Magnesium in PDB 6s84: Tsabde Complex From Thermotoga Maritima

All present enzymatic activity of Tsabde Complex From Thermotoga Maritima:
2.3.1.234;

The structure of Tsabde Complex From Thermotoga Maritima, PDB code: 6s84 was solved by S.Missoury, I.Li-De-La-Sierra-Gallay, H.Van Tilbeurgh, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.43 / 2.89
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	85.160, 108.210, 176.650, 90.00, 90.00, 90.00
R / Rfree (%)	20.9 / 28.2

The binding sites of Magnesium atom in the Tsabde Complex From Thermotoga Maritima (pdb code 6s84). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Tsabde Complex From Thermotoga Maritima, PDB code: 6s84:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Tsabde Complex From Thermotoga Maritima


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Tsabde Complex From Thermotoga Maritima within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg200 b:67.7 occ:1.00 OE2 E:GLU108 1.9 77.9 1.0 OG1 E:THR42 2.0 78.0 1.0 O2G E:APC201 2.6 87.5 1.0 O2B E:APC201 2.8 81.0 1.0 CD E:GLU108 3.0 86.3 1.0 OG E:SER61 3.1 93.4 1.0 O1G E:APC201 3.1 89.4 1.0 PG E:APC201 3.2 91.6 1.0 CB E:THR42 3.3 80.7 1.0 PB E:APC201 3.5 85.5 1.0 OE1 E:GLU108 3.6 87.3 1.0 CB E:SER61 3.6 86.7 1.0 O3B E:APC201 3.6 84.4 1.0 C3A E:APC201 3.6 87.7 1.0 OD2 E:ASP80 3.8 89.8 1.0 CG2 E:THR42 3.9 75.8 1.0 CG E:GLU108 4.3 86.4 1.0 N E:THR42 4.3 82.6 1.0 CA E:SER61 4.3 82.8 1.0 CA E:THR42 4.3 82.8 1.0 OG1 E:THR63 4.6 0.3 1.0 O3G E:APC201 4.7 94.9 1.0 PA E:APC201 4.8 89.4 1.0 CD E:PRO62 4.9 94.8 1.0 O2A E:APC201 4.9 93.8 1.0 NZ D:LYS166 4.9 83.0 1.0 O1A E:APC201 4.9 84.9 1.0 CG E:ASP80 5.0 89.5 1.0 O1B E:APC201 5.0 86.8 1.0 OD1 D:ASP158 5.0 0.3 1.0 NZ D:LYS213 5.0 94.2 1.0

Magnesium binding site 2 out of 2 in the Tsabde Complex From Thermotoga Maritima


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Tsabde Complex From Thermotoga Maritima within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg202 b:52.4 occ:1.00 OG1 B:THR42 2.1 62.7 1.0 O1G B:APC203 2.3 83.5 1.0 OE2 B:GLU108 2.6 65.6 1.0 O1B B:APC203 2.7 71.7 1.0 O3B B:APC203 3.1 78.3 1.0 PG B:APC203 3.2 85.4 1.0 OG B:SER61 3.4 72.0 1.0 CB B:THR42 3.4 66.2 1.0 CD B:GLU108 3.4 67.5 1.0 OE1 B:GLU108 3.5 67.5 1.0 PB B:APC203 3.5 73.3 1.0 O2G B:APC203 3.7 95.2 1.0 OD2 B:ASP80 3.8 85.2 1.0 CG2 B:THR42 4.0 61.9 1.0 CB B:SER61 4.1 70.3 1.0 O1A B:APC203 4.1 70.8 1.0 NZ A:LYS166 4.4 69.0 1.0 OG1 B:THR63 4.5 86.9 1.0 O2B B:APC203 4.5 69.5 1.0 O3G B:APC203 4.5 81.6 1.0 CA B:THR42 4.5 69.9 1.0 OE1 A:GLU162 4.5 78.5 1.0 N B:THR42 4.6 73.4 1.0 CA B:SER61 4.7 69.2 1.0 C3A B:APC203 4.8 71.5 1.0 NZ A:LYS213 4.8 82.9 1.0 OD1 A:ASP158 4.8 1.0 1.0 CG B:GLU108 4.9 68.1 1.0 PA B:APC203 4.9 73.3 1.0 CD B:PRO62 4.9 66.8 1.0 CG B:ASP80 5.0 77.8 1.0

S.Missoury, S.Plancqueel, I.Li De La Sierra-Gallay, W.Zhang, D.Liger, D.Durand, R.Dammak, B.Collinet, H.Van Tilbeurgh. The Structure of the Tsab/Tsad/Tsae Complex Reveals An Unexpected Mechanism For the Bacterial T6A Trna-Modification. Nucleic Acids Res. V. 46 5850 2018.
ISSN: ESSN 1362-4962
PubMed: 29741707
DOI: 10.1093/NAR/GKY323