Magnesium in PDB 7obq: Srp-Sr at the Distal Site Conformation

The binding sites of Magnesium atom in the Srp-Sr at the Distal Site Conformation (pdb code 7obq). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Srp-Sr at the Distal Site Conformation, PDB code: 7obq:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Srp-Sr at the Distal Site Conformation


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Srp-Sr at the Distal Site Conformation within 5.0Å range: probe atom residue distance (Å) B Occ v:Mg300 b:75.1 occ:1.00 OG1 v:THR78 2.1 72.2 1.0 OG v:SER95 2.1 77.2 1.0 O1G v:GTP301 2.1 88.0 1.0 O1B v:GTP301 2.1 88.0 1.0 PB v:GTP301 2.9 88.0 1.0 O2B v:GTP301 3.0 88.0 1.0 CB v:THR78 3.1 72.2 1.0 CB v:SER95 3.3 77.2 1.0 PG v:GTP301 3.4 88.0 1.0 O3B v:GTP301 3.5 88.0 1.0 CG v:LYS77 3.7 72.6 1.0 N v:THR78 3.7 72.2 1.0 N v:SER95 3.7 77.2 1.0 CA v:THR78 4.0 72.2 1.0 OD2 v:ASP117 4.0 69.7 1.0 CA v:SER95 4.0 77.2 1.0 O v:GLN93 4.1 76.3 1.0 CD v:LYS77 4.2 72.6 1.0 O2A v:GTP301 4.3 88.0 1.0 CG2 v:THR78 4.3 72.2 1.0 O2G v:GTP301 4.3 88.0 1.0 O3G v:GTP301 4.4 88.0 1.0 O3A v:GTP301 4.4 88.0 1.0 C v:THR94 4.6 73.3 1.0 C v:LYS77 4.8 72.6 1.0 CG v:ASP117 4.9 69.7 1.0 CB v:LYS77 4.9 72.6 1.0 OD1 v:ASP117 4.9 69.7 1.0 CA v:THR94 4.9 73.3 1.0 O y:GLY11 4.9 69.8 1.0

Magnesium binding site 2 out of 3 in the Srp-Sr at the Distal Site Conformation


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Srp-Sr at the Distal Site Conformation within 5.0Å range: probe atom residue distance (Å) B Occ x:Mg602 b:82.6 occ:1.00 O1B x:GNP601 2.1 78.1 1.0 O1G x:GNP601 2.1 78.1 1.0 OG1 x:THR115 2.1 75.6 1.0 O2B x:GNP601 2.8 78.1 1.0 PB x:GNP601 2.9 78.1 1.0 CG x:LYS114 3.1 80.1 1.0 PG x:GNP601 3.3 78.1 1.0 CB x:THR115 3.4 75.6 1.0 N x:THR115 3.5 75.6 1.0 N3B x:GNP601 3.6 78.1 1.0 CD x:LYS114 3.9 80.1 1.0 CA x:THR115 4.0 75.6 1.0 O3G x:GNP601 4.0 78.1 1.0 OD2 x:ASP190 4.0 88.4 1.0 O1A x:GNP601 4.2 78.1 1.0 OD2 x:ASP138 4.3 97.0 1.0 O3A x:GNP601 4.3 78.1 1.0 CB x:LYS114 4.4 80.1 1.0 OD1 x:ASP190 4.4 88.4 1.0 C x:LYS114 4.4 80.1 1.0 O2G x:GNP601 4.5 78.1 1.0 CG2 x:THR115 4.5 75.6 1.0 CG x:ASP190 4.6 88.4 1.0 N x:LYS114 4.6 80.1 1.0 CA x:LYS114 4.7 80.1 1.0 PA x:GNP601 5.0 78.1 1.0

Magnesium binding site 3 out of 3 in the Srp-Sr at the Distal Site Conformation


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Srp-Sr at the Distal Site Conformation within 5.0Å range: probe atom residue distance (Å) B Occ y:Mg702 b:85.2 occ:1.00 O1G y:GNP701 2.1 76.5 1.0 OG y:SER431 2.1 75.7 1.0 O1B y:GNP701 2.1 76.5 1.0 OD2 y:ASP454 3.2 91.8 1.0 PG y:GNP701 3.2 76.5 1.0 PB y:GNP701 3.3 76.5 1.0 CB y:SER431 3.4 75.7 1.0 N3B y:GNP701 3.5 76.5 1.0 O3G y:GNP701 3.8 76.5 1.0 N y:SER431 3.8 75.7 1.0 OD2 y:ASP519 3.9 83.2 1.0 O2A y:GNP701 3.9 76.5 1.0 NH1 y:ARG457 4.2 83.0 1.0 CA y:SER431 4.2 75.7 1.0 O3A y:GNP701 4.3 76.5 1.0 O1A y:GNP701 4.3 76.5 1.0 PA y:GNP701 4.4 76.5 1.0 O2B y:GNP701 4.4 76.5 1.0 CG y:ASP454 4.4 91.8 1.0 O2G y:GNP701 4.5 76.5 1.0 OE1 y:GLN463 4.6 89.0 1.0 CB y:LYS430 4.7 71.4 1.0 CG y:ASP519 4.7 83.2 1.0 OD1 y:ASP519 4.7 83.2 1.0 C y:LYS430 4.8 71.4 1.0 CZ y:ARG457 4.9 83.0 1.0

A.Jomaa, S.Eitzinger, Z.Zhu, S.Chandrasekar, K.Kobayashi, S.Shan, N.Ban. Molecular Mechanism of Cargo Recognition and Handover By the Mammalian Signal Recognition Particle Cell Rep V. 36 2021.
ISSN: ESSN 2211-1247
DOI: DOI.ORG/10.1016/J.CELREP.2021.109350