Iron 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:

Magnesium

(Mg)

2 atoms

The binding sites of Iron 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 Iron atom.
In total 2 binding sites of Iron where determined in the Crystal Structure of E. Coli Ygjd-Yeaz Heterodimer in Complex with Adp, PDB code: 4ydu:
Jump to Iron binding site number: 1; 2;

Iron 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 Iron with other atoms in the Fe 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:Fe403 b:25.1 occ:1.00 O2B A:ADP401 1.6 34.1 1.0 OD1 A:ASP300 1.9 27.6 1.0 NE2 A:HIS111 2.1 30.2 1.0 NE2 A:HIS115 2.1 27.2 1.0 O2A A:ADP401 2.9 24.6 1.0 PB A:ADP401 2.9 38.3 1.0 CG A:ASP300 2.9 27.3 1.0 CE1 A:HIS111 3.0 33.6 1.0 CD2 A:HIS115 3.1 28.1 1.0 CE1 A:HIS115 3.1 28.1 1.0 CD2 A:HIS111 3.1 30.3 1.0 OD2 A:ASP300 3.2 28.3 1.0 O3A A:ADP401 3.4 31.0 1.0 PA A:ADP401 3.6 24.7 1.0 O A:HOH522 3.7 30.3 1.0 O1B A:ADP401 3.7 37.7 1.0 O3B A:ADP401 4.1 36.3 1.0 ND1 A:HIS111 4.1 30.3 1.0 ND1 A:HIS115 4.2 28.0 1.0 CG A:HIS115 4.2 26.8 1.0 CG A:HIS111 4.2 28.3 1.0 CB A:ASP300 4.2 25.0 1.0 O1A A:ADP401 4.3 27.9 1.0 O A:HOH592 4.5 32.2 1.0 CA A:ASP300 4.5 24.1 1.0 CE A:MET304 4.6 31.2 1.0 N A:ASP300 4.6 25.3 1.0 O A:HOH604 4.9 34.2 1.0 O5' A:ADP401 5.0 24.3 1.0 CB A:SER136 5.0 32.4 1.0

Iron 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 Iron with other atoms in the Fe 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:Fe403 b:23.5 occ:1.00 O2B B:ADP401 1.7 38.4 1.0 OD1 B:ASP300 2.0 27.8 1.0 NE2 B:HIS111 2.1 19.9 1.0 NE2 B:HIS115 2.1 20.3 1.0 O1A B:ADP401 2.9 28.6 1.0 CG B:ASP300 2.9 31.4 1.0 PB B:ADP401 3.0 36.0 1.0 CD2 B:HIS111 3.1 24.1 1.0 CE1 B:HIS115 3.1 20.7 1.0 CE1 B:HIS111 3.1 21.4 1.0 CD2 B:HIS115 3.1 19.2 1.0 OD2 B:ASP300 3.3 35.4 1.0 O3A B:ADP401 3.3 29.6 1.0 PA B:ADP401 3.6 24.6 1.0 O3B B:ADP401 3.7 32.1 1.0 O B:HOH566 3.9 23.6 1.0 O B:HOH608 4.0 35.8 1.0 O1B B:ADP401 4.2 29.5 1.0 ND1 B:HIS111 4.2 22.3 1.0 CG B:HIS111 4.2 21.7 1.0 ND1 B:HIS115 4.2 20.9 1.0 CG B:HIS115 4.3 18.2 1.0 CB B:ASP300 4.3 29.8 1.0 O2A B:ADP401 4.4 25.5 1.0 CE B:MET112 4.4 41.0 1.0 CA B:ASP300 4.6 26.3 1.0 CE B:MET304 4.7 30.6 1.0 N B:ASP300 4.7 25.2 1.0 CB B:SER136 4.8 25.8 1.0 O5' B:ADP401 4.9 22.5 1.0 O B:HOH606 4.9 18.4 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