Magnesium in PDB 2q0f: Terminal Uridylyl Transferase 4 From Trypanosoma Brucei with Bound Utp and Ump

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

The structure of Terminal Uridylyl Transferase 4 From Trypanosoma Brucei with Bound Utp and Ump, PDB code: 2q0f was solved by J.Stagno, H.Luecke, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	38.98 / 2.40
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	80.620, 41.924, 106.017, 90.00, 94.37, 90.00
R / Rfree (%)	22.3 / 29.3

The binding sites of Magnesium atom in the Terminal Uridylyl Transferase 4 From Trypanosoma Brucei with Bound Utp and Ump (pdb code 2q0f). 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 Utp and Ump, PDB code: 2q0f:
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 Utp and Ump


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 Utp and Ump within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg401 b:14.3 occ:1.00 O1B A:UTP501 2.1 34.2 1.0 OD2 A:ASP68 2.2 27.5 1.0 O A:HOH574 2.4 31.3 1.0 O A:HOH503 2.5 33.1 1.0 O3G A:UTP501 2.5 33.9 1.0 OD2 A:ASP66 2.5 29.5 1.0 O1A A:UTP501 2.8 32.4 1.0 CG A:ASP68 3.2 26.7 1.0 PB A:UTP501 3.3 37.0 1.0 OD1 A:ASP68 3.4 26.5 1.0 CG A:ASP66 3.5 33.5 1.0 PA A:UTP501 3.6 32.3 1.0 C5' A:UTP501 3.7 30.1 1.0 OD1 A:ASP66 3.7 32.5 1.0 O3A A:UTP501 3.7 34.5 1.0 PG A:UTP501 3.9 33.0 1.0 O5' A:UTP501 3.9 33.5 1.0 O3B A:UTP501 4.0 34.3 1.0 MG A:MG402 4.2 24.0 1.0 O A:HOH534 4.4 44.7 1.0 CB A:ASP68 4.6 25.9 1.0 O3' A:U5P502 4.6 48.9 1.0 O A:HOH504 4.6 35.7 1.0 O2B A:UTP501 4.7 35.2 1.0 N A:SER54 4.7 25.9 1.0 O1G A:UTP501 4.7 30.4 1.0 O A:HOH512 4.9 16.3 1.0 O2G A:UTP501 4.9 32.5 1.0 O A:ASP66 4.9 33.0 1.0 OG A:SER54 4.9 29.4 1.0 CB A:ASP66 4.9 33.9 1.0

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


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 Utp and Ump within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg402 b:24.0 occ:1.00 O1A A:UTP501 2.3 32.4 1.0 O A:HOH604 2.3 33.3 1.0 O A:HOH503 2.5 33.1 1.0 O3' A:U5P502 2.6 48.9 1.0 O A:HOH504 2.6 35.7 1.0 O A:HOH603 2.7 23.9 1.0 PA A:UTP501 3.5 32.3 1.0 C3' A:U5P502 3.5 49.8 1.0 O3P A:U5P502 3.9 47.5 1.0 O2A A:UTP501 4.0 33.3 1.0 O5' A:UTP501 4.1 33.5 1.0 MG A:MG401 4.2 14.3 1.0 OD2 A:ASP136 4.3 40.6 1.0 C4' A:U5P502 4.3 50.3 1.0 C5' A:U5P502 4.3 50.0 1.0 OD1 A:ASP66 4.5 32.5 1.0 OD1 A:ASP68 4.5 26.5 1.0 NH2 A:ARG126 4.6 49.0 1.0 O A:HOH534 4.6 44.7 1.0 O3G A:UTP501 4.7 33.9 1.0 O A:HOH572 4.7 24.6 1.0 C2' A:U5P502 4.8 50.9 1.0 O A:HOH551 4.8 27.6 1.0 O3A A:UTP501 4.9 34.5 1.0 O5' A:U5P502 4.9 49.1 1.0

J.Stagno, I.Aphasizheva, R.Aphasizhev, H.Luecke. Dual Role of the Rna Substrate in Selectivity and Catalysis By Terminal Uridylyl Transferases. Proc.Natl.Acad.Sci.Usa V. 104 14634 2007.
ISSN: ISSN 0027-8424
PubMed: 17785418
DOI: 10.1073/PNAS.0704259104