Magnesium in PDB 6slo: Crystal Structure of PUF60 Uhm Domain in Complex with 7,8 Dimethoxyperphenazine

The structure of Crystal Structure of PUF60 Uhm Domain in Complex with 7,8 Dimethoxyperphenazine, PDB code: 6slo was solved by P.K.A.Jagtap, T.Kubelka, T.Bach, M.Sattler, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	55.04 / 1.94
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	81.520, 89.400, 149.210, 90.00, 90.00, 90.00
R / Rfree (%)	17.6 / 20.7

The structure of Crystal Structure of PUF60 Uhm Domain in Complex with 7,8 Dimethoxyperphenazine also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Magnesium atom in the Crystal Structure of PUF60 Uhm Domain in Complex with 7,8 Dimethoxyperphenazine (pdb code 6slo). 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 PUF60 Uhm Domain in Complex with 7,8 Dimethoxyperphenazine, PDB code: 6slo:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of PUF60 Uhm Domain in Complex with 7,8 Dimethoxyperphenazine


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 PUF60 Uhm Domain in Complex with 7,8 Dimethoxyperphenazine within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg601 b:31.9 occ:1.00 OG D:SER552 2.6 29.7 1.0 OG1 A:THR421 2.7 23.9 1.0 MG A:MG602 2.9 40.8 1.0 N A:ARG417 2.9 24.3 1.0 O A:GLY418 3.5 27.2 1.0 CG2 A:VAL435 3.6 31.7 1.0 CA A:ILE416 3.7 23.6 1.0 N A:GLY418 3.7 21.9 1.0 CB D:SER552 3.8 28.8 1.0 CB A:THR421 3.8 25.0 1.0 C A:ILE416 3.8 25.5 1.0 CA A:ARG417 3.8 20.3 1.0 CG2 A:THR421 3.9 25.1 1.0 CB A:ARG417 3.9 19.9 1.0 CG2 A:ILE416 4.0 23.5 1.0 C A:ARG417 4.1 26.6 1.0 O A:GLY415 4.3 26.0 1.0 CD1 A:ILE416 4.4 27.1 1.0 CB A:ILE416 4.4 23.7 1.0 C A:GLY418 4.4 27.1 1.0 CG A:ARG417 4.6 21.5 1.0 CA A:GLY418 4.6 21.3 1.0 CB A:VAL435 4.8 40.6 1.0 N A:ILE416 4.8 24.9 1.0 CG1 A:VAL435 4.8 47.3 1.0 N D:SER552 4.9 25.2 1.0 CA D:SER552 4.9 24.2 1.0 O A:ILE416 5.0 25.5 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of PUF60 Uhm Domain in Complex with 7,8 Dimethoxyperphenazine


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 PUF60 Uhm Domain in Complex with 7,8 Dimethoxyperphenazine within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg602 b:40.8 occ:1.00 MG A:MG601 2.9 31.9 1.0 N A:GLY418 2.9 21.9 1.0 NE2 C:GLN546 2.9 24.0 1.0 O D:HOH774 3.3 35.4 1.0 CG1 A:VAL435 3.5 47.3 1.0 SD C:MET456 3.6 37.1 1.0 CA A:GLY418 3.6 21.3 1.0 CB A:ARG417 3.6 19.9 1.0 CE C:MET456 3.8 30.9 1.0 CG2 A:VAL435 3.9 31.7 1.0 O A:GLY418 3.9 27.2 1.0 C A:ARG417 4.0 26.6 1.0 CD C:GLN546 4.1 28.5 1.0 C A:GLY418 4.1 27.1 1.0 CA A:ARG417 4.2 20.3 1.0 O D:ASP550 4.2 24.1 1.0 CB A:VAL435 4.3 40.6 1.0 N A:ARG417 4.3 24.3 1.0 OG1 A:THR421 4.3 23.9 1.0 OE1 C:GLN546 4.5 26.0 1.0 CG A:ARG417 4.6 21.5 1.0 CD A:ARG417 4.7 25.7 1.0 OG D:SER552 4.7 29.7 1.0 NH1 A:ARG417 4.9 19.8 1.0 CG C:MET456 4.9 30.5 1.0

P.K.A.Jagtap, T.Kubelka, K.Soni, C.L.Will, D.Garg, C.Sippel, T.G.Kapp, H.K.Potukuchi, K.Schorpp, K.Hadian, H.Kessler, R.Luhrmann, F.Hausch, T.Bach, M.Sattler. Identification of Phenothiazine Derivatives As Uhm-Binding Inhibitors of Early Spliceosome Assembly. Nat Commun V. 11 5621 2020.
ISSN: ESSN 2041-1723
PubMed: 33159082
DOI: 10.1038/S41467-020-19514-1