Iron in PDB 4wq4: E. Coli Ygjd(E12A)-Yeaz Heterodimer in Complex with Atp

All present enzymatic activity of E. Coli Ygjd(E12A)-Yeaz Heterodimer in Complex with Atp:
2.6.99.4;

The structure of E. Coli Ygjd(E12A)-Yeaz Heterodimer in Complex with Atp, PDB code: 4wq4 was solved by W.Zhang, B.Collinet, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.04 / 2.33
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	63.270, 68.070, 87.130, 109.30, 92.98, 117.23
R / Rfree (%)	20.2 / 25.3

The binding sites of Iron atom in the E. Coli Ygjd(E12A)-Yeaz Heterodimer in Complex with Atp (pdb code 4wq4). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 2 binding sites of Iron where determined in the E. Coli Ygjd(E12A)-Yeaz Heterodimer in Complex with Atp, PDB code: 4wq4:
Jump to Iron binding site number: 1; 2;

Iron binding site 1 out of 2 in the E. Coli Ygjd(E12A)-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 E. Coli Ygjd(E12A)-Yeaz Heterodimer in Complex with Atp within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe401 b:48.7 occ:1.00 NE2 A:HIS115 2.3 29.0 1.0 OD1 A:ASP300 2.4 43.1 1.0 NE2 A:HIS111 2.5 18.7 1.0 O2A A:ATP402 2.7 38.2 1.0 O2G A:ATP402 2.9 52.0 1.0 O2B A:ATP402 3.0 42.9 1.0 CD2 A:HIS111 3.1 20.3 1.0 O1A A:ATP402 3.1 42.5 1.0 PA A:ATP402 3.2 36.9 1.0 CE1 A:HIS115 3.3 30.0 1.0 CD2 A:HIS115 3.3 30.0 1.0 CG A:ASP300 3.5 30.9 1.0 CE1 A:HIS111 3.7 20.6 1.0 O3A A:ATP402 3.8 40.3 1.0 PB A:ATP402 3.8 52.4 1.0 OD2 A:ASP300 3.9 30.1 1.0 CE A:MET112 3.9 40.1 1.0 O3B A:ATP402 4.1 52.8 1.0 PG A:ATP402 4.1 62.0 1.0 CG A:HIS111 4.4 18.8 1.0 ND1 A:HIS115 4.4 29.6 1.0 CG A:HIS115 4.4 23.5 1.0 ND1 A:HIS111 4.6 19.1 1.0 O A:HOH538 4.7 30.5 1.0 O5' A:ATP402 4.8 42.4 1.0 CB A:ASP300 4.8 27.4 1.0 O3G A:ATP402 4.9 51.7 1.0 CB A:SER136 4.9 30.5 1.0 N A:ASP300 5.0 24.1 1.0 CA A:ASP300 5.0 24.6 1.0

Iron binding site 2 out of 2 in the E. Coli Ygjd(E12A)-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 E. Coli Ygjd(E12A)-Yeaz Heterodimer in Complex with Atp within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe401 b:51.5 occ:1.00 NE2 B:HIS115 2.3 26.9 1.0 OD1 B:ASP300 2.4 31.2 1.0 O1B B:ATP402 2.5 47.6 1.0 NE2 B:HIS111 2.5 31.9 1.0 O2G B:ATP402 2.7 47.2 1.0 O B:HOH527 2.9 46.9 1.0 O2A B:ATP402 2.9 39.2 1.0 O1A B:ATP402 3.0 44.6 1.0 PA B:ATP402 3.1 40.9 1.0 CD2 B:HIS115 3.2 29.9 1.0 CG B:ASP300 3.3 27.0 1.0 CE1 B:HIS115 3.3 32.1 1.0 CD2 B:HIS111 3.3 28.3 1.0 O3A B:ATP402 3.5 48.1 1.0 PB B:ATP402 3.5 67.1 1.0 OD2 B:ASP300 3.6 37.5 1.0 CE1 B:HIS111 3.6 28.9 1.0 PG B:ATP402 3.9 57.8 1.0 O3B B:ATP402 4.1 53.8 1.0 CE B:MET112 4.2 42.4 1.0 O1G B:ATP402 4.4 59.1 1.0 CG B:HIS115 4.4 25.1 1.0 ND1 B:HIS115 4.4 29.0 1.0 CG B:HIS111 4.6 27.0 1.0 CB B:ASP300 4.6 26.1 1.0 ND1 B:HIS111 4.7 29.7 1.0 O5' B:ATP402 4.7 45.8 1.0 N B:ASP300 4.8 23.7 1.0 CA B:ASP300 4.9 24.7 1.0 O2B B:ATP402 4.9 62.2 1.0 OG B:SER136 5.0 50.6 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