Sodium in PDB 1w16: Rat Synaptotagmin 4 C2B Domain in the Absence of Calcium

The structure of Rat Synaptotagmin 4 C2B Domain in the Absence of Calcium, PDB code: 1w16 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 / 2.30
Space group	P 63 2 2
Cell size a, b, c (Å), α, β, γ (°)	91.061, 91.061, 122.860, 90.00, 90.00, 120.00
R / Rfree (%)	21.3 / 25.7

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

Chlorine

(Cl)

7 atoms

The binding sites of Sodium atom in the Rat Synaptotagmin 4 C2B Domain in the Absence of Calcium (pdb code 1w16). 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 Absence of Calcium, PDB code: 1w16:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Rat Synaptotagmin 4 C2B Domain in the Absence 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 Absence of Calcium within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1001 b:47.5 occ:1.00 OG A:SER339 3.2 51.8 1.0 N A:ASP361 3.3 52.4 1.0 CA A:PHE360 3.6 52.2 1.0 CD1 A:PHE360 3.8 53.1 1.0 CB A:SER339 3.8 51.1 1.0 C A:PHE360 4.0 52.6 1.0 O A:VAL359 4.0 51.8 1.0 O A:HOH2021 4.0 65.0 1.0 CB A:ASP361 4.2 53.7 1.0 NZ A:LYS341 4.2 52.2 1.0 CB A:PHE360 4.2 52.1 1.0 CA A:ASP361 4.3 53.5 1.0 OD2 A:ASP361 4.4 61.4 1.0 CG A:PHE360 4.5 54.2 1.0 CE A:LYS341 4.5 49.8 1.0 CG A:ASP361 4.5 56.6 1.0 O A:ASP361 4.6 53.3 1.0 N A:PHE360 4.7 52.1 1.0 CE1 A:PHE360 4.7 55.7 1.0 C A:VAL359 4.7 51.8 1.0 C A:ASP361 5.0 52.6 1.0

Sodium binding site 2 out of 2 in the Rat Synaptotagmin 4 C2B Domain in the Absence 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 Absence of Calcium within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1002 b:60.9 occ:1.00 O A:GLU380 2.3 58.8 1.0 O A:SER383 2.4 48.5 1.0 OD1 A:ASN385 2.5 46.5 1.0 O A:HOH2033 2.6 64.9 1.0 O A:HOH2035 3.0 57.7 1.0 CG A:ASN385 3.4 49.0 1.0 C A:GLU380 3.4 58.7 1.0 C A:SER383 3.6 48.6 1.0 ND2 A:ASN385 3.8 48.2 1.0 N A:ASN385 4.0 47.1 1.0 N A:SER383 4.0 50.1 1.0 N A:GLU380 4.1 59.2 1.0 N A:ARG381 4.3 58.3 1.0 O A:HOH2037 4.3 27.4 0.5 CA A:ARG381 4.3 58.2 1.0 CA A:GLU380 4.4 59.3 1.0 N A:GLY382 4.4 54.5 1.0 C A:ARG384 4.4 46.7 1.0 CA A:SER383 4.4 49.6 1.0 N A:ARG384 4.5 48.2 1.0 CA A:ASN385 4.6 48.3 1.0 CB A:ASN385 4.6 48.4 1.0 CA A:ARG384 4.6 47.4 1.0 C A:ARG381 4.6 56.2 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