Magnesium in PDB 5w0n: Structure of Human TUT7 Catalytic Module (Cm) in Complex with Umpnpp and U2 Rna

All present enzymatic activity of Structure of Human TUT7 Catalytic Module (Cm) in Complex with Umpnpp and U2 Rna:
2.7.7.52;

The structure of Structure of Human TUT7 Catalytic Module (Cm) in Complex with Umpnpp and U2 Rna, PDB code: 5w0n was solved by C.R.Faehnle, J.Walleshauser, L.Joshua-Tor, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	58.88 / 2.50
Space group	P 61
Cell size a, b, c (Å), α, β, γ (°)	135.972, 135.972, 181.574, 90.00, 90.00, 120.00
R / Rfree (%)	18.7 / 21.5

The structure of Structure of Human TUT7 Catalytic Module (Cm) in Complex with Umpnpp and U2 Rna also contains other interesting chemical elements:

Zinc	(Zn)	2 atoms
Iodine	(I)	3 atoms

The binding sites of Magnesium atom in the Structure of Human TUT7 Catalytic Module (Cm) in Complex with Umpnpp and U2 Rna (pdb code 5w0n). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Structure of Human TUT7 Catalytic Module (Cm) in Complex with Umpnpp and U2 Rna, PDB code: 5w0n:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Structure of Human TUT7 Catalytic Module (Cm) in Complex with Umpnpp and U2 Rna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of Human TUT7 Catalytic Module (Cm) in Complex with Umpnpp and U2 Rna within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1401 b:78.4 occ:1.00 O2A A:2KH1402 2.0 82.8 1.0 O A:HOH1512 2.0 83.3 1.0 OD1 A:ASP1058 2.1 51.7 1.0 O1B A:2KH1402 2.1 87.4 1.0 OD2 A:ASP1060 2.1 47.1 1.0 O3G A:2KH1402 2.2 87.0 1.0 CG A:ASP1060 3.1 39.0 1.0 CG A:ASP1058 3.1 42.4 1.0 H7 A:2KH1402 3.1 92.3 1.0 PB A:2KH1402 3.3 79.0 0.9 PA A:2KH1402 3.3 73.2 1.0 OD1 A:ASP1060 3.4 40.8 1.0 H A:SER1047 3.5 50.0 1.0 OD2 A:ASP1058 3.5 40.7 1.0 PG A:2KH1402 3.5 80.5 0.9 N3A A:2KH1402 3.7 79.9 0.9 O3B A:2KH1402 3.8 84.5 1.0 C5' A:2KH1402 3.8 77.0 1.0 O A:HOH1520 3.8 39.0 1.0 H6 A:2KH1402 3.8 92.3 1.0 O A:ASP1058 3.9 37.2 1.0 OG A:SER1047 4.0 37.5 1.0 O A:HOH1526 4.0 36.1 1.0 HG A:SER1047 4.0 45.0 1.0 H A:ASP1058 4.1 49.2 1.0 HB3 A:SER1057 4.1 46.6 1.0 HA3 A:GLY1046 4.1 54.7 1.0 O5' A:2KH1402 4.1 75.5 1.0 H3AO A:UPU1403 4.2 51.6 1.0 N A:SER1047 4.3 41.7 1.0 HB3 A:SER1047 4.4 39.9 1.0 O1G A:2KH1402 4.4 84.7 0.9 C A:ASP1058 4.4 42.2 1.0 O1A A:2KH1402 4.4 75.3 1.0 CB A:ASP1058 4.4 44.7 1.0 CB A:ASP1060 4.4 41.4 1.0 O2G A:2KH1402 4.5 84.0 1.0 N A:ASP1058 4.5 41.0 1.0 O2B A:2KH1402 4.5 82.8 1.0 H2 A:2KH1402 4.5 95.8 0.9 HB2 A:ASP1060 4.5 49.6 1.0 H A:ASP1060 4.6 49.0 1.0 CA A:ASP1058 4.7 44.3 1.0 CB A:SER1047 4.7 33.2 1.0 O3'A A:UPU1403 4.8 43.0 1.0 HB3 A:ASP1058 4.9 53.6 1.0 CA A:GLY1046 4.9 45.6 1.0 N A:ASP1060 5.0 40.8 1.0

Magnesium binding site 2 out of 3 in the Structure of Human TUT7 Catalytic Module (Cm) in Complex with Umpnpp and U2 Rna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of Human TUT7 Catalytic Module (Cm) in Complex with Umpnpp and U2 Rna within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1401 b:37.8 occ:1.00 OD1 B:ASP1058 2.0 43.3 1.0 O2B B:2KH1402 2.0 28.7 1.0 O B:HOH1502 2.1 42.4 1.0 OD2 B:ASP1060 2.1 38.9 1.0 O3G B:2KH1402 2.2 27.3 1.0 O1A B:2KH1402 2.2 32.5 1.0 CG B:ASP1058 3.1 41.8 1.0 CG B:ASP1060 3.2 39.5 1.0 PB B:2KH1402 3.2 34.1 0.9 H6 B:2KH1402 3.2 42.6 1.0 H B:SER1047 3.3 46.7 1.0 PG B:2KH1402 3.4 28.6 0.9 PA B:2KH1402 3.5 35.0 1.0 OD1 B:ASP1060 3.5 38.0 1.0 OD2 B:ASP1058 3.5 43.9 1.0 OG B:SER1047 3.7 40.6 1.0 O3B B:2KH1402 3.7 36.4 1.0 HG B:SER1047 3.7 48.8 1.0 N3A B:2KH1402 3.8 39.5 0.9 O B:ASP1058 3.8 37.9 1.0 HB3 B:SER1057 3.9 51.9 1.0 H B:ASP1058 4.0 40.8 1.0 C5' B:2KH1402 4.0 35.5 1.0 O B:HOH1506 4.0 35.5 1.0 O B:HOH1524 4.0 40.1 1.0 H7 B:2KH1402 4.0 42.6 1.0 HA3 B:GLY1046 4.1 50.1 1.0 N B:SER1047 4.1 38.9 1.0 HB3 B:SER1047 4.2 45.9 1.0 O2G B:2KH1402 4.2 32.3 1.0 O5' B:2KH1402 4.3 35.6 1.0 C B:ASP1058 4.3 40.2 1.0 N B:ASP1058 4.4 34.0 1.0 CB B:ASP1058 4.4 38.7 1.0 H3AO B:UPU1403 4.4 56.9 1.0 CB B:SER1047 4.4 38.2 1.0 O1B B:2KH1402 4.4 38.2 1.0 H B:ASP1060 4.5 50.2 1.0 CB B:ASP1060 4.5 40.6 1.0 O1G B:2KH1402 4.5 33.3 0.9 HB2 B:ASP1060 4.5 48.7 1.0 H2 B:2KH1402 4.5 47.4 0.9 O2A B:2KH1402 4.6 39.3 1.0 CA B:ASP1058 4.6 38.8 1.0 H B:SER1048 4.8 53.2 1.0 CB B:SER1057 4.9 43.2 1.0 CA B:GLY1046 4.9 41.8 1.0 CA B:SER1047 4.9 44.4 1.0 N B:ASP1060 4.9 41.8 1.0 HB3 B:ASP1058 4.9 46.4 1.0 HB2 B:ASP1058 5.0 46.4 1.0

Magnesium binding site 3 out of 3 in the Structure of Human TUT7 Catalytic Module (Cm) in Complex with Umpnpp and U2 Rna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structure of Human TUT7 Catalytic Module (Cm) in Complex with Umpnpp and U2 Rna within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg1401 b:45.9 occ:1.00 O C:HOH1504 2.0 47.0 1.0 O1A C:2KH1402 2.1 41.7 1.0 OD1 C:ASP1058 2.1 47.6 1.0 OD2 C:ASP1060 2.1 44.7 1.0 O1G C:2KH1402 2.1 42.0 1.0 O1B C:2KH1402 2.2 43.2 1.0 CG C:ASP1060 3.1 44.5 1.0 H6 C:2KH1402 3.1 57.7 1.0 CG C:ASP1058 3.1 47.5 1.0 PB C:2KH1402 3.3 44.1 0.9 PA C:2KH1402 3.3 43.5 1.0 H C:SER1047 3.3 47.8 1.0 OD1 C:ASP1060 3.4 42.0 1.0 PG C:2KH1402 3.4 38.3 0.9 OD2 C:ASP1058 3.5 47.8 1.0 N3A C:2KH1402 3.7 41.1 0.9 OG C:SER1047 3.7 47.6 1.0 HG C:SER1047 3.7 57.2 1.0 O3B C:2KH1402 3.8 41.2 1.0 O C:ASP1058 3.8 48.1 1.0 C5' C:2KH1402 3.9 48.1 1.0 O C:HOH1520 3.9 54.6 1.0 HB3 C:SER1057 4.0 48.5 1.0 H7 C:2KH1402 4.0 57.7 1.0 H C:ASP1058 4.1 57.7 1.0 O C:HOH1505 4.1 37.1 1.0 HA3 C:GLY1046 4.1 47.5 1.0 O5' C:2KH1402 4.2 50.0 1.0 HB3 C:SER1047 4.2 53.9 1.0 N C:SER1047 4.2 39.9 1.0 H3AO C:UPU1403 4.2 60.0 1.0 O2G C:2KH1402 4.2 39.5 0.9 C C:ASP1058 4.4 45.9 1.0 CB C:ASP1060 4.4 43.3 1.0 CB C:SER1047 4.4 44.9 1.0 CB C:ASP1058 4.4 47.6 1.0 N C:ASP1058 4.5 48.1 1.0 O3G C:2KH1402 4.5 40.6 1.0 H2 C:2KH1402 4.5 49.4 0.9 O2A C:2KH1402 4.5 47.9 1.0 HB2 C:ASP1060 4.5 52.0 1.0 H C:ASP1060 4.5 51.9 1.0 O2B C:2KH1402 4.6 41.4 1.0 CA C:ASP1058 4.7 49.1 1.0 O3'A C:UPU1403 4.9 50.0 1.0 CA C:GLY1046 4.9 39.6 1.0 CB C:SER1057 4.9 40.5 1.0 N C:ASP1060 4.9 43.2 1.0 H C:SER1048 4.9 50.0 1.0 CA C:SER1047 4.9 42.1 1.0 HB3 C:ASP1058 5.0 57.1 1.0

C.R.Faehnle, J.Walleshauser, L.Joshua-Tor. Multi-Domain Utilization By TUT4 and TUT7 in Control of Let-7 Biogenesis. Nat. Struct. Mol. Biol. V. 24 658 2017.
ISSN: ESSN 1545-9985
PubMed: 28671666
DOI: 10.1038/NSMB.3428