Iron in PDB 6io9: The Structure of Apo-Udgx

The structure of The Structure of Apo-Udgx, PDB code: 6io9 was solved by W.Xie, J.Tu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	36.61 / 1.90
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	36.572, 50.958, 54.367, 90.00, 104.56, 90.00
R / Rfree (%)	19 / 22.5

The binding sites of Iron atom in the The Structure of Apo-Udgx (pdb code 6io9). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the The Structure of Apo-Udgx, PDB code: 6io9:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the The Structure of Apo-Udgx


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of The Structure of Apo-Udgx within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe301 b:22.7 occ:1.00 FE1 A:SF4301 0.0 22.7 1.0 S2 A:SF4301 2.2 27.8 1.0 S3 A:SF4301 2.2 28.6 1.0 S4 A:SF4301 2.2 27.3 1.0 SG A:CYS120 2.2 22.4 1.0 FE2 A:SF4301 2.8 25.1 1.0 FE4 A:SF4301 2.8 24.3 1.0 FE3 A:SF4301 2.8 28.4 1.0 CB A:CYS120 3.1 24.4 1.0 S1 A:SF4301 3.7 29.1 1.0 CA A:CYS120 3.8 22.9 1.0 N A:LYS94 4.1 22.8 1.0 CD1 A:TRP123 4.2 22.0 1.0 CB A:LYS94 4.5 23.0 1.0 NE1 A:TRP123 4.5 23.5 1.0 ND1 A:HIS95 4.6 23.4 1.0 N A:CYS120 4.7 23.7 1.0 SG A:CYS27 4.7 28.0 1.0 CG1 A:VAL93 4.7 37.5 1.0 SG A:CYS24 4.7 24.9 1.0 CA A:LYS94 4.8 18.9 1.0 C A:CYS120 4.9 24.7 1.0 N A:HIS95 5.0 22.4 1.0 O A:CYS120 5.0 22.8 1.0

Iron binding site 2 out of 4 in the The Structure of Apo-Udgx


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of The Structure of Apo-Udgx within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe301 b:25.1 occ:1.00 FE2 A:SF4301 0.0 25.1 1.0 S3 A:SF4301 2.2 28.6 1.0 S4 A:SF4301 2.2 27.3 1.0 S1 A:SF4301 2.2 29.1 1.0 SG A:CYS24 2.3 24.9 1.0 FE1 A:SF4301 2.8 22.7 1.0 FE3 A:SF4301 2.8 28.4 1.0 FE4 A:SF4301 2.8 24.3 1.0 CB A:CYS24 3.2 25.6 1.0 N A:GLY26 3.7 29.7 1.0 S2 A:SF4301 3.8 27.8 1.0 NE1 A:TRP123 4.0 23.5 1.0 CA A:GLY26 4.1 27.3 1.0 C A:CYS24 4.1 29.6 1.0 O A:CYS24 4.2 28.8 1.0 CA A:CYS24 4.3 24.1 1.0 N A:CYS27 4.3 26.1 1.0 ND1 A:HIS95 4.4 23.4 1.0 CB A:ALA4 4.4 25.4 1.0 N A:ARG25 4.5 23.9 1.0 CE1 A:HIS95 4.5 26.5 1.0 CD1 A:TRP123 4.5 22.0 1.0 C A:GLY26 4.6 27.1 1.0 C A:ARG25 4.6 28.3 1.0 SG A:CYS120 4.7 22.4 1.0 CA A:ARG25 4.9 26.9 1.0

Iron binding site 3 out of 4 in the The Structure of Apo-Udgx


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of The Structure of Apo-Udgx within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe301 b:28.4 occ:1.00 FE3 A:SF4301 0.0 28.4 1.0 ND1 A:HIS95 1.9 23.4 1.0 S2 A:SF4301 2.2 27.8 1.0 S4 A:SF4301 2.2 27.3 1.0 S1 A:SF4301 2.2 29.1 1.0 CE1 A:HIS95 2.7 26.5 1.0 FE2 A:SF4301 2.8 25.1 1.0 FE4 A:SF4301 2.8 24.3 1.0 FE1 A:SF4301 2.8 22.7 1.0 CG A:HIS95 3.1 22.6 1.0 CB A:HIS95 3.6 27.7 1.0 S3 A:SF4301 3.7 28.6 1.0 NE2 A:HIS95 3.9 21.3 1.0 N A:HIS95 4.0 22.4 1.0 CD2 A:HIS95 4.1 25.0 1.0 C A:LYS94 4.4 24.7 1.0 CA A:HIS95 4.4 24.4 1.0 N A:TYR30 4.6 26.6 1.0 SG A:CYS27 4.7 28.0 1.0 CB A:TYR30 4.7 27.6 1.0 SG A:CYS24 4.8 24.9 1.0 SG A:CYS120 4.8 22.4 1.0 CB A:LEU29 4.8 23.3 1.0 O A:LYS94 4.8 23.1 1.0 CA A:TYR30 4.8 27.5 1.0 N A:LYS94 4.8 22.8 1.0 O A:CYS24 4.9 28.8 1.0 CB A:LYS94 4.9 23.0 1.0 CB A:CYS24 4.9 25.6 1.0 CA A:LYS94 4.9 18.9 1.0

Iron binding site 4 out of 4 in the The Structure of Apo-Udgx


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of The Structure of Apo-Udgx within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe301 b:24.3 occ:1.00 FE4 A:SF4301 0.0 24.3 1.0 S3 A:SF4301 2.2 28.6 1.0 S1 A:SF4301 2.2 29.1 1.0 S2 A:SF4301 2.2 27.8 1.0 SG A:CYS27 2.2 28.0 1.0 FE1 A:SF4301 2.8 22.7 1.0 FE3 A:SF4301 2.8 28.4 1.0 FE2 A:SF4301 2.8 25.1 1.0 N A:CYS27 3.4 26.1 1.0 CB A:CYS27 3.4 29.4 1.0 CA A:CYS27 3.8 28.3 1.0 S4 A:SF4301 3.8 27.3 1.0 C A:GLY26 4.1 27.1 1.0 C A:CYS27 4.2 29.2 1.0 O A:CYS27 4.3 27.3 1.0 ND1 A:HIS95 4.4 23.4 1.0 CB A:LEU29 4.5 23.3 1.0 N A:GLY26 4.6 29.7 1.0 CA A:GLY26 4.7 27.3 1.0 N A:LEU29 4.7 27.3 1.0 SG A:CYS120 4.7 22.4 1.0 CB A:CYS120 4.8 24.4 1.0 O A:GLY26 4.9 26.1 1.0 CG A:LEU29 4.9 26.6 1.0 N A:GLY28 4.9 25.7 1.0 SG A:CYS24 5.0 24.9 1.0 CD1 A:LEU29 5.0 25.2 1.0

J.Tu, R.Chen, Y.Yang, W.Cao, W.Xie. Suicide Inactivation of the Uracil Dna Glycosylase Udgx By Covalent Complex Formation. Nat.Chem.Biol. V. 15 615 2019.
ISSN: ESSN 1552-4469
PubMed: 31101915
DOI: 10.1038/S41589-019-0290-X