Magnesium in PDB 4ydu: Crystal Structure of E. Coli Ygjd-Yeaz Heterodimer in Complex with Adp

All present enzymatic activity of Crystal Structure of E. Coli Ygjd-Yeaz Heterodimer in Complex with Adp:
2.6.99.4;

The structure of Crystal Structure of E. Coli Ygjd-Yeaz Heterodimer in Complex with Adp, PDB code: 4ydu was solved by W.Zhang, B.Collinet, L.Perrochia, D.Durand, H.Van Tilbeurgh, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.38 / 2.33
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	63.620, 68.480, 87.070, 109.38, 92.66, 117.66
R / Rfree (%)	20.2 / 25.3

The structure of Crystal Structure of E. Coli Ygjd-Yeaz Heterodimer in Complex with Adp also contains other interesting chemical elements:

Iron

(Fe)

2 atoms

The binding sites of Magnesium atom in the Crystal Structure of E. Coli Ygjd-Yeaz Heterodimer in Complex with Adp (pdb code 4ydu). 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 E. Coli Ygjd-Yeaz Heterodimer in Complex with Adp, PDB code: 4ydu:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of E. Coli Ygjd-Yeaz Heterodimer in Complex with Adp


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 E. Coli Ygjd-Yeaz Heterodimer in Complex with Adp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg402 b:33.7 occ:1.00 O A:HOH604 1.7 34.2 1.0 OE1 A:GLU12 2.0 31.9 1.0 OD1 A:ASP11 2.2 28.3 1.0 O A:HOH586 2.3 24.5 1.0 O A:HOH580 2.4 29.1 1.0 CD A:GLU12 3.2 32.1 1.0 CG A:ASP11 3.3 32.3 1.0 OE2 A:GLU12 3.6 30.6 1.0 OD2 A:ASP11 3.8 32.4 1.0 O1B A:ADP401 3.9 37.7 1.0 O3A A:ADP401 4.0 31.0 1.0 OD2 A:ASP300 4.1 28.3 1.0 N A:ASP11 4.4 26.6 1.0 O1A A:ADP401 4.4 27.9 1.0 CG A:ASP300 4.4 27.3 1.0 CG A:GLU12 4.4 28.3 1.0 CB A:ASP300 4.6 25.0 1.0 CB A:ASP11 4.6 29.3 1.0 CB A:CYS10 4.7 24.5 1.0 N A:GLU12 4.7 26.1 1.0 C A:ASP11 4.8 27.7 1.0 CA A:ASP11 4.8 27.2 1.0 CB A:GLU12 4.8 26.3 1.0 SG A:CYS10 4.8 25.9 1.0 PB A:ADP401 4.9 38.3 1.0 O A:HOH519 4.9 20.2 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of E. Coli Ygjd-Yeaz Heterodimer in Complex with Adp


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 E. Coli Ygjd-Yeaz Heterodimer in Complex with Adp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg402 b:35.5 occ:1.00 O B:HOH606 2.0 18.4 1.0 OE1 B:GLU12 2.3 36.0 1.0 O B:HOH605 2.3 25.6 1.0 OD1 B:ASP11 2.4 33.0 1.0 CD B:GLU12 3.4 37.5 1.0 CG B:ASP11 3.4 35.5 1.0 OE2 B:GLU12 3.8 34.9 1.0 OD2 B:ASP11 3.8 38.0 1.0 O3A B:ADP401 4.0 29.6 1.0 O B:HOH609 4.0 29.3 1.0 O3B B:ADP401 4.1 32.1 1.0 O2A B:ADP401 4.3 25.5 1.0 OD2 B:ASP300 4.5 35.4 1.0 N B:ASP11 4.7 26.6 1.0 CG B:GLU12 4.7 30.8 1.0 CB B:ASP11 4.8 32.5 1.0 CG B:ASP300 4.8 31.4 1.0 PB B:ADP401 4.8 36.0 1.0 C5' B:ADP401 4.9 22.4 1.0 CB B:CYS10 4.9 28.9 1.0 PA B:ADP401 4.9 24.6 1.0 SG B:CYS10 4.9 32.5 1.0 O B:HOH607 4.9 31.1 1.0 CB B:ASP300 5.0 29.8 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. V. 43 1804 2015.
ISSN: ISSN 0305-1048
PubMed: 25578970
DOI: 10.1093/NAR/GKU1397