Magnesium in PDB 8orj: Cryo-Em Structure of Human Trna Ligase Rtcb in Complex with Human PYROXD1.

All present enzymatic activity of Cryo-Em Structure of Human Trna Ligase Rtcb in Complex with Human PYROXD1.:
6.5.1.8;

The binding sites of Magnesium atom in the Cryo-Em Structure of Human Trna Ligase Rtcb in Complex with Human PYROXD1. (pdb code 8orj). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Cryo-Em Structure of Human Trna Ligase Rtcb in Complex with Human PYROXD1., PDB code: 8orj:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Cryo-Em Structure of Human Trna Ligase Rtcb in Complex with Human PYROXD1.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Cryo-Em Structure of Human Trna Ligase Rtcb in Complex with Human PYROXD1. within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg601 b:49.4 occ:1.00 NE2 A:HIS353 2.0 68.6 1.0 NE2 A:HIS259 2.1 53.0 1.0 SG A:CYS122 2.1 51.2 1.0 CE1 A:HIS353 2.8 71.2 1.0 CB A:CYS122 3.0 69.3 1.0 CE1 A:HIS259 3.1 56.2 1.0 CD2 A:HIS259 3.1 55.0 1.0 CD2 A:HIS353 3.3 70.4 1.0 MG A:MG602 3.3 9.0 1.0 OD2 B:ASP500 3.7 83.0 1.0 ND1 A:HIS353 4.0 68.1 1.0 CA A:CYS122 4.1 66.9 1.0 ND1 A:HIS259 4.2 47.6 1.0 CG A:HIS353 4.2 66.4 1.0 CG A:HIS259 4.2 44.4 1.0 CE1 A:HIS428 4.3 72.7 1.0 C A:CYS122 4.3 65.2 1.0 OD2 A:ASP119 4.4 80.8 1.0 NE2 A:HIS227 4.5 57.8 1.0 N A:GLY123 4.6 58.3 1.0 CD2 A:HIS227 4.6 68.5 1.0 NE2 A:HIS428 4.6 69.8 1.0 ND2 A:ASN354 4.8 73.5 1.0 O A:CYS122 4.9 76.6 1.0 CG B:ASP500 4.9 79.5 1.0

Magnesium binding site 2 out of 2 in the Cryo-Em Structure of Human Trna Ligase Rtcb in Complex with Human PYROXD1.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Cryo-Em Structure of Human Trna Ligase Rtcb in Complex with Human PYROXD1. within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg602 b:9.0 occ:1.00 OD2 A:ASP119 1.9 80.8 1.0 OD2 B:ASP500 2.0 83.0 1.0 SG A:CYS122 2.2 51.2 1.0 NE2 A:HIS227 2.4 57.8 1.0 CG B:ASP500 2.6 79.5 1.0 OD1 B:ASP500 2.7 75.2 1.0 CG A:ASP119 3.2 82.4 1.0 CE1 A:HIS227 3.3 66.3 1.0 MG A:MG601 3.3 49.4 1.0 CB A:CYS122 3.4 69.3 1.0 CD2 A:HIS227 3.4 68.5 1.0 CB A:ASP119 3.9 75.8 1.0 CB B:ASP500 4.0 75.5 1.0 OD1 A:ASP119 4.1 86.6 1.0 O B:ASP500 4.4 89.3 1.0 ND1 A:HIS227 4.5 72.5 1.0 CG A:HIS227 4.5 65.3 1.0 CA A:CYS122 4.6 66.9 1.0 C B:ASP500 4.6 88.2 1.0 NE2 A:HIS259 4.7 53.0 1.0 ND2 A:ASN354 4.8 73.5 1.0 CA B:ASP500 4.8 76.9 1.0 NE2 A:HIS353 4.9 68.6 1.0

L.Loeff, A.Kroupova, I.Asanovic, F.Boneberg, M.M.Pfleiderer, A.Ferdigg, F.Ackle, J.Martinez, M.Jinek. Mechanistic Basis For Oxidative Stress Protection of the Human Trna Ligase Complex By the Oxidoreductase PYROXD1 Biorxiv 2023.
ISSN: ISSN 2692-8205
DOI: 10.1101/2023.04.06.535761