Chlorine 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:

Sodium

(Na)

1 atom

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

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


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Extended-Synaptotagmin 2, C2A- and C2B-Domains within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl801 b:79.6 occ:1.00 HE A:ARG419 2.4 83.0 1.0 HD21 B:LEU378 3.1 65.7 1.0 HB2 A:ARG419 3.2 74.8 1.0 NE A:ARG419 3.2 69.2 1.0 OE1 B:GLU585 3.4 69.4 1.0 HD2 A:ARG419 3.4 66.1 1.0 HD11 A:ILE424 3.4 1.0 1.0 HB3 A:ARG419 3.6 74.8 1.0 HH21 A:ARG419 3.8 79.0 1.0 CB A:ARG419 3.8 62.4 1.0 CD A:ARG419 3.8 55.1 1.0 OE1 A:GLU455 3.9 99.9 1.0 HG22 A:ILE417 4.0 58.3 1.0 CD2 B:LEU378 4.0 54.7 1.0 HD12 A:ILE424 4.1 1.0 1.0 CD1 A:ILE424 4.1 85.8 1.0 HG21 A:ILE417 4.2 58.3 1.0 CZ A:ARG419 4.2 69.5 1.0 HD23 B:LEU378 4.3 65.7 1.0 HB2 A:GLU455 4.3 70.6 1.0 NH2 A:ARG419 4.4 65.8 1.0 HD13 A:ILE424 4.4 1.0 1.0 HD22 B:LEU378 4.4 65.7 1.0 HB3 A:GLU455 4.4 70.6 1.0 CG A:ARG419 4.4 64.8 1.0 CD B:GLU585 4.4 53.1 1.0 OE1 A:GLU457 4.5 67.7 1.0 CG2 A:ILE417 4.5 48.5 1.0 HD11 B:LEU378 4.6 84.5 1.0 OE2 B:GLU585 4.7 71.6 1.0 HD3 A:ARG419 4.7 66.1 1.0 HG3 A:GLU457 4.7 78.4 1.0 CB A:GLU455 4.8 58.8 1.0 HG3 A:ARG419 4.9 77.8 1.0 HB3 B:ALA376 4.9 71.1 1.0

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


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Extended-Synaptotagmin 2, C2A- and C2B-Domains within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl802 b:80.0 occ:1.00 H A:PHE591 2.3 45.3 1.0 O A:HOH922 3.0 44.3 1.0 HA A:PHE590 3.0 53.0 1.0 HD2 A:LYS569 3.0 98.2 1.0 HB2 A:PHE591 3.0 57.5 1.0 HD2 A:PHE591 3.1 55.8 1.0 N A:PHE591 3.1 37.8 1.0 HB3 A:LYS569 3.1 0.6 1.0 HG3 A:LYS569 3.4 0.8 1.0 HD2 A:PHE590 3.6 59.2 1.0 CD A:LYS569 3.7 81.8 1.0 HE3 A:LYS569 3.7 0.1 1.0 CA A:PHE590 3.8 44.2 1.0 CG A:LYS569 3.8 96.5 1.0 CB A:PHE591 3.8 47.9 1.0 CB A:LYS569 3.9 98.9 1.0 CD2 A:PHE591 3.9 46.5 1.0 C A:PHE590 4.0 42.8 1.0 CA A:PHE591 4.0 40.0 1.0 HB3 A:PHE590 4.0 64.1 1.0 HE21 A:GLN571 4.1 47.9 1.0 HZ2 A:LYS569 4.1 0.2 1.0 CE A:LYS569 4.2 0.6 1.0 HB2 A:LYS569 4.2 0.6 1.0 CD2 A:PHE590 4.3 49.3 1.0 CG A:PHE591 4.4 40.5 1.0 CB A:PHE590 4.4 53.4 1.0 O A:PHE591 4.4 61.5 1.0 HE22 A:GLN571 4.5 47.9 1.0 O A:THR589 4.5 35.6 1.0 HD3 A:LYS569 4.5 98.2 1.0 HB3 A:PHE591 4.6 57.5 1.0 NE2 A:GLN571 4.6 39.9 1.0 NZ A:LYS569 4.7 0.8 1.0 CG A:PHE590 4.7 52.4 1.0 C A:PHE591 4.7 41.8 1.0 HG2 A:LYS569 4.8 0.8 1.0 HA A:PHE591 4.8 48.0 1.0 N A:PHE590 4.9 41.1 1.0

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


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Extended-Synaptotagmin 2, C2A- and C2B-Domains within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl702 b:52.8 occ:1.00 H B:PHE591 2.3 43.2 1.0 HA B:PHE590 2.9 44.8 1.0 HG2 B:LYS569 2.9 0.9 1.0 HD2 B:PHE591 2.9 60.0 1.0 N B:PHE591 3.1 36.0 1.0 HB3 B:LYS569 3.2 0.3 1.0 HB2 B:PHE591 3.2 47.9 1.0 HD2 B:PHE590 3.6 48.1 1.0 CG B:LYS569 3.7 0.2 1.0 HB2 B:LYS569 3.7 0.3 1.0 CB B:LYS569 3.7 0.6 1.0 CA B:PHE590 3.7 37.4 1.0 CD2 B:PHE591 3.8 50.0 1.0 C B:PHE590 3.9 45.2 1.0 CB B:PHE591 3.9 39.9 1.0 HB3 B:PHE590 4.0 42.3 1.0 HG3 B:LYS569 4.1 0.9 1.0 CA B:PHE591 4.1 38.5 1.0 CD2 B:PHE590 4.3 40.1 1.0 CB B:PHE590 4.3 35.2 1.0 CG B:PHE591 4.4 46.7 1.0 O B:PHE591 4.4 38.0 1.0 H1 B:ACT704 4.4 0.0 1.0 O B:THR589 4.4 30.6 1.0 OE1 B:GLN571 4.6 40.1 1.0 CG B:PHE590 4.7 39.9 1.0 C B:PHE591 4.8 42.0 1.0 HB3 B:PHE591 4.8 47.9 1.0 CE2 B:PHE591 4.8 62.5 1.0 N B:PHE590 4.9 34.3 1.0 HE2 B:PHE591 4.9 75.0 1.0 HA B:PHE591 4.9 46.2 1.0 CD B:LYS569 4.9 0.3 1.0 HD3 B:LYS569 4.9 0.6 1.0 HE2 B:LYS569 5.0 0.3 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