Magnesium in PDB 6agg: Crystal Structure of Agmatine-Amppcp-Mg Complexed Tias (TRNAILE2 Agmatidine Synthetase)

All present enzymatic activity of Crystal Structure of Agmatine-Amppcp-Mg Complexed Tias (TRNAILE2 Agmatidine Synthetase):
6.3.4.22;

The structure of Crystal Structure of Agmatine-Amppcp-Mg Complexed Tias (TRNAILE2 Agmatidine Synthetase), PDB code: 6agg was solved by J.S.Dong, W.M.Gong, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.10 / 2.71
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	69.786, 69.786, 210.822, 90.00, 90.00, 90.00
R / Rfree (%)	21.1 / 29.8

The structure of Crystal Structure of Agmatine-Amppcp-Mg Complexed Tias (TRNAILE2 Agmatidine Synthetase) also contains other interesting chemical elements:

Zinc

(Zn)

1 atom

The binding sites of Magnesium atom in the Crystal Structure of Agmatine-Amppcp-Mg Complexed Tias (TRNAILE2 Agmatidine Synthetase) (pdb code 6agg). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of Agmatine-Amppcp-Mg Complexed Tias (TRNAILE2 Agmatidine Synthetase), PDB code: 6agg:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of Agmatine-Amppcp-Mg Complexed Tias (TRNAILE2 Agmatidine Synthetase)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Agmatine-Amppcp-Mg Complexed Tias (TRNAILE2 Agmatidine Synthetase) within 5.0Å range: probe atom residue distance (Å) B Occ Z:Mg507 b:0.1 occ:1.00 O1P Z:TPO18 2.3 99.2 1.0 O1A Z:ACP502 2.5 1.0 1.0 OD2 Z:ASP11 2.5 0.5 1.0 CA Z:ASP9 2.8 64.7 1.0 O2A Z:ACP502 2.9 96.8 1.0 N Z:THR10 2.9 84.2 1.0 O2P Z:TPO18 2.9 81.7 1.0 P Z:TPO18 3.1 67.9 1.0 PA Z:ACP502 3.1 96.9 1.0 C Z:ASP9 3.1 88.7 1.0 N Z:ASP9 3.4 58.1 1.0 OD1 Z:ASP9 3.5 67.7 1.0 N Z:ASP11 3.5 90.6 1.0 O3A Z:ACP502 3.6 75.7 1.0 CG Z:ASP11 3.6 0.3 1.0 OG1 Z:TPO18 3.8 75.7 1.0 O Z:ASP11 4.0 97.2 1.0 CB Z:ASP9 4.0 56.8 1.0 CA Z:THR10 4.1 87.5 1.0 O Z:ASP9 4.1 57.9 1.0 CG Z:ASP9 4.1 78.6 1.0 C3B Z:ACP502 4.2 0.0 1.0 CB Z:ASP11 4.2 99.2 1.0 C Z:THR10 4.2 89.7 1.0 CA Z:ASP11 4.3 94.2 1.0 MG Z:MG508 4.4 63.2 1.0 PB Z:ACP502 4.4 0.8 1.0 C Z:ASP11 4.4 94.4 1.0 O3P Z:TPO18 4.5 0.6 1.0 C Z:ASP8 4.6 65.7 1.0 OD1 Z:ASP11 4.6 0.7 1.0 O1G Z:ACP502 4.7 0.6 1.0 O5' Z:ACP502 4.7 0.5 1.0 OG1 Z:THR10 4.8 70.0 1.0 PG Z:ACP502 4.9 0.5 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of Agmatine-Amppcp-Mg Complexed Tias (TRNAILE2 Agmatidine Synthetase)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Agmatine-Amppcp-Mg Complexed Tias (TRNAILE2 Agmatidine Synthetase) within 5.0Å range: probe atom residue distance (Å) B Occ Z:Mg508 b:63.2 occ:1.00 O2P Z:TPO18 2.4 81.7 1.0 O1B Z:ACP502 2.5 0.3 1.0 OD2 Z:ASP8 2.5 62.2 1.0 O Z:GLY57 2.7 72.2 1.0 PB Z:ACP502 2.7 0.8 1.0 O2A Z:ACP502 2.8 96.8 1.0 CB Z:ASP8 2.9 60.8 1.0 CG Z:ASP8 3.1 68.3 1.0 C Z:GLY57 3.2 70.6 1.0 N Z:ALA58 3.6 72.1 1.0 N Z:ASP9 3.6 58.1 1.0 CA Z:ALA58 3.7 68.2 1.0 O3A Z:ACP502 3.8 75.7 1.0 P Z:TPO18 3.8 67.9 1.0 C3B Z:ACP502 3.9 0.0 1.0 PA Z:ACP502 3.9 96.9 1.0 O2B Z:ACP502 4.0 0.2 1.0 CA Z:ASP8 4.1 66.6 1.0 N Z:GLY57 4.1 68.3 1.0 CA Z:GLY57 4.2 64.0 1.0 CB Z:ALA58 4.2 58.1 1.0 OD1 Z:ASP8 4.3 84.5 1.0 C Z:ASP8 4.4 65.7 1.0 MG Z:MG507 4.4 0.1 1.0 OG1 Z:TPO18 4.5 75.7 1.0 OD1 Z:ASN56 4.5 83.8 1.0 O3P Z:TPO18 4.5 0.6 1.0 CA Z:ASP9 4.6 64.7 1.0 C5' Z:ACP502 4.7 0.5 1.0 O1P Z:TPO18 4.8 99.2 1.0 CB Z:TPO18 4.8 66.0 1.0 C Z:ASN56 4.8 77.1 1.0 CG2 Z:TPO18 4.9 59.3 1.0 O1A Z:ACP502 4.9 1.0 1.0 O5' Z:ACP502 4.9 0.5 1.0

J.Dong, F.Li, F.Gao, J.Wei, Y.Lin, Y.Zhang, J.Lou, G.Liu, Y.Dong, L.Liu, H.Liu, J.Wang, W.Gong. Structure of Trna-Modifying Enzyme Tias and Motions of Its Substrate Binding Zinc Ribbon. J. Mol. Biol. V. 430 4183 2018.
ISSN: ESSN 1089-8638
PubMed: 30121296
DOI: 10.1016/J.JMB.2018.08.015