Calcium in PDB 4l9o: Crystal Structure of the SEC13-SEC16 Blade-Inserted Complex From Pichia Pastoris

The structure of Crystal Structure of the SEC13-SEC16 Blade-Inserted Complex From Pichia Pastoris, PDB code: 4l9o was solved by C.Mcmahon, P.D.Jeffrey, F.M.Hughson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.42 / 1.60
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	70.509, 49.320, 90.904, 90.00, 111.70, 90.00
R / Rfree (%)	17.3 / 20.5

The structure of Crystal Structure of the SEC13-SEC16 Blade-Inserted Complex From Pichia Pastoris also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Calcium atom in the Crystal Structure of the SEC13-SEC16 Blade-Inserted Complex From Pichia Pastoris (pdb code 4l9o). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Crystal Structure of the SEC13-SEC16 Blade-Inserted Complex From Pichia Pastoris, PDB code: 4l9o:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Crystal Structure of the SEC13-SEC16 Blade-Inserted Complex From Pichia Pastoris


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of the SEC13-SEC16 Blade-Inserted Complex From Pichia Pastoris within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca2401 b:11.2 occ:1.00 O A:ILE2157 2.3 12.8 1.0 O A:SER2132 2.3 10.3 1.0 O1 A:EDO2406 2.4 15.2 1.0 O2 A:EDO2406 2.6 14.7 1.0 C1 A:EDO2406 3.2 16.0 1.0 H11 A:EDO2406 3.2 19.2 1.0 C2 A:EDO2406 3.4 15.4 1.0 C A:ILE2157 3.5 10.9 1.0 HA A:ASP2133 3.5 14.0 1.0 C A:SER2132 3.5 9.9 1.0 H22 A:EDO2406 3.8 18.5 1.0 HA A:ILE2157 3.8 15.5 1.0 HB3 A:SER2132 3.9 15.8 1.0 HO2 A:EDO2407 4.2 21.8 1.0 HA2 A:GLY2158 4.2 14.6 1.0 H12 A:EDO2406 4.2 19.2 1.0 HA3 A:GLY2158 4.3 14.6 1.0 CA A:ASP2133 4.3 11.7 1.0 HG23 A:ILE2157 4.3 18.9 1.0 CA A:ILE2157 4.3 12.9 1.0 H21 A:EDO2406 4.3 18.5 1.0 N A:ASP2133 4.4 10.7 1.0 O2 A:EDO2407 4.4 18.2 1.0 HG22 A:ILE2157 4.4 18.9 1.0 N A:GLY2158 4.5 11.4 1.0 CA A:GLY2158 4.5 12.2 1.0 CA A:SER2132 4.5 9.8 1.0 HA A:SER2132 4.5 11.7 1.0 CB A:SER2132 4.6 13.2 1.0 C A:ASP2133 4.6 13.1 1.0 CG2 A:ILE2157 4.8 15.8 1.0 H A:GLY2134 4.9 14.1 1.0 N A:GLY2134 4.9 11.7 1.0

Calcium binding site 2 out of 3 in the Crystal Structure of the SEC13-SEC16 Blade-Inserted Complex From Pichia Pastoris


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of the SEC13-SEC16 Blade-Inserted Complex From Pichia Pastoris within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca2402 b:20.0 occ:1.00 O A:HOH2570 2.3 28.9 1.0 O A:HOH2562 2.3 25.6 1.0 O A:HOH2576 2.3 30.2 1.0 O1 A:EDO2405 2.4 21.6 1.0 O A:HOH2557 2.4 26.6 1.0 O2 A:EDO2405 2.4 20.1 1.0 O A:HOH2537 2.5 20.2 1.0 O A:HOH2510 2.5 25.6 1.0 C1 A:EDO2405 3.5 20.2 1.0 C2 A:EDO2405 3.5 19.7 1.0 HE22 A:GLN2069 3.9 32.6 1.0 H11 A:EDO2405 3.9 24.3 1.0 HG A:SER2163 4.0 22.4 1.0 H22 A:EDO2405 4.1 23.6 1.0 OG A:SER2163 4.3 18.6 1.0 H21 A:EDO2405 4.3 23.6 1.0 H12 A:EDO2405 4.3 24.3 1.0 O A:ALA2263 4.5 13.3 1.0 OD2 A:ASP2212 4.5 12.2 1.0 OD1 A:ASP2212 4.5 14.1 1.0 NE2 A:GLN2069 4.6 27.2 1.0 O A:HOH2573 4.6 20.4 1.0 O A:HOH2605 4.6 23.3 1.0 O A:VAL2213 4.6 12.4 1.0 HE21 A:GLN2069 4.7 32.6 1.0 HB3 A:SER2264 5.0 23.8 1.0

Calcium binding site 3 out of 3 in the Crystal Structure of the SEC13-SEC16 Blade-Inserted Complex From Pichia Pastoris


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of the SEC13-SEC16 Blade-Inserted Complex From Pichia Pastoris within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca2401 b:15.2 occ:1.00 O B:SER2132 2.2 14.4 1.0 O B:ILE2157 2.3 18.7 1.0 C B:ILE2157 3.4 18.6 1.0 C B:SER2132 3.5 14.1 1.0 HA B:ASP2133 3.5 19.4 1.0 HA B:ILE2157 3.8 19.4 1.0 HB3 B:SER2132 3.9 17.0 1.0 HA3 B:GLY2158 4.0 19.7 1.0 HA2 B:GLY2158 4.0 19.7 1.0 CA B:ILE2157 4.2 16.2 1.0 CA B:ASP2133 4.2 16.1 1.0 CA B:GLY2158 4.3 16.4 1.0 N B:GLY2158 4.3 14.6 1.0 N B:ASP2133 4.3 14.1 1.0 HA B:SER2132 4.4 17.1 1.0 CA B:SER2132 4.4 14.3 1.0 HG22 B:ILE2157 4.5 21.2 1.0 C B:ASP2133 4.5 17.1 1.0 HG23 B:ILE2157 4.6 21.2 1.0 CB B:SER2132 4.6 14.2 1.0 N B:GLY2134 4.8 15.0 1.0 H B:GLY2134 4.8 18.0 1.0 CG2 B:ILE2157 4.9 17.6 1.0

N.Bharucha, Y.Liu, E.Papanikou, C.Mcmahon, M.Esaki, P.D.Jeffrey, F.M.Hughson, B.S.Glick. SEC16 Influences Transitional Er Sites By Regulating Rather Than Organizing Copii. Mol Biol Cell V. 24 3406 2013.
PubMed: 24006484
DOI: 10.1091/MBC.E13-04-0185