Iron in PDB 8iim: H109K Mutant of Uracil Dna Glycosylase X

All present enzymatic activity of H109K Mutant of Uracil Dna Glycosylase X:
3.2.2.27;

The structure of H109K Mutant of Uracil Dna Glycosylase X, PDB code: 8iim was solved by S.Aroli, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	26.41 / 1.60
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	36.45, 51.75, 54.63, 90, 104.83, 90
R / Rfree (%)	16.4 / 18.2

The binding sites of Iron atom in the H109K Mutant of Uracil Dna Glycosylase X (pdb code 8iim). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the H109K Mutant of Uracil Dna Glycosylase X, PDB code: 8iim:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the H109K Mutant of Uracil Dna Glycosylase X


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of H109K Mutant of Uracil Dna Glycosylase X within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe301 b:12.4 occ:1.00 FE1 A:SF4301 0.0 12.4 1.0 SG A:CYS120 2.2 10.7 1.0 S3 A:SF4301 2.3 10.9 1.0 S2 A:SF4301 2.3 10.8 1.0 S4 A:SF4301 2.3 11.2 1.0 FE3 A:SF4301 2.7 12.6 1.0 FE4 A:SF4301 2.7 13.3 1.0 FE2 A:SF4301 2.7 12.9 1.0 CB A:CYS120 3.1 11.6 1.0 CA A:CYS120 3.8 11.9 1.0 S1 A:SF4301 3.9 11.8 1.0 N A:LYS94 4.0 11.2 1.0 CD1 A:TRP123 4.2 12.1 1.0 CB A:LYS94 4.3 13.4 1.0 NE1 A:TRP123 4.5 12.6 1.0 SG A:CYS24 4.6 11.8 1.0 SG A:CYS27 4.7 12.8 1.0 N A:CYS120 4.7 11.2 1.0 ND1 A:HIS95 4.7 11.1 1.0 CA A:LYS94 4.7 11.8 1.0 CA A:VAL93 4.9 12.9 1.0 N A:HIS95 4.9 10.5 1.0 CB A:VAL93 5.0 16.6 1.0 C A:CYS120 5.0 11.7 1.0 C A:VAL93 5.0 13.2 1.0

Iron binding site 2 out of 4 in the H109K Mutant of Uracil Dna Glycosylase X


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of H109K Mutant of Uracil Dna Glycosylase X within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe301 b:12.9 occ:1.00 FE2 A:SF4301 0.0 12.9 1.0 S4 A:SF4301 2.3 11.2 1.0 SG A:CYS27 2.3 12.8 1.0 S1 A:SF4301 2.3 11.8 1.0 S3 A:SF4301 2.3 10.9 1.0 FE4 A:SF4301 2.7 13.3 1.0 FE1 A:SF4301 2.7 12.4 1.0 FE3 A:SF4301 2.8 12.6 1.0 CB A:CYS27 3.4 13.8 1.0 N A:CYS27 3.4 13.0 1.0 CA A:CYS27 3.8 13.0 1.0 S2 A:SF4301 3.9 10.8 1.0 C A:CYS27 4.2 12.6 1.0 C A:GLY26 4.2 15.2 1.0 O A:CYS27 4.3 15.8 1.0 CB A:LEU29 4.5 11.8 1.0 N A:LEU29 4.6 13.2 1.0 N A:GLY26 4.6 12.4 1.0 CA A:GLY26 4.7 13.5 1.0 SG A:CYS120 4.7 10.7 1.0 ND1 A:HIS95 4.7 11.1 1.0 CB A:CYS120 4.8 11.6 1.0 N A:GLY28 4.9 16.0 1.0 SG A:CYS24 4.9 11.8 1.0 CG A:LEU29 4.9 12.6 1.0 N A:TYR30 5.0 13.0 1.0

Iron binding site 3 out of 4 in the H109K Mutant of Uracil Dna Glycosylase X


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of H109K Mutant of Uracil Dna Glycosylase X within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe301 b:12.6 occ:1.00 FE3 A:SF4301 0.0 12.6 1.0 S4 A:SF4301 2.3 11.2 1.0 S1 A:SF4301 2.3 11.8 1.0 SG A:CYS24 2.3 11.8 1.0 S2 A:SF4301 2.3 10.8 1.0 FE4 A:SF4301 2.7 13.3 1.0 FE1 A:SF4301 2.7 12.4 1.0 FE2 A:SF4301 2.8 12.9 1.0 CB A:CYS24 3.2 12.1 1.0 N A:GLY26 3.6 12.4 1.0 S3 A:SF4301 3.9 10.9 1.0 CA A:GLY26 4.0 13.5 1.0 NE1 A:TRP123 4.1 12.6 1.0 C A:CYS24 4.2 12.7 1.0 N A:CYS27 4.3 13.0 1.0 CA A:CYS24 4.3 12.2 1.0 O A:CYS24 4.4 14.9 1.0 N A:ARG25 4.5 13.4 1.0 CB A:ALA4 4.5 13.8 1.0 C A:GLY26 4.5 15.2 1.0 ND1 A:HIS95 4.5 11.1 1.0 C A:ARG25 4.6 14.2 1.0 CD1 A:TRP123 4.6 12.1 1.0 SG A:CYS120 4.7 10.7 1.0 CE1 A:HIS95 4.8 12.9 1.0 CA A:ARG25 4.8 14.2 1.0 SG A:CYS27 5.0 12.8 1.0

Iron binding site 4 out of 4 in the H109K Mutant of Uracil Dna Glycosylase X


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of H109K Mutant of Uracil Dna Glycosylase X within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe301 b:13.3 occ:1.00 FE4 A:SF4301 0.0 13.3 1.0 ND1 A:HIS95 2.2 11.1 1.0 S3 A:SF4301 2.3 10.9 1.0 S1 A:SF4301 2.3 11.8 1.0 S2 A:SF4301 2.3 10.8 1.0 FE2 A:SF4301 2.7 12.9 1.0 FE3 A:SF4301 2.7 12.6 1.0 FE1 A:SF4301 2.7 12.4 1.0 CE1 A:HIS95 3.1 12.9 1.0 CG A:HIS95 3.3 11.3 1.0 CB A:HIS95 3.6 11.2 1.0 S4 A:SF4301 3.8 11.2 1.0 N A:HIS95 4.1 10.5 1.0 NE2 A:HIS95 4.2 14.3 1.0 CD2 A:HIS95 4.3 13.2 1.0 N A:TYR30 4.4 13.0 1.0 CA A:HIS95 4.4 11.2 1.0 C A:LYS94 4.5 11.9 1.0 CB A:LYS94 4.6 13.4 1.0 SG A:CYS27 4.6 12.8 1.0 CB A:TYR30 4.6 12.9 1.0 SG A:CYS24 4.7 11.8 1.0 CB A:LEU29 4.7 11.8 1.0 CA A:TYR30 4.8 13.2 1.0 SG A:CYS120 4.8 10.7 1.0 N A:LYS94 4.8 11.2 1.0 CB A:CYS24 4.9 12.1 1.0 CA A:LYS94 4.9 11.8 1.0 C A:LEU29 4.9 13.6 1.0

S.Aroli, E.J.Woo, B.Gopal, U.Varshney. Mutational and Structural Analyses of Udgx: Insights Into the Active Site Pocket Architecture and Its Evolution. Nucleic Acids Res. 2023.
ISSN: ESSN 1362-4962
PubMed: 37283083
DOI: 10.1093/NAR/GKAD486