Calcium in PDB 4npk: Extended-Synaptotagmin 2, C2A- and C2B-Domains, Calcium Bound

The structure of Extended-Synaptotagmin 2, C2A- and C2B-Domains, Calcium Bound, PDB code: 4npk 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)	28.99 / 2.55
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	95.840, 53.194, 85.276, 90.00, 99.95, 90.00
R / Rfree (%)	22.2 / 28.6

The binding sites of Calcium atom in the Extended-Synaptotagmin 2, C2A- and C2B-Domains, Calcium Bound (pdb code 4npk). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Extended-Synaptotagmin 2, C2A- and C2B-Domains, Calcium Bound, PDB code: 4npk:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Extended-Synaptotagmin 2, C2A- and C2B-Domains, Calcium Bound


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Extended-Synaptotagmin 2, C2A- and C2B-Domains, Calcium Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca801 b:0.9 occ:1.00 OD1 A:ASP462 2.3 0.4 1.0 OD2 A:ASP413 2.3 0.1 1.0 OD1 A:ASP460 2.4 0.1 1.0 OD1 A:ASP401 2.4 0.8 1.0 O A:HOH903 2.4 0.2 1.0 OD2 A:ASP401 2.5 0.5 1.0 O A:GLU461 2.6 0.9 1.0 CG A:ASP401 2.8 0.1 1.0 OD2 A:ASP460 2.8 0.4 1.0 CG A:ASP460 2.9 0.5 1.0 HA A:ASP462 3.3 0.1 1.0 C A:GLU461 3.4 0.3 1.0 CG A:ASP413 3.5 0.1 1.0 CG A:ASP462 3.5 1.0 1.0 H A:ASP413 3.8 0.7 1.0 HA A:SER412 3.8 0.1 1.0 HB2 A:ASP413 3.9 0.8 1.0 CA A:CA802 3.9 0.4 1.0 CA A:ASP462 3.9 0.1 1.0 N A:ASP462 4.0 0.8 1.0 O A:HOH904 4.2 95.4 1.0 N A:ASP413 4.2 0.7 1.0 CB A:ASP413 4.2 0.5 1.0 CB A:ASP462 4.3 0.8 1.0 CB A:ASP401 4.3 0.4 1.0 CB A:ASP460 4.4 0.1 1.0 OD1 A:ASP413 4.4 0.1 1.0 HB3 A:SER412 4.4 0.5 1.0 N A:GLU461 4.4 0.4 1.0 OD2 A:ASP462 4.5 0.2 1.0 CA A:GLU461 4.5 0.3 1.0 C A:ASP460 4.5 0.5 1.0 HD3 A:PRO463 4.5 0.5 1.0 HB3 A:ASP401 4.6 0.3 1.0 CA A:SER412 4.6 0.7 1.0 HB3 A:ASP462 4.6 0.9 1.0 H A:GLU461 4.7 0.2 1.0 C A:SER412 4.7 0.4 1.0 H A:ASP462 4.7 0.7 1.0 HB2 A:ASP401 4.7 0.3 1.0 HB3 A:GLU461 4.8 0.5 1.0 O A:ASP460 4.8 1.0 1.0 HB3 A:ASP460 4.8 0.7 1.0 CA A:ASP413 4.9 0.6 1.0 HB2 A:ASP460 4.9 0.7 1.0 CA A:ASP460 4.9 0.8 1.0 CB A:SER412 5.0 0.6 1.0

Calcium binding site 2 out of 3 in the Extended-Synaptotagmin 2, C2A- and C2B-Domains, Calcium Bound


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Extended-Synaptotagmin 2, C2A- and C2B-Domains, Calcium Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca802 b:0.4 occ:1.00 OD2 A:ASP460 2.3 0.4 1.0 OD2 A:ASP467 2.4 0.4 1.0 OD2 A:ASP401 2.4 0.5 1.0 O A:HOH904 2.4 95.4 1.0 OD1 A:ASP462 2.5 0.4 1.0 OD2 A:ASP462 2.5 0.2 1.0 O A:LYS400 2.6 0.2 1.0 CG A:ASP462 2.7 1.0 1.0 HA A:ASP401 3.3 0.4 1.0 C A:LYS400 3.3 0.4 1.0 HB3 A:LYS400 3.4 0.4 1.0 CG A:ASP467 3.5 0.9 1.0 HB2 A:LYS400 3.5 0.4 1.0 CG A:ASP460 3.6 0.5 1.0 CG A:ASP401 3.6 0.1 1.0 HB2 A:ASP467 3.7 0.3 1.0 CB A:LYS400 3.8 0.0 1.0 CA A:CA801 3.9 0.9 1.0 CA A:ASP401 4.0 1.0 1.0 N A:ASP401 4.0 0.1 1.0 CB A:ASP462 4.1 0.8 1.0 HB3 A:ASP460 4.1 0.7 1.0 HB3 A:ASP462 4.2 0.9 1.0 CB A:ASP467 4.2 0.6 1.0 CA A:LYS400 4.2 86.0 1.0 H A:ASP467 4.4 0.9 1.0 CB A:ASP401 4.4 0.4 1.0 OD1 A:ASP467 4.4 0.2 1.0 OD1 A:ASP460 4.4 0.1 1.0 CB A:ASP460 4.4 0.1 1.0 OD1 A:ASP401 4.5 0.8 1.0 HB2 A:ASP462 4.6 0.9 1.0 H A:ASP401 4.7 0.1 1.0 HB3 A:ASP467 4.7 0.3 1.0 HA A:LYS400 4.9 0.1 1.0 HB3 A:ASP401 4.9 0.3 1.0 HB2 A:ASP460 4.9 0.7 1.0 HA A:ASP462 4.9 0.1 1.0

Calcium binding site 3 out of 3 in the Extended-Synaptotagmin 2, C2A- and C2B-Domains, Calcium Bound


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Extended-Synaptotagmin 2, C2A- and C2B-Domains, Calcium Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca803 b:0.4 occ:1.00 OD1 A:ASP466 2.4 0.0 1.0 O A:ASP464 2.4 0.7 1.0 O A:ASP462 2.4 0.8 1.0 O A:HOH901 2.4 0.5 1.0 O A:HOH902 2.4 0.4 1.0 C A:ASP462 3.5 0.5 1.0 C A:ASP464 3.5 0.0 1.0 CG A:ASP466 3.5 0.4 1.0 H A:ASP462 3.6 0.7 1.0 O A:PRO463 3.7 0.3 1.0 C A:PRO463 3.7 0.4 1.0 N A:ASP464 3.9 0.9 1.0 HA A:PRO463 4.0 0.0 1.0 OD2 A:ASP466 4.1 0.8 1.0 H A:ASP466 4.1 0.6 1.0 CA A:ASP464 4.2 0.5 1.0 CA A:PRO463 4.2 0.3 1.0 N A:ASP462 4.2 0.8 1.0 N A:ASP466 4.3 0.3 1.0 H A:ASP464 4.3 0.7 1.0 N A:PRO463 4.3 0.3 1.0 HA A:ASP464 4.3 0.1 1.0 HB2 A:ASP462 4.3 0.9 1.0 CA A:ASP462 4.4 0.1 1.0 HA A:LYS465 4.5 0.9 1.0 HA A:ASP466 4.5 0.5 1.0 C A:LYS465 4.6 0.3 1.0 N A:LYS465 4.6 0.6 1.0 HA A:GLU461 4.7 0.8 1.0 CB A:ASP466 4.7 0.8 1.0 HG2 A:GLU461 4.7 0.9 1.0 HG3 A:GLU461 4.7 0.9 1.0 CA A:ASP466 4.8 0.9 1.0 CA A:LYS465 4.8 0.9 1.0 CB A:ASP462 4.9 0.8 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