Magnesium in PDB 4kr7: Crystal Structure of A 4-Thiouridine Synthetase - Rna Complex with Bound Atp

All present enzymatic activity of Crystal Structure of A 4-Thiouridine Synthetase - Rna Complex with Bound Atp:
2.8.1.4;

The structure of Crystal Structure of A 4-Thiouridine Synthetase - Rna Complex with Bound Atp, PDB code: 4kr7 was solved by P.Neumann, R.Ficner, K.Lakomek, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.39 / 3.42
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	103.170, 113.220, 133.180, 90.00, 90.00, 90.00
R / Rfree (%)	23 / 27.4

The binding sites of Magnesium atom in the Crystal Structure of A 4-Thiouridine Synthetase - Rna Complex with Bound Atp (pdb code 4kr7). 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 A 4-Thiouridine Synthetase - Rna Complex with Bound Atp, PDB code: 4kr7:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of A 4-Thiouridine Synthetase - Rna Complex with Bound Atp


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 A 4-Thiouridine Synthetase - Rna Complex with Bound Atp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg402 b:71.7 occ:1.00 O3B A:ATP401 2.7 0.7 1.0 O3G A:ATP401 2.7 0.8 1.0 O2A A:ATP401 3.3 0.6 1.0 PG A:ATP401 3.4 0.8 1.0 O3A A:ATP401 3.8 1.0 1.0 O5' A:ATP401 3.8 0.1 1.0 C8 A:ATP401 3.9 0.2 1.0 PA A:ATP401 3.9 0.3 1.0 PB A:ATP401 4.0 0.7 1.0 OG A:SER182 4.0 90.2 1.0 N7 A:ATP401 4.0 0.3 1.0 CB A:SER182 4.1 91.4 1.0 O2G A:ATP401 4.3 99.8 1.0 NH2 A:ARG264 4.4 82.2 1.0 O1G A:ATP401 4.6 0.5 1.0 O1B A:ATP401 4.7 0.1 1.0 N9 A:ATP401 4.9 0.4 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of A 4-Thiouridine Synthetase - Rna Complex with Bound Atp


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 A 4-Thiouridine Synthetase - Rna Complex with Bound Atp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg402 b:65.1 occ:1.00 O1G B:ATP401 2.9 89.3 1.0 PG B:ATP401 4.2 88.2 1.0 O2B B:ATP401 4.3 89.9 1.0 O2G B:ATP401 4.4 88.7 1.0 CA B:PRO339 4.5 0.1 1.0 CA B:GLY184 4.5 77.3 1.0 O2A B:ATP401 4.6 89.8 1.0 O B:PRO339 4.7 0.1 1.0 CB B:PRO339 4.9 0.6 1.0

P.Neumann, K.Lakomek, P.T.Naumann, W.M.Erwin, C.T.Lauhon, R.Ficner. Crystal Structure of A 4-Thiouridine Synthetase-Rna Complex Reveals Specificity of Trna U8 Modification. Nucleic Acids Res. V. 42 6673 2014.
ISSN: ISSN 0305-1048
PubMed: 24705700
DOI: 10.1093/NAR/GKU249