Iron in PDB 6ioc: The Structure of the H109Q Mutant of Udgx in Complex with Uracil

All present enzymatic activity of The Structure of the H109Q Mutant of Udgx in Complex with Uracil:
2.7.7.7;

The structure of The Structure of the H109Q Mutant of Udgx in Complex with Uracil, PDB code: 6ioc 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)	30.83 / 1.62
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	38.683, 50.711, 38.826, 90.00, 90.62, 90.00
R / Rfree (%)	15.5 / 18.2

The binding sites of Iron atom in the The Structure of the H109Q Mutant of Udgx in Complex with Uracil (pdb code 6ioc). 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 the H109Q Mutant of Udgx in Complex with Uracil, PDB code: 6ioc:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the The Structure of the H109Q Mutant of Udgx in Complex with Uracil


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 the H109Q Mutant of Udgx in Complex with Uracil within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe301 b:7.4 occ:1.00 FE1 A:SF4301 0.0 7.4 1.0 S4 A:SF4301 2.2 6.7 1.0 S2 A:SF4301 2.2 7.2 1.0 SG A:CYS120 2.2 7.1 1.0 S3 A:SF4301 2.3 6.2 1.0 FE2 A:SF4301 2.7 7.5 1.0 FE3 A:SF4301 2.7 8.3 1.0 FE4 A:SF4301 2.7 6.8 1.0 CB A:CYS120 3.0 6.9 1.0 CA A:CYS120 3.8 6.4 1.0 S1 A:SF4301 3.8 7.9 1.0 N A:LYS94 4.1 7.8 1.0 CD1 A:TRP123 4.2 6.4 1.0 CB A:LYS94 4.3 11.8 1.0 NE1 A:TRP123 4.4 6.4 1.0 ND1 A:HIS95 4.5 10.2 1.0 N A:CYS120 4.6 6.8 1.0 CG A:LYS94 4.6 22.8 1.0 SG A:CYS24 4.7 7.5 1.0 SG A:CYS27 4.7 10.0 1.0 CA A:LYS94 4.7 7.1 1.0 N A:HIS95 4.9 6.0 1.0 C A:CYS120 4.9 8.6 1.0

Iron binding site 2 out of 4 in the The Structure of the H109Q Mutant of Udgx in Complex with Uracil


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 the H109Q Mutant of Udgx in Complex with Uracil within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe301 b:7.5 occ:1.00 FE2 A:SF4301 0.0 7.5 1.0 S3 A:SF4301 2.2 6.2 1.0 S1 A:SF4301 2.2 7.9 1.0 S4 A:SF4301 2.3 6.7 1.0 SG A:CYS24 2.3 7.5 1.0 FE3 A:SF4301 2.6 8.3 1.0 FE1 A:SF4301 2.7 7.4 1.0 FE4 A:SF4301 2.7 6.8 1.0 CB A:CYS24 3.2 7.5 1.0 N A:GLY26 3.6 8.9 1.0 S2 A:SF4301 3.8 7.2 1.0 CA A:GLY26 4.0 8.7 1.0 NE1 A:TRP123 4.1 6.4 1.0 C A:CYS24 4.2 9.6 1.0 N A:CYS27 4.3 8.2 1.0 CA A:CYS24 4.3 6.7 1.0 ND1 A:HIS95 4.3 10.2 1.0 O A:CYS24 4.4 8.0 1.0 CB A:ALA4 4.5 9.2 1.0 N A:ARG25 4.6 9.4 1.0 C A:GLY26 4.6 8.9 1.0 CE1 A:HIS95 4.6 11.2 1.0 CD1 A:TRP123 4.6 6.4 1.0 C A:ARG25 4.7 12.2 1.0 SG A:CYS120 4.7 7.1 1.0 CA A:ARG25 4.9 6.7 1.0 SG A:CYS27 4.9 10.0 1.0

Iron binding site 3 out of 4 in the The Structure of the H109Q Mutant of Udgx in Complex with Uracil


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 the H109Q Mutant of Udgx in Complex with Uracil within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe301 b:8.3 occ:1.00 FE3 A:SF4301 0.0 8.3 1.0 ND1 A:HIS95 2.0 10.2 1.0 S2 A:SF4301 2.2 7.2 1.0 S4 A:SF4301 2.2 6.7 1.0 S1 A:SF4301 2.2 7.9 1.0 FE2 A:SF4301 2.6 7.5 1.0 FE4 A:SF4301 2.7 6.8 1.0 FE1 A:SF4301 2.7 7.4 1.0 CE1 A:HIS95 2.9 11.2 1.0 CG A:HIS95 3.2 11.5 1.0 CB A:HIS95 3.6 9.3 1.0 S3 A:SF4301 3.7 6.2 1.0 NE2 A:HIS95 4.1 9.9 1.0 N A:HIS95 4.1 6.0 1.0 CD2 A:HIS95 4.2 9.4 1.0 N A:TYR30 4.5 9.6 1.0 CA A:HIS95 4.5 6.8 1.0 C A:LYS94 4.6 8.5 1.0 SG A:CYS27 4.7 10.0 1.0 SG A:CYS24 4.7 7.5 1.0 CB A:CYS24 4.7 7.5 1.0 CB A:TYR30 4.7 10.8 1.0 CB A:LYS94 4.7 11.8 1.0 SG A:CYS120 4.7 7.1 1.0 CB A:LEU29 4.8 8.4 1.0 CA A:TYR30 4.8 12.7 1.0 O A:CYS24 4.9 8.0 1.0 C A:LEU29 4.9 11.6 1.0 N A:LYS94 4.9 7.8 1.0

Iron binding site 4 out of 4 in the The Structure of the H109Q Mutant of Udgx in Complex with Uracil


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 the H109Q Mutant of Udgx in Complex with Uracil within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe301 b:6.8 occ:1.00 FE4 A:SF4301 0.0 6.8 1.0 S3 A:SF4301 2.2 6.2 1.0 S1 A:SF4301 2.2 7.9 1.0 S2 A:SF4301 2.3 7.2 1.0 SG A:CYS27 2.3 10.0 1.0 FE3 A:SF4301 2.7 8.3 1.0 FE2 A:SF4301 2.7 7.5 1.0 FE1 A:SF4301 2.7 7.4 1.0 CB A:CYS27 3.4 8.9 1.0 N A:CYS27 3.4 8.2 1.0 S4 A:SF4301 3.8 6.7 1.0 CA A:CYS27 3.8 8.7 1.0 C A:CYS27 4.2 10.5 1.0 C A:GLY26 4.2 8.9 1.0 O A:CYS27 4.3 13.7 1.0 CB A:LEU29 4.5 8.4 1.0 N A:LEU29 4.6 9.7 1.0 ND1 A:HIS95 4.6 10.2 1.0 N A:GLY26 4.6 8.9 1.0 CA A:GLY26 4.6 8.7 1.0 SG A:CYS120 4.7 7.1 1.0 CB A:CYS120 4.7 6.9 1.0 SG A:CYS24 4.9 7.5 1.0 N A:GLY28 5.0 11.6 1.0 CG A:LEU29 5.0 10.2 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