Magnesium in PDB 3din: Crystal Structure of the Protein-Translocation Complex Formed By the Secy Channel and the Seca Atpase

The structure of Crystal Structure of the Protein-Translocation Complex Formed By the Secy Channel and the Seca Atpase, PDB code: 3din was solved by J.Zimmer, Y.Nam, T.A.Rapoport, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	15.00 / 4.50
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	101.616, 156.003, 358.155, 90.00, 90.00, 90.00
R / Rfree (%)	27.9 / 30.3

The structure of Crystal Structure of the Protein-Translocation Complex Formed By the Secy Channel and the Seca Atpase also contains other interesting chemical elements:

Fluorine

(F)

6 atoms

The binding sites of Magnesium atom in the Crystal Structure of the Protein-Translocation Complex Formed By the Secy Channel and the Seca Atpase (pdb code 3din). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of the Protein-Translocation Complex Formed By the Secy Channel and the Seca Atpase, PDB code: 3din:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of the Protein-Translocation Complex Formed By the Secy Channel and the Seca Atpase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of the Protein-Translocation Complex Formed By the Secy Channel and the Seca Atpase within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg872 b:0.7 occ:1.00 F3 A:BEF874 2.0 0.2 1.0 CB A:LYS101 2.3 0.0 1.0 NH2 A:ARG131 2.6 0.6 1.0 BE A:BEF874 2.9 0.1 1.0 C A:LYS101 2.9 0.6 1.0 N A:THR102 3.0 0.8 1.0 CA A:LYS101 3.2 0.6 1.0 OD2 A:ASP252 3.2 0.3 1.0 F2 A:BEF874 3.3 0.4 1.0 O A:LYS101 3.4 0.6 1.0 CG A:LYS101 3.5 0.0 1.0 O2B A:ADP873 3.5 0.4 1.0 CZ A:ARG131 3.6 0.6 1.0 CA A:THR102 3.8 0.8 1.0 O2A A:ADP873 3.8 0.1 1.0 OD1 A:ASP252 3.8 0.3 1.0 CG2 A:THR102 3.9 0.4 1.0 CG A:ASP252 3.9 0.3 1.0 NH1 A:ARG131 4.0 0.6 1.0 OD1 A:ASP132 4.1 0.4 1.0 CD A:LYS101 4.1 0.0 1.0 N A:LYS101 4.1 0.6 1.0 F1 A:BEF874 4.2 0.8 1.0 O1A A:ADP873 4.2 0.5 1.0 PA A:ADP873 4.3 0.8 1.0 O3A A:ADP873 4.3 0.8 1.0 CB A:THR102 4.4 0.4 1.0 CE A:LYS101 4.5 0.0 1.0 NE A:ARG131 4.6 0.6 1.0 NZ A:LYS101 4.6 0.0 1.0 PB A:ADP873 4.7 0.5 1.0 OD2 A:ASP132 4.8 0.4 1.0 CG A:ASP132 4.9 0.4 1.0 C A:GLY100 5.0 0.8 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of the Protein-Translocation Complex Formed By the Secy Channel and the Seca Atpase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of the Protein-Translocation Complex Formed By the Secy Channel and the Seca Atpase within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg872 b:0.7 occ:1.00 F3 B:BEF874 2.0 0.2 1.0 CB B:LYS101 2.2 0.0 1.0 NH2 B:ARG131 2.6 0.6 1.0 BE B:BEF874 2.9 0.1 1.0 C B:LYS101 2.9 0.6 1.0 N B:THR102 3.1 0.8 1.0 OD2 B:ASP252 3.1 0.3 1.0 CA B:LYS101 3.2 0.6 1.0 F2 B:BEF874 3.3 0.4 1.0 O B:LYS101 3.4 0.6 1.0 CG B:LYS101 3.4 0.0 1.0 O2B B:ADP873 3.5 0.4 1.0 CD B:LYS101 3.6 0.0 1.0 CZ B:ARG131 3.6 0.6 1.0 OD1 B:ASP252 3.7 0.3 1.0 CG B:ASP252 3.8 0.3 1.0 O2A B:ADP873 3.8 0.1 1.0 CA B:THR102 3.8 0.8 1.0 NH1 B:ARG131 4.0 0.6 1.0 CG2 B:THR102 4.0 0.4 1.0 CE B:LYS101 4.1 0.0 1.0 OD1 B:ASP132 4.1 0.4 1.0 N B:LYS101 4.2 0.6 1.0 F1 B:BEF874 4.2 0.8 1.0 O1A B:ADP873 4.2 0.5 1.0 PA B:ADP873 4.3 0.8 1.0 O3A B:ADP873 4.3 0.8 1.0 CB B:THR102 4.6 0.4 1.0 NZ B:LYS101 4.6 0.0 1.0 NE B:ARG131 4.6 0.6 1.0 PB B:ADP873 4.7 0.5 1.0 OD2 B:ASP132 4.8 0.4 1.0 CG B:ASP132 4.9 0.4 1.0 SD B:MET415 5.0 0.3 1.0

J.Zimmer, Y.Nam, T.A.Rapoport. Structure of A Complex of the Atpase Seca and the Protein-Translocation Channel. Nature V. 455 936 2008.
ISSN: ISSN 0028-0836
PubMed: 18923516
DOI: 10.1038/NATURE07335