Magnesium in PDB 4ycp: E. Coli Dihydrouridine Synthase C (Dusc) in Complex with Trnatrp

The structure of E. Coli Dihydrouridine Synthase C (Dusc) in Complex with Trnatrp, PDB code: 4ycp was solved by R.T.Byrne, H.T.Jenkins, D.T.Peters, F.Whelan, J.Stowell, N.Aziz, P.Kasatsky, M.V.Rodnina, E.V.Koonin, A.L.Konevega, A.A.Antson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.26 / 2.55
Space group	P 65 2 2
Cell size a, b, c (Å), α, β, γ (°)	98.516, 98.516, 231.172, 90.00, 90.00, 120.00
R / Rfree (%)	20.8 / 23.5

The binding sites of Magnesium atom in the E. Coli Dihydrouridine Synthase C (Dusc) in Complex with Trnatrp (pdb code 4ycp). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total only one binding site of Magnesium was determined in the E. Coli Dihydrouridine Synthase C (Dusc) in Complex with Trnatrp, PDB code: 4ycp:

Magnesium binding site 1 out of 1 in the E. Coli Dihydrouridine Synthase C (Dusc) in Complex with Trnatrp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of E. Coli Dihydrouridine Synthase C (Dusc) in Complex with Trnatrp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg101 b:48.1 occ:1.00 OP2 B:G19 2.0 39.4 1.0 OP2 B:U17 2.0 41.7 1.0 O A:HOH542 2.2 45.9 1.0 O B:HOH207 2.2 47.5 1.0 O B:HOH208 2.2 49.0 1.0 O A:HOH543 2.2 44.1 1.0 P B:G19 3.2 39.2 1.0 P B:U17 3.5 42.7 1.0 OP1 B:G19 3.6 39.7 1.0 O3' B:U16 4.1 43.5 1.0 C3' B:U16 4.1 43.2 1.0 O3' B:G18 4.2 39.9 1.0 O B:HOH206 4.3 37.1 1.0 OE1 A:GLN275 4.3 37.7 1.0 C3' B:G18 4.3 40.2 1.0 O5' B:G19 4.3 38.9 1.0 OP1 B:U17 4.4 42.8 1.0 O5' B:U17 4.4 43.0 1.0 O A:GLU9 4.5 40.1 1.0 O2' B:U16 4.5 44.2 1.0 OE1 A:GLU9 4.6 46.0 1.0 O A:HOH544 4.6 36.1 1.0 C2' B:U16 4.8 44.1 1.0 C7M A:FMN401 4.8 32.7 1.0

R.T.Byrne, H.T.Jenkins, D.T.Peters, F.Whelan, J.Stowell, N.Aziz, P.Kasatsky, M.V.Rodnina, E.V.Koonin, A.L.Konevega, A.A.Antson. Major Reorientation of Trna Substrates Defines Specificity of Dihydrouridine Synthases. Proc.Natl.Acad.Sci.Usa V. 112 6033 2015.
ISSN: ESSN 1091-6490
PubMed: 25902496
DOI: 10.1073/PNAS.1500161112