Magnesium in PDB 6k0r: RUVBL1-RUVBL2 with Truncated Domain II in Complex with Phosphorylated Cordycepin

All present enzymatic activity of RUVBL1-RUVBL2 with Truncated Domain II in Complex with Phosphorylated Cordycepin:
3.6.4.12;

The structure of RUVBL1-RUVBL2 with Truncated Domain II in Complex with Phosphorylated Cordycepin, PDB code: 6k0r was solved by W.Zhang, L.Chen, W.Li, D.Ju, N.Huang, E.Zhang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.72 / 2.50
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	110.304, 186.424, 235.176, 90.00, 91.04, 90.00
R / Rfree (%)	22.8 / 26.9

The binding sites of Magnesium atom in the RUVBL1-RUVBL2 with Truncated Domain II in Complex with Phosphorylated Cordycepin (pdb code 6k0r). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the RUVBL1-RUVBL2 with Truncated Domain II in Complex with Phosphorylated Cordycepin, PDB code: 6k0r:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the RUVBL1-RUVBL2 with Truncated Domain II in Complex with Phosphorylated Cordycepin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of RUVBL1-RUVBL2 with Truncated Domain II in Complex with Phosphorylated Cordycepin within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg502 b:55.2 occ:1.00 O3B D:CUU501 2.6 77.0 1.0 O2B D:CUU501 3.0 77.6 1.0 PB D:CUU501 3.5 77.0 1.0 OD2 C:ASP356 3.7 76.4 1.0 OD2 D:ASP299 4.1 77.9 1.0 O1B D:CUU501 4.3 76.5 1.0 CB D:PRO79 4.6 61.6 1.0 N D:GLY80 4.6 61.1 1.0 CG C:ASP356 4.7 69.2 1.0 O3A D:CUU501 4.7 77.4 1.0 CA D:PRO79 4.8 59.8 1.0 OD1 C:ASP356 4.8 70.2 1.0 OG1 D:THR84 5.0 67.4 1.0

Magnesium binding site 2 out of 2 in the RUVBL1-RUVBL2 with Truncated Domain II in Complex with Phosphorylated Cordycepin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of RUVBL1-RUVBL2 with Truncated Domain II in Complex with Phosphorylated Cordycepin within 5.0Å range: probe atom residue distance (Å) B Occ L:Mg502 b:56.0 occ:1.00 O3B L:CU0501 2.5 61.8 1.0 O1B L:CU0501 3.2 60.0 1.0 PB L:CU0501 3.4 61.8 1.0 OD2 H:ASP356 4.1 68.2 1.0 OD1 L:ASP299 4.2 75.4 1.0 CB L:PRO79 4.3 64.3 1.0 O2B L:CU0501 4.4 59.0 1.0 CA L:PRO79 4.5 62.6 1.0 OD2 L:ASP299 4.6 81.5 1.0 O3A L:CU0501 4.6 64.3 1.0 N L:GLY80 4.6 63.9 1.0 NZ L:LYS83 4.7 81.3 1.0 CG L:ASP299 4.8 74.4 1.0

D.Ju, W.Zhang, J.Yan, H.Zhao, W.Li, J.Wang, M.Liao, Z.Xu, Z.Wang, G.Zhou, L.Mei, N.Hou, S.Ying, T.Cai, S.Chen, X.Xie, L.Lai, C.Tang, N.Park, J.S.Takahashi, N.Huang, X.Qi, E.E.Zhang. Chemical Perturbations Reveal That RUVBL2 Regulates the Circadian Phase in Mammals. Sci Transl Med 2020.
ISSN: ESSN 1946-6242
DOI: 10.1126/SCITRANSLMED.ABA0769