Magnesium in PDB 2nom: Terminal Uridylyl Transferase 4 From Trypanosoma Brucei with Bound Dutp

All present enzymatic activity of Terminal Uridylyl Transferase 4 From Trypanosoma Brucei with Bound Dutp:
2.7.7.52;

The structure of Terminal Uridylyl Transferase 4 From Trypanosoma Brucei with Bound Dutp, PDB code: 2nom was solved by H.Luecke, J.Stagno, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	41.20 / 2.40
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	79.142, 41.659, 104.286, 90.00, 96.46, 90.00
R / Rfree (%)	23 / 30.1

The binding sites of Magnesium atom in the Terminal Uridylyl Transferase 4 From Trypanosoma Brucei with Bound Dutp (pdb code 2nom). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Terminal Uridylyl Transferase 4 From Trypanosoma Brucei with Bound Dutp, PDB code: 2nom:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Terminal Uridylyl Transferase 4 From Trypanosoma Brucei with Bound Dutp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Terminal Uridylyl Transferase 4 From Trypanosoma Brucei with Bound Dutp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg401 b:18.5 occ:1.00 O A:HOH556 1.9 19.7 1.0 OD2 A:ASP66 2.1 19.0 1.0 O3G A:DUT501 2.2 16.2 1.0 OD2 A:ASP68 2.2 11.5 1.0 O1B A:DUT501 2.3 18.6 1.0 O A:HOH590 2.5 37.6 1.0 CG A:ASP66 3.3 21.5 1.0 O A:ASP66 3.4 17.2 1.0 CG A:ASP68 3.4 11.2 1.0 MG A:MG402 3.5 27.6 1.0 PG A:DUT501 3.6 14.2 1.0 PB A:DUT501 3.6 18.6 1.0 C A:ASP66 3.7 16.9 1.0 O A:HOH587 3.9 21.8 1.0 O3B A:DUT501 4.0 16.2 1.0 OD1 A:ASP66 4.0 25.1 1.0 OD1 A:ASP68 4.1 16.6 1.0 N A:ASP66 4.2 20.1 1.0 N A:SER54 4.2 20.0 1.0 N A:VAL67 4.2 15.4 1.0 OG A:SER54 4.3 18.6 1.0 CA A:ASP66 4.3 18.7 1.0 O A:HOH506 4.4 7.9 1.0 N A:ASP68 4.4 11.6 1.0 CB A:ASP66 4.4 18.5 1.0 CA A:VAL67 4.4 13.3 1.0 O3A A:DUT501 4.5 14.8 1.0 O2G A:DUT501 4.5 14.2 1.0 C A:VAL67 4.5 12.1 1.0 CB A:ASP68 4.5 11.8 1.0 O1G A:DUT501 4.6 19.2 1.0 O1A A:DUT501 4.7 17.0 1.0 CA A:GLY53 4.7 21.5 1.0 O2B A:DUT501 4.8 20.9 1.0 O A:HOH540 4.8 25.4 1.0 CB A:SER54 4.8 19.4 1.0 C A:SER65 4.9 21.9 1.0 C A:GLY53 4.9 21.1 1.0 CB A:SER65 4.9 23.1 1.0 O A:HOH589 4.9 27.4 1.0

Magnesium binding site 2 out of 2 in the Terminal Uridylyl Transferase 4 From Trypanosoma Brucei with Bound Dutp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Terminal Uridylyl Transferase 4 From Trypanosoma Brucei with Bound Dutp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg402 b:27.6 occ:1.00 O A:HOH590 2.1 37.6 1.0 OD2 A:ASP136 2.2 25.0 1.0 OD1 A:ASP68 2.2 16.6 1.0 OD1 A:ASP66 2.4 25.1 1.0 O A:HOH589 2.4 27.4 1.0 O A:HOH588 2.4 29.1 1.0 OD2 A:ASP68 2.9 11.5 1.0 CG A:ASP68 2.9 11.2 1.0 OD2 A:ASP66 3.0 19.0 1.0 CG A:ASP66 3.0 21.5 1.0 CG A:ASP136 3.4 24.1 1.0 MG A:MG401 3.5 18.5 1.0 O1A A:DUT501 3.7 17.0 1.0 O A:HOH581 3.8 14.9 1.0 O A:HOH540 4.1 25.4 1.0 CB A:ASP136 4.2 21.6 1.0 O1B A:DUT501 4.3 18.6 1.0 CB A:ASP68 4.3 11.8 1.0 OD1 A:ASP136 4.4 27.8 1.0 O3G A:DUT501 4.4 16.2 1.0 O A:HOH587 4.4 21.8 1.0 CB A:ASP66 4.5 18.5 1.0 O A:HOH558 4.6 22.4 1.0 NH2 A:ARG126 4.8 40.7 1.0 PA A:DUT501 5.0 15.9 1.0 CA A:ASP68 5.0 11.8 1.0

J.Stagno, I.Aphasizheva, A.Rosengarth, H.Luecke, R.Aphasizhev. Utp-Bound and Apo Structures of A Minimal Rna Uridylyltransferase. J.Mol.Biol. V. 366 882 2007.
ISSN: ISSN 0022-2836
PubMed: 17189640
DOI: 10.1016/J.JMB.2006.11.065