Magnesium in PDB 4wq5: Ygjd(V85E)-Yeaz Heterodimer in Complex with Atp

All present enzymatic activity of Ygjd(V85E)-Yeaz Heterodimer in Complex with Atp:
2.6.99.4;

The structure of Ygjd(V85E)-Yeaz Heterodimer in Complex with Atp, PDB code: 4wq5 was solved by W.Zhang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	42.62 / 2.33
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	63.690, 68.080, 87.340, 109.31, 92.56, 117.94
R / Rfree (%)	18 / 23.3

The structure of Ygjd(V85E)-Yeaz Heterodimer in Complex with Atp also contains other interesting chemical elements:

Iron

(Fe)

2 atoms

The binding sites of Magnesium atom in the Ygjd(V85E)-Yeaz Heterodimer in Complex with Atp (pdb code 4wq5). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Ygjd(V85E)-Yeaz Heterodimer in Complex with Atp, PDB code: 4wq5:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Ygjd(V85E)-Yeaz Heterodimer in Complex with Atp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Ygjd(V85E)-Yeaz Heterodimer in Complex with Atp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg401 b:62.8 occ:1.00 OE1 A:GLU12 2.6 60.3 1.0 OD1 A:ASP11 2.8 45.7 1.0 OD2 A:ASP300 2.9 54.4 1.0 O2B A:ATP403 2.9 51.0 1.0 CG A:ASP300 3.5 53.8 1.0 CD A:GLU12 3.8 59.0 1.0 O1B A:ATP403 3.9 53.0 1.0 PB A:ATP403 3.9 45.8 1.0 CB A:CYS10 3.9 38.9 1.0 CG A:ASP11 4.0 44.9 1.0 O2A A:ATP403 4.1 39.9 1.0 CB A:ASP300 4.1 44.7 1.0 OD1 A:ASP300 4.2 55.0 1.0 N A:ASP11 4.2 36.8 1.0 OE2 A:GLU12 4.5 64.4 1.0 O A:HOH511 4.5 31.6 1.0 N A:GLU12 4.6 36.8 1.0 SG A:CYS10 4.6 47.0 1.0 CB A:GLU12 4.6 38.9 1.0 OD2 A:ASP11 4.7 54.1 1.0 O3A A:ATP403 4.8 43.9 1.0 CG A:GLU12 4.8 49.7 1.0 CA A:ASP11 4.9 36.2 1.0 C A:ASP11 4.9 33.4 1.0 CB A:ASP11 5.0 43.1 1.0

Magnesium binding site 2 out of 2 in the Ygjd(V85E)-Yeaz Heterodimer in Complex with Atp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Ygjd(V85E)-Yeaz Heterodimer in Complex with Atp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg401 b:53.9 occ:1.00 O1B B:ATP403 2.7 56.1 1.0 OD1 B:ASP11 2.8 48.3 1.0 O B:HOH515 2.9 55.5 1.0 OD2 B:ASP300 3.0 70.7 1.0 OE1 B:GLU12 3.2 59.6 1.0 CG B:ASP300 3.5 54.9 1.0 O2B B:ATP403 3.6 64.6 1.0 PB B:ATP403 3.6 47.8 1.0 CB B:CYS10 3.7 42.5 1.0 CB B:ASP300 3.9 49.8 1.0 CG B:ASP11 3.9 48.9 1.0 O1A B:ATP403 4.0 38.2 1.0 N B:ASP11 4.2 36.9 1.0 OD1 B:ASP300 4.3 71.2 1.0 SG B:CYS10 4.4 49.8 1.0 CD B:GLU12 4.4 58.6 1.0 O3A B:ATP403 4.5 58.6 1.0 OD2 B:ASP11 4.6 53.0 1.0 CA B:CYS10 4.8 35.1 1.0 N B:GLU12 4.9 39.8 1.0 FE B:FE402 4.9 56.5 1.0 CA B:ASP11 4.9 36.8 1.0 CB B:ASP11 4.9 44.0 1.0 PA B:ATP403 5.0 35.8 1.0 O3B B:ATP403 5.0 55.1 1.0

W.Zhang, B.Collinet, L.Perrochia, D.Durand, H.Van Tilbeurgh. The Atp-Mediated Formation of the Ygjd-Yeaz-Yjee Complex Is Required For the Biosynthesis of Trna T6A in Escherichia Coli. Nucleic Acids Res. 2015.
ISSN: ESSN 1362-4962
PubMed: 25578970
DOI: 10.1093/NAR/GKU1397