2.5 34.6 0.5 O A:HOH2054 2.9 51.2 1.0 CG A:ASN385 3.3 34.3 1.0 C A:GLU380 3.4 37.0 1.0 C A:SER383 3.5 33.0 1.0 N A:ASN385 3.8 32.4 1.0 ND2 A:ASN385 3.9 37.4 1.0 N A:GLU380 4.0 37.6 1.0 N A:SER383 4.1 34.0 1.0 C A:ARG384 4.2 32.7 1.0 CA A:GLU380 4.2 37.8 1.0 O A:HOH2060 4.2 34.3 0.5 N A:ARG381 4.3 35.8 1.0 CA A:ASN385 4.3 33.0 1.0 CA A:ARG384 4.4 31.7 1.0 CB A:ASN385 4.4 33.0 1.0 CA A:ARG381 4.4 36.4 1.0 N A:ARG384 4.4 32.5 1.0 N A:GLY382 4.4 34.8 1.0 CA A:SER383 4.4 34.9 1.0 CB A:GLU380 4.6 38.6 1.0 C A:ARG381 4.6 35.0 1.0 OG A:SER383 4.8 39.4 1.0 O A:ARG384 4.9 33.5 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