Magnesium in PDB 6i0u: Crystal Structure of Dmtailor in Complex with U6 Rna

All present enzymatic activity of Crystal Structure of Dmtailor in Complex with U6 Rna:
2.7.7.52;

The structure of Crystal Structure of Dmtailor in Complex with U6 Rna, PDB code: 6i0u was solved by A.Kroupova, A.Ivascu, M.Jinek, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.55 / 2.00
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	60.783, 60.783, 167.216, 90.00, 90.00, 120.00
R / Rfree (%)	20.6 / 24

The binding sites of Magnesium atom in the Crystal Structure of Dmtailor in Complex with U6 Rna (pdb code 6i0u). 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 Dmtailor in Complex with U6 Rna, PDB code: 6i0u:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of Dmtailor in Complex with U6 Rna


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 Dmtailor in Complex with U6 Rna within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg601 b:40.3 occ:1.00 OD2 A:ASP280 2.2 37.9 1.0 OP1 B:U4 2.2 62.6 1.0 OD2 A:ASP278 2.4 81.3 1.0 O B:HOH106 2.4 35.8 1.0 O A:HOH716 2.5 38.6 1.0 O B:HOH107 2.6 43.5 1.0 CG A:ASP280 3.1 36.4 1.0 O5' B:U4 3.2 60.9 1.0 P B:U4 3.3 52.2 1.0 CG A:ASP278 3.3 77.8 1.0 OD1 A:ASP280 3.3 35.5 1.0 H A:SER267 3.5 31.2 1.0 OD1 A:ASP278 3.6 76.9 1.0 MG A:MG602 3.6 50.2 1.0 O B:HOH108 3.6 52.0 1.0 HA3 A:GLY266 3.8 39.0 1.0 O A:ASP278 4.1 38.0 1.0 OG A:SER267 4.1 39.3 1.0 O3' B:U3 4.2 60.6 1.0 HG A:SER267 4.3 47.4 1.0 O A:HOH724 4.4 42.0 1.0 N A:SER267 4.4 26.2 1.0 O A:HOH732 4.4 43.8 1.0 C5' B:U4 4.4 54.1 1.0 H A:ASP278 4.5 45.0 1.0 OP2 B:U4 4.5 71.0 1.0 H A:ASP280 4.5 36.4 1.0 C A:ASP278 4.5 40.4 1.0 H5' B:U4 4.5 65.1 1.0 CB A:ASP280 4.5 30.7 1.0 HA2 A:GLY266 4.5 39.0 1.0 CA A:GLY266 4.6 32.3 1.0 O A:HOH771 4.6 58.7 1.0 H4' B:U4 4.6 54.1 1.0 HB2 A:ASP280 4.7 37.0 1.0 O B:HOH105 4.7 42.8 1.0 CB A:ASP278 4.7 65.2 1.0 N A:ASP280 4.8 30.1 1.0 HA A:LEU279 4.8 49.3 1.0 HB3 A:SER277 4.9 44.3 1.0 HB3 A:SER267 4.9 41.1 1.0 N A:ASP278 4.9 37.4 1.0 CA A:ASP278 5.0 48.9 1.0 HO2' B:U3 5.0 52.1 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of Dmtailor in Complex with U6 Rna


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 Dmtailor in Complex with U6 Rna within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg602 b:50.2 occ:1.00 O3' B:U3 2.1 60.6 1.0 OD1 A:ASP278 2.3 76.9 1.0 OD1 A:ASP280 2.3 35.5 1.0 OD2 A:ASP343 2.3 41.4 1.0 OP1 B:U4 2.3 62.6 1.0 P B:U4 2.7 52.2 1.0 HB2 A:ASP343 3.0 59.3 1.0 CG A:ASP343 3.0 51.0 1.0 CG A:ASP278 3.3 77.8 1.0 H4' B:U3 3.3 65.1 1.0 C3' B:U3 3.3 52.1 1.0 HO2' B:U3 3.4 52.1 1.0 CG A:ASP280 3.4 36.4 1.0 CB A:ASP343 3.4 49.2 1.0 MG A:MG601 3.6 40.3 1.0 OD2 A:ASP278 3.7 81.3 1.0 O2' B:U3 3.7 43.2 1.0 O5' B:U4 3.7 60.9 1.0 HB3 A:ASP343 3.8 59.3 1.0 C4' B:U3 3.8 54.1 1.0 OD2 A:ASP280 3.8 37.9 1.0 OP2 B:U4 3.9 71.0 1.0 HZ1 A:LYS332 3.9 94.4 1.0 H5'' B:U3 3.9 62.7 1.0 OD1 A:ASP343 4.0 50.7 1.0 HZ2 A:LYS332 4.0 94.4 1.0 H3' B:U3 4.0 62.7 1.0 C2' B:U3 4.1 50.6 1.0 NZ A:LYS332 4.4 78.5 1.0 C5' B:U3 4.4 53.0 1.0 HB2 A:ASP278 4.5 78.4 1.0 CB A:ASP278 4.6 65.2 1.0 H2' B:U3 4.6 60.9 1.0 CB A:ASP280 4.6 30.7 1.0 HA A:ASP280 4.7 40.9 1.0 H A:ASP343 4.7 57.6 1.0 HB3 A:ASP280 4.7 37.0 1.0 O B:HOH102 4.8 76.0 1.0 CA A:ASP343 4.8 51.3 1.0 HZ3 A:LYS332 4.9 94.4 1.0 HB3 A:ASP278 4.9 78.4 1.0 H5' B:U3 4.9 62.7 1.0

A.Kroupova, A.Ivascu, M.M.Reimao-Pinto, S.L.Ameres, M.Jinek. Structural Basis For Acceptor Rna Substrate Selectivity of the 3' Terminal Uridylyl Transferase Tailor. Nucleic Acids Res. V. 47 1030 2019.
ISSN: ESSN 1362-4962
PubMed: 30462292
DOI: 10.1093/NAR/GKY1164