Magnesium in PDB 5ck3: Signal Recognition Particle Receptor Srb-Gtp/Srx Complex From Chaetomium Thermophilum

The structure of Signal Recognition Particle Receptor Srb-Gtp/Srx Complex From Chaetomium Thermophilum, PDB code: 5ck3 was solved by B.R.Jadhav, K.Wild, I.Sinning, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.47 / 3.20
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	88.277, 83.609, 90.213, 90.00, 105.23, 90.00
R / Rfree (%)	27.6 / 30

The binding sites of Magnesium atom in the Signal Recognition Particle Receptor Srb-Gtp/Srx Complex From Chaetomium Thermophilum (pdb code 5ck3). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Signal Recognition Particle Receptor Srb-Gtp/Srx Complex From Chaetomium Thermophilum, PDB code: 5ck3:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Signal Recognition Particle Receptor Srb-Gtp/Srx Complex From Chaetomium Thermophilum


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Signal Recognition Particle Receptor Srb-Gtp/Srx Complex From Chaetomium Thermophilum within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg401 b:42.1 occ:1.00 OG1 B:THR64 2.0 47.8 1.0 O1B B:GTP402 2.2 46.7 1.0 OG B:SER107 2.4 53.4 1.0 O1G B:GTP402 2.6 43.5 1.0 CB B:THR64 2.7 43.4 1.0 N B:SER107 2.8 51.7 1.0 O B:HIS105 2.8 51.9 1.0 PB B:GTP402 3.1 46.5 1.0 O3A B:GTP402 3.1 51.0 1.0 CB B:SER107 3.4 56.9 1.0 C B:THR106 3.5 51.3 1.0 CA B:SER107 3.6 61.9 1.0 CA B:THR106 3.6 61.6 1.0 CG2 B:THR64 3.6 42.9 1.0 PG B:GTP402 3.7 47.4 1.0 C B:HIS105 3.7 51.8 1.0 O1A B:GTP402 3.7 39.3 1.0 PA B:GTP402 3.8 36.3 1.0 O3B B:GTP402 3.8 45.7 1.0 CA B:THR64 3.9 36.4 1.0 N B:THR64 4.0 42.2 1.0 NZ B:LYS63 4.0 55.6 1.0 O2A B:GTP402 4.0 26.5 1.0 N B:THR106 4.1 60.0 1.0 O A:SER12 4.1 56.0 1.0 O2G B:GTP402 4.2 59.3 1.0 O2B B:GTP402 4.4 40.1 1.0 O B:THR106 4.5 45.8 1.0 CA A:GLY13 4.6 55.5 1.0 OG1 B:THR104 4.7 45.9 1.0 CB B:THR104 4.7 42.2 1.0 CB B:THR106 4.9 59.1 1.0 CA B:HIS105 4.9 48.9 1.0 N B:HIS105 4.9 55.2 1.0 C B:THR64 4.9 37.9 1.0 O3G B:GTP402 4.9 48.7 1.0 C B:SER107 5.0 64.9 1.0

Magnesium binding site 2 out of 3 in the Signal Recognition Particle Receptor Srb-Gtp/Srx Complex From Chaetomium Thermophilum


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Signal Recognition Particle Receptor Srb-Gtp/Srx Complex From Chaetomium Thermophilum within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg400 b:53.6 occ:1.00 O1B D:GTP401 1.9 67.4 1.0 OG D:SER107 2.0 58.9 1.0 O1G D:GTP401 2.1 64.1 1.0 OG1 D:THR64 2.2 63.9 1.0 PG D:GTP401 2.8 58.3 1.0 CB D:SER107 2.8 57.7 1.0 O3G D:GTP401 2.8 59.4 1.0 PB D:GTP401 3.0 65.5 1.0 O3B D:GTP401 3.3 56.1 1.0 O D:THR147 3.5 66.6 1.0 CB D:THR64 3.5 60.5 1.0 OD2 D:ASP146 3.5 58.7 1.0 OD1 D:ASP146 3.7 64.2 1.0 O2B D:GTP401 3.8 61.8 1.0 N D:SER107 3.9 56.8 1.0 N D:THR64 4.0 61.0 1.0 CA D:SER107 4.0 55.3 1.0 CG D:ASP146 4.0 58.6 1.0 O2G D:GTP401 4.2 66.0 1.0 NZ D:LYS63 4.2 63.2 1.0 CA D:THR64 4.3 55.7 1.0 O3A D:GTP401 4.3 55.0 1.0 O1A D:GTP401 4.3 63.4 1.0 C D:THR147 4.5 67.5 1.0 CG2 D:THR64 4.6 59.4 1.0 CB D:LYS63 4.6 57.6 1.0 CA D:PRO148 4.7 71.9 1.0 PA D:GTP401 4.7 57.0 1.0 O2A D:GTP401 4.7 60.8 1.0 O C:SER12 4.7 60.7 1.0 CE D:LYS63 4.8 61.9 1.0 O D:SER107 4.9 67.8 1.0 C D:SER107 4.9 62.2 1.0 C D:LYS63 5.0 62.0 1.0

Magnesium binding site 3 out of 3 in the Signal Recognition Particle Receptor Srb-Gtp/Srx Complex From Chaetomium Thermophilum


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Signal Recognition Particle Receptor Srb-Gtp/Srx Complex From Chaetomium Thermophilum within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg400 b:0.3 occ:1.00 OG1 F:THR64 2.1 92.3 1.0 O3G F:GTP401 2.2 100.0 1.0 O F:THR147 2.3 1.0 1.0 OG F:SER107 2.3 0.9 1.0 OD2 F:ASP146 2.5 0.2 1.0 O1B F:GTP401 2.6 0.3 1.0 OD1 F:ASP146 2.8 0.6 1.0 CG F:ASP146 3.0 1.0 1.0 CB F:SER107 3.1 99.1 1.0 PG F:GTP401 3.3 1.0 1.0 NZ F:LYS63 3.4 0.4 1.0 O1G F:GTP401 3.4 0.8 1.0 CB F:THR64 3.4 93.3 1.0 C F:THR147 3.4 0.8 1.0 N F:THR64 3.6 0.6 1.0 CE F:LYS63 3.7 0.9 1.0 CA F:THR64 3.8 0.4 1.0 PB F:GTP401 3.8 0.4 1.0 CB F:LYS63 3.9 0.2 1.0 CA F:PRO148 3.9 0.2 1.0 O3B F:GTP401 4.0 0.2 1.0 N F:PRO148 4.1 0.5 1.0 N F:THR147 4.1 0.8 1.0 CG2 F:THR64 4.2 95.8 1.0 CG F:LYS63 4.4 0.9 1.0 C F:LYS63 4.4 0.0 1.0 C F:PRO148 4.4 0.3 1.0 CA F:THR147 4.4 1.0 1.0 CA F:SER107 4.5 96.3 1.0 CB F:ASP146 4.5 0.6 1.0 O2G F:GTP401 4.5 99.7 1.0 O2B F:GTP401 4.5 1.0 1.0 CD F:LYS63 4.6 0.9 1.0 N F:SER107 4.6 95.9 1.0 N F:GLY149 4.7 0.1 1.0 CA F:LYS63 4.7 0.6 1.0 O2A F:GTP401 4.8 96.9 1.0

B.Jadhav, K.Wild, M.R.Pool, I.Sinning. Structure and Switch Cycle of Sr Beta As Ancestral Eukaryotic Gtpase Associated with Secretory Membranes. Structure V. 23 1838 2015.
ISSN: ISSN 0969-2126
PubMed: 26299945
DOI: 10.1016/J.STR.2015.07.010