Magnesium in PDB 5ck5: Signal Recognition Particle Receptor Srb-Gdp-Mg From Chaetomium Thermophilum

The structure of Signal Recognition Particle Receptor Srb-Gdp-Mg From Chaetomium Thermophilum, PDB code: 5ck5 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)	64.20 / 2.40
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	64.100, 137.970, 64.310, 90.00, 93.12, 90.00
R / Rfree (%)	18.6 / 22.3

The binding sites of Magnesium atom in the Signal Recognition Particle Receptor Srb-Gdp-Mg From Chaetomium Thermophilum (pdb code 5ck5). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Signal Recognition Particle Receptor Srb-Gdp-Mg From Chaetomium Thermophilum, PDB code: 5ck5:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Signal Recognition Particle Receptor Srb-Gdp-Mg 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-Gdp-Mg From Chaetomium Thermophilum within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg402 b:25.9 occ:1.00 OG1 A:THR64 2.0 50.3 1.0 O1B A:GDP401 2.0 26.2 1.0 PB A:GDP401 3.4 31.1 1.0 CB A:THR64 3.4 53.1 1.0 O2B A:GDP401 3.8 42.3 1.0 O A:HOH522 3.9 31.6 1.0 NZ A:LYS63 4.0 51.5 1.0 CG2 A:THR64 4.2 52.4 1.0 N A:THR64 4.2 27.5 1.0 O3B A:GDP401 4.2 37.3 1.0 O A:THR147 4.2 53.7 1.0 O2A A:GDP401 4.3 43.5 1.0 O A:HOH509 4.3 30.4 1.0 CA A:THR64 4.3 29.1 1.0 OD2 A:ASP146 4.4 43.5 1.0 O3A A:GDP401 4.6 49.1 1.0 OD1 A:ASP146 4.6 31.4 1.0 CE A:LYS63 4.7 47.5 1.0 CB A:LYS63 4.8 25.6 1.0 PA A:GDP401 4.9 37.8 1.0 CG A:ASP146 4.9 38.8 1.0

Magnesium binding site 2 out of 4 in the Signal Recognition Particle Receptor Srb-Gdp-Mg 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-Gdp-Mg From Chaetomium Thermophilum within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg402 b:22.4 occ:1.00 O1B B:GDP401 2.0 27.9 1.0 OG1 B:THR64 2.1 27.7 1.0 O B:HOH516 3.1 29.9 1.0 PB B:GDP401 3.4 33.6 1.0 CB B:THR64 3.4 37.8 1.0 O3B B:GDP401 3.6 47.1 1.0 N B:THR64 4.2 24.9 1.0 O2B B:GDP401 4.2 22.6 1.0 OD2 B:ASP146 4.2 31.4 1.0 CG2 B:THR64 4.3 30.2 1.0 CA B:THR64 4.3 38.7 1.0 O3A B:GDP401 4.4 18.4 1.0 O2A B:GDP401 4.4 40.9 1.0 O B:HOH502 4.8 17.5 1.0 O B:THR147 4.8 30.1 1.0 PA B:GDP401 4.8 30.9 1.0 NZ B:LYS63 5.0 25.3 1.0

Magnesium binding site 3 out of 4 in the Signal Recognition Particle Receptor Srb-Gdp-Mg 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-Gdp-Mg From Chaetomium Thermophilum within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg402 b:40.1 occ:1.00 OG1 C:THR64 2.0 64.2 1.0 O C:HOH506 2.0 39.0 1.0 O1B C:GDP401 2.4 54.1 1.0 CB C:THR64 3.2 62.9 1.0 PB C:GDP401 3.7 58.6 1.0 CG2 C:THR64 3.8 67.0 1.0 O3B C:GDP401 4.0 51.5 1.0 CA C:THR64 4.4 57.8 1.0 O2B C:GDP401 4.5 60.4 1.0 N C:THR64 4.5 54.4 1.0 O2A C:GDP401 4.6 55.7 1.0 OD2 C:ASP146 4.7 85.6 1.0 O1A C:GDP401 4.7 37.8 1.0 O3A C:GDP401 4.8 65.7 1.0 PA C:GDP401 4.9 47.0 1.0

Magnesium binding site 4 out of 4 in the Signal Recognition Particle Receptor Srb-Gdp-Mg From Chaetomium Thermophilum


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Signal Recognition Particle Receptor Srb-Gdp-Mg From Chaetomium Thermophilum within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg402 b:69.5 occ:1.00 O D:HOH507 2.2 67.4 1.0 OG1 D:THR64 2.6 62.8 1.0 O1B D:GDP401 2.6 58.1 1.0 PB D:GDP401 3.9 56.9 1.0 CB D:THR64 4.0 62.5 1.0 O D:THR147 4.0 73.9 1.0 OD2 D:ASP146 4.1 99.8 1.0 O2B D:GDP401 4.2 57.4 1.0 O3B D:GDP401 4.5 54.6 1.0 OD1 D:ASP146 4.6 97.7 1.0 CG D:ASP146 4.6 96.6 1.0 N D:THR64 4.7 54.7 1.0 CG2 D:THR64 4.7 64.2 1.0 NZ D:LYS63 4.8 47.2 1.0 CA D:THR64 4.9 55.8 1.0 CE D:LYS63 5.0 46.7 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