Magnesium in PDB 5wu4: Crystal Structure of Human TUT1 Bound with Mgatp, Form II

All present enzymatic activity of Crystal Structure of Human TUT1 Bound with Mgatp, Form II:
2.7.7.19; 2.7.7.52;

The structure of Crystal Structure of Human TUT1 Bound with Mgatp, Form II, PDB code: 5wu4 was solved by S.Yamashita, K.Tomita, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.98 / 2.80
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	77.660, 88.560, 93.820, 90.00, 98.66, 90.00
R / Rfree (%)	24.1 / 28.2

The structure of Crystal Structure of Human TUT1 Bound with Mgatp, Form II also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Magnesium atom in the Crystal Structure of Human TUT1 Bound with Mgatp, Form II (pdb code 5wu4). 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 Human TUT1 Bound with Mgatp, Form II, PDB code: 5wu4:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of Human TUT1 Bound with Mgatp, Form II


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 Human TUT1 Bound with Mgatp, Form II within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1002 b:1.0 occ:1.00 O2B A:ATP1001 2.0 0.5 1.0 OD2 A:ASP218 2.0 67.1 1.0 O3G A:ATP1001 2.1 0.7 1.0 O1A A:ATP1001 2.5 0.8 1.0 CB A:SER205 3.2 58.4 1.0 CG A:ASP218 3.2 60.7 1.0 N A:SER205 3.2 52.3 1.0 PB A:ATP1001 3.3 0.4 1.0 PG A:ATP1001 3.4 1.0 1.0 O A:ASP216 3.5 48.4 1.0 PA A:ATP1001 3.5 1.0 1.0 O5' A:ATP1001 3.6 0.6 1.0 O3B A:ATP1001 3.7 0.7 1.0 CB A:ASP216 3.8 64.5 1.0 CA A:SER205 3.8 55.0 1.0 O3A A:ATP1001 3.9 0.7 1.0 OD1 A:ASP218 3.9 62.3 1.0 C A:ASP216 4.1 51.0 1.0 O2G A:ATP1001 4.1 0.8 1.0 C A:GLY204 4.3 50.0 1.0 CA A:ASP216 4.3 54.9 1.0 CB A:ASP218 4.3 52.6 1.0 CA A:GLY204 4.4 49.5 1.0 N A:ASP216 4.4 53.8 1.0 OG A:SER205 4.4 62.5 1.0 O1G A:ATP1001 4.5 0.8 1.0 O1B A:ATP1001 4.5 0.4 1.0 O A:PHE203 4.7 50.6 1.0 N A:ASP218 4.8 46.0 1.0 N A:SER206 4.8 59.2 1.0 O A:HOH1101 4.8 86.0 1.0 C A:SER205 4.8 58.8 1.0 C5' A:ATP1001 4.9 0.4 1.0 O2A A:ATP1001 4.9 0.3 1.0 CG A:ASP216 4.9 78.8 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of Human TUT1 Bound with Mgatp, Form II


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 Human TUT1 Bound with Mgatp, Form II within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1002 b:0.0 occ:1.00 O1G B:ATP1001 2.0 0.3 1.0 O2A B:ATP1001 2.1 0.3 1.0 O1B B:ATP1001 2.2 0.3 1.0 OD2 B:ASP218 2.5 62.4 1.0 CB B:SER205 3.2 72.5 1.0 O B:ASP216 3.3 66.1 1.0 PA B:ATP1001 3.4 0.5 1.0 PB B:ATP1001 3.4 0.7 1.0 CB B:ASP216 3.4 80.0 1.0 PG B:ATP1001 3.4 0.7 1.0 N B:SER205 3.4 62.5 1.0 O3A B:ATP1001 3.7 0.9 1.0 CG B:ASP218 3.7 60.7 1.0 O3B B:ATP1001 3.7 0.0 1.0 C B:ASP216 3.8 62.9 1.0 N B:ASP216 3.8 62.3 1.0 CA B:ASP216 3.8 67.4 1.0 O5' B:ATP1001 3.9 0.2 1.0 CA B:SER205 3.9 66.6 1.0 O2G B:ATP1001 4.3 0.8 1.0 OD1 B:ASP218 4.3 64.8 1.0 OG B:SER205 4.3 77.2 1.0 O3G B:ATP1001 4.3 1.0 1.0 O B:HOH1101 4.4 99.6 1.0 CG B:ASP216 4.4 96.7 1.0 C B:GLY204 4.5 60.1 1.0 CA B:GLY204 4.6 57.9 1.0 O2B B:ATP1001 4.7 0.3 1.0 O1A B:ATP1001 4.7 0.7 1.0 C B:CYS215 4.8 57.1 1.0 N B:SER206 4.8 64.6 1.0 CB B:ASP218 4.8 54.1 1.0 CB B:CYS215 4.8 50.3 1.0 N B:LEU217 4.8 54.8 1.0 C B:SER205 4.9 69.0 1.0 N B:ASP218 5.0 47.1 1.0

S.Yamashita, Y.Takagi, T.Nagaike, K.Tomita. Crystal Structures of U6 Snrna-Specific Terminal Uridylyltransferase Nat Commun V. 8 15788 2017.
ISSN: ESSN 2041-1723
PubMed: 28589955
DOI: 10.1038/NCOMMS15788