Chlorine in PDB 5kc1: Structure of the C-Terminal Dimerization Domain of ATG38

The structure of Structure of the C-Terminal Dimerization Domain of ATG38, PDB code: 5kc1 was solved by Y.Ohashi, N.Soler, M.Garcia-Ortegon, L.Zhang, O.Perisic, G.R.Masson, C.M.Johnson, R.J.Williams, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	58.00 / 2.20
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	81.383, 249.385, 50.197, 90.00, 90.00, 90.00
R / Rfree (%)	20.5 / 24.1

The structure of Structure of the C-Terminal Dimerization Domain of ATG38 also contains other interesting chemical elements:

Iodine	(I)	1 atom
Sodium	(Na)	14 atoms

The binding sites of Chlorine atom in the Structure of the C-Terminal Dimerization Domain of ATG38 (pdb code 5kc1). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 6 binding sites of Chlorine where determined in the Structure of the C-Terminal Dimerization Domain of ATG38, PDB code: 5kc1:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6;

Chlorine binding site 1 out of 6 in the Structure of the C-Terminal Dimerization Domain of ATG38


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Structure of the C-Terminal Dimerization Domain of ATG38 within 5.0Å range: probe atom residue distance (Å) B Occ D:Cl305 b:87.1 occ:1.00 NE2 D:GLN169 3.3 60.4 1.0 CD1 D:LEU176 4.0 46.0 1.0 CG D:GLU173 4.2 53.0 1.0 CB D:LYS172 4.4 40.3 1.0 CD D:GLN169 4.6 76.8 1.0 N D:GLU173 4.7 37.2 1.0 CA D:GLU173 4.9 45.8 1.0 C D:LYS172 4.9 48.9 1.0

Chlorine binding site 2 out of 6 in the Structure of the C-Terminal Dimerization Domain of ATG38


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Structure of the C-Terminal Dimerization Domain of ATG38 within 5.0Å range: probe atom residue distance (Å) B Occ D:Cl306 b:90.8 occ:1.00 O D:LYS172 3.1 49.4 1.0 CB D:LYS172 3.5 40.3 1.0 CA D:LYS172 3.5 45.8 1.0 CG D:LEU176 3.6 54.6 1.0 C D:LYS172 3.7 48.9 1.0 CG D:LYS172 3.8 53.8 1.0 CG1 D:VAL175 3.9 47.7 1.0 CD2 D:LEU176 4.0 54.1 1.0 CB D:VAL175 4.0 57.3 1.0 CD1 D:LEU176 4.1 46.0 1.0 N D:LEU176 4.5 51.4 1.0 CD D:LYS172 4.5 90.1 1.0 CB D:LEU176 4.8 44.7 1.0 N D:LYS172 4.9 43.8 1.0 N D:GLU173 4.9 37.2 1.0 CG2 D:VAL175 5.0 55.7 1.0 C D:VAL175 5.0 49.1 1.0

Chlorine binding site 3 out of 6 in the Structure of the C-Terminal Dimerization Domain of ATG38


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Structure of the C-Terminal Dimerization Domain of ATG38 within 5.0Å range: probe atom residue distance (Å) B Occ E:Cl302 b:0.8 occ:1.00 NA E:NA301 3.2 69.3 1.0 CD2 E:LEU130 4.0 41.6 1.0 CB E:LEU130 4.3 39.5 1.0 NZ F:LYS180 4.4 67.4 1.0 CD2 A:LEU130 4.6 46.6 1.0 CG E:LEU130 4.7 47.0 1.0

Chlorine binding site 4 out of 6 in the Structure of the C-Terminal Dimerization Domain of ATG38


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Structure of the C-Terminal Dimerization Domain of ATG38 within 5.0Å range:

Chlorine binding site 5 out of 6 in the Structure of the C-Terminal Dimerization Domain of ATG38


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Structure of the C-Terminal Dimerization Domain of ATG38 within 5.0Å range: probe atom residue distance (Å) B Occ F:Cl306 b:0.3 occ:1.00 CE F:LYS180 4.5 82.8 1.0 NZ F:LYS180 4.9 67.4 1.0

Chlorine binding site 6 out of 6 in the Structure of the C-Terminal Dimerization Domain of ATG38


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Structure of the C-Terminal Dimerization Domain of ATG38 within 5.0Å range: probe atom residue distance (Å) B Occ F:Cl307 b:0.3 occ:1.00 NA F:NA304 3.5 66.0 1.0 CG F:LYS172 4.0 51.6 1.0 CA F:LYS172 4.3 39.9 1.0 CB F:LYS172 4.5 50.9 1.0 CG2 F:VAL175 4.5 34.9 1.0 CB F:VAL175 4.7 47.2 1.0 CD F:LYS172 4.8 70.0 1.0 CG1 F:VAL175 4.8 40.0 1.0

Y.Ohashi, N.Soler, M.Garcia Ortegon, L.Zhang, M.L.Kirsten, O.Perisic, G.R.Masson, J.E.Burke, A.J.Jakobi, A.A.Apostolakis, C.M.Johnson, M.Ohashi, N.T.Ktistakis, C.Sachse, R.L.Williams. Characterization of ATG38 and NRBF2, A Fifth Subunit of the Autophagic VPS34/PIK3C3 Complex. Autophagy V. 12 2129 2016.
ISSN: ESSN 1554-8635
PubMed: 27630019
DOI: 10.1080/15548627.2016.1226736