Iron 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:

Magnesium

(Mg)

2 atoms

The binding sites of Iron 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 Iron atom.
In total 2 binding sites of Iron where determined in the Ygjd(V85E)-Yeaz Heterodimer in Complex with Atp, PDB code: 4wq5:
Jump to Iron binding site number: 1; 2;

Iron 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 Iron with other atoms in the Fe 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:Fe402 b:50.2 occ:1.00 O3B A:ATP403 2.2 62.7 1.0 NE2 A:HIS111 2.3 33.5 1.0 OD1 A:ASP300 2.3 55.0 1.0 NE2 A:HIS115 2.4 33.6 1.0 O2B A:ATP403 2.4 51.0 1.0 PB A:ATP403 2.8 45.8 1.0 CD2 A:HIS111 3.2 35.0 1.0 CD2 A:HIS115 3.2 33.7 1.0 CE1 A:HIS111 3.3 38.3 1.0 CG A:ASP300 3.4 53.8 1.0 CE1 A:HIS115 3.4 31.7 1.0 O1A A:ATP403 3.4 46.2 1.0 O3A A:ATP403 3.6 43.9 1.0 PG A:ATP403 3.6 48.2 1.0 PA A:ATP403 3.7 36.8 1.0 OD2 A:ASP300 3.8 54.4 1.0 O2A A:ATP403 3.9 39.9 1.0 O2G A:ATP403 3.9 53.6 1.0 O1B A:ATP403 4.1 53.0 1.0 CE A:MET112 4.1 50.1 1.0 CG A:HIS111 4.3 33.6 1.0 ND1 A:HIS111 4.3 38.0 1.0 O1G A:ATP403 4.4 54.8 1.0 CG A:HIS115 4.4 30.1 1.0 ND1 A:HIS115 4.5 35.4 1.0 CB A:ASP300 4.6 44.7 1.0 O3G A:ATP403 4.6 54.9 1.0 N A:ASP300 4.7 34.7 1.0 CE A:MET304 4.7 41.7 1.0 CA A:ASP300 4.8 35.4 1.0 CB A:SER136 4.9 37.4 1.0

Iron 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 Iron with other atoms in the Fe 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:Fe402 b:56.5 occ:1.00 O3B B:ATP403 2.2 55.1 1.0 NE2 B:HIS111 2.3 42.1 1.0 NE2 B:HIS115 2.4 38.8 1.0 O1B B:ATP403 2.4 56.1 1.0 OD1 B:ASP300 2.6 71.2 1.0 PB B:ATP403 2.7 47.8 1.0 CD2 B:HIS111 3.1 39.2 1.0 CE1 B:HIS115 3.3 36.8 1.0 CE1 B:HIS111 3.3 43.2 1.0 CD2 B:HIS115 3.4 38.1 1.0 O2A B:ATP403 3.4 33.4 1.0 CG B:ASP300 3.5 54.9 1.0 PG B:ATP403 3.6 47.1 1.0 O3A B:ATP403 3.6 58.6 1.0 PA B:ATP403 3.8 35.8 1.0 CE B:MET112 4.0 55.3 1.0 O1A B:ATP403 4.0 38.2 1.0 O1G B:ATP403 4.0 57.3 1.0 O2B B:ATP403 4.1 64.6 1.0 OD2 B:ASP300 4.1 70.7 1.0 O3G B:ATP403 4.1 55.7 1.0 CG B:HIS111 4.3 43.3 1.0 ND1 B:HIS111 4.4 47.7 1.0 ND1 B:HIS115 4.4 35.9 1.0 CB B:ASP300 4.5 49.8 1.0 CG B:HIS115 4.5 34.2 1.0 CA B:ASP300 4.6 39.4 1.0 N B:ASP300 4.6 42.8 1.0 O2G B:ATP403 4.7 51.9 1.0 CE B:MET304 4.8 49.2 1.0 MG B:MG401 4.9 53.9 1.0 CB B:SER136 5.0 44.0 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