Sodium in PDB 4npj: Extended-Synaptotagmin 2, C2A- and C2B-Domains

The structure of Extended-Synaptotagmin 2, C2A- and C2B-Domains, PDB code: 4npj was solved by D.R.Tomchick, J.Rizo, J.Xu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	41.89 / 2.10
Space group	P 43
Cell size a, b, c (Å), α, β, γ (°)	62.300, 62.300, 226.395, 90.00, 90.00, 90.00
R / Rfree (%)	20 / 23.9

The structure of Extended-Synaptotagmin 2, C2A- and C2B-Domains also contains other interesting chemical elements:

Chlorine

(Cl)

3 atoms

The binding sites of Sodium atom in the Extended-Synaptotagmin 2, C2A- and C2B-Domains (pdb code 4npj). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the Extended-Synaptotagmin 2, C2A- and C2B-Domains, PDB code: 4npj:

Sodium binding site 1 out of 1 in the Extended-Synaptotagmin 2, C2A- and C2B-Domains


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Extended-Synaptotagmin 2, C2A- and C2B-Domains within 5.0Å range: probe atom residue distance (Å) B Occ B:Na701 b:91.8 occ:1.00 OE2 A:GLU581 2.4 0.2 1.0 O B:ASP464 2.4 75.1 1.0 O A:HOH968 2.5 65.9 1.0 OD1 B:ASP466 2.5 50.5 1.0 HE A:ARG546 2.8 0.2 1.0 O B:ASP462 3.0 86.3 1.0 HD3 A:ARG546 3.3 87.0 1.0 NE A:ARG546 3.4 86.0 1.0 CG B:ASP466 3.4 53.8 1.0 HG2 A:ARG546 3.6 88.0 1.0 CD A:GLU581 3.6 0.7 1.0 H B:ASP462 3.6 86.8 1.0 C B:ASP464 3.6 83.7 1.0 CD A:ARG546 3.8 72.5 1.0 H B:ASP466 3.8 86.2 1.0 OD2 B:ASP466 3.9 57.4 1.0 C B:ASP462 4.0 72.2 1.0 HA B:LYS465 4.0 86.8 1.0 O B:PRO463 4.1 94.0 1.0 N B:ASP466 4.1 71.9 1.0 HG3 A:GLU581 4.1 0.8 1.0 CG A:ARG546 4.2 73.3 1.0 HH21 A:ARG546 4.2 0.4 1.0 C B:PRO463 4.3 83.0 1.0 O B:HOH864 4.3 54.8 1.0 N B:ASP462 4.4 72.3 1.0 HB2 B:ASP462 4.4 98.3 1.0 CZ A:ARG546 4.4 93.1 1.0 CG A:GLU581 4.4 97.3 1.0 C B:LYS465 4.5 77.4 1.0 N B:ASP464 4.5 70.7 1.0 OE1 A:GLU581 4.5 95.8 1.0 CA B:LYS465 4.5 72.3 1.0 N B:LYS465 4.5 76.3 1.0 CB B:ASP466 4.5 48.4 1.0 CA B:ASP464 4.6 94.0 1.0 HG3 A:ARG546 4.6 88.0 1.0 HA B:ASP464 4.7 0.8 1.0 NH2 A:ARG546 4.7 89.5 1.0 HA B:ASP466 4.7 61.0 1.0 CA B:ASP462 4.7 70.5 1.0 HD2 A:ARG546 4.7 87.0 1.0 CA B:ASP466 4.7 50.9 1.0 HB2 B:ASP466 4.7 58.0 1.0 HG2 A:GLU581 4.8 0.8 1.0 HG2 B:GLU461 4.8 83.8 1.0 HA B:PRO463 4.9 90.9 1.0 N B:PRO463 4.9 68.2 1.0 CA B:PRO463 4.9 75.8 1.0 H B:ASP464 4.9 84.9 1.0 CB B:ASP462 5.0 81.9 1.0 HA B:GLU461 5.0 57.6 1.0

J.Xu, T.Bacaj, A.Zhou, D.R.Tomchick, T.C.Sudhof, J.Rizo. Structure and Ca(2+)-Binding Properties of the Tandem C2 Domains of E-SYT2. Structure V. 22 269 2014.
ISSN: ISSN 0969-2126
PubMed: 24373768
DOI: 10.1016/J.STR.2013.11.011