Iron in PDB 8iij: H109G Mutant of Uracil Dna Glycosylase X

All present enzymatic activity of H109G Mutant of Uracil Dna Glycosylase X:
3.2.2.27;

The structure of H109G Mutant of Uracil Dna Glycosylase X, PDB code: 8iij was solved by S.Aroli, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	24.35 / 1.83
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	36.71, 50.58, 54.83, 90, 104.22, 90
R / Rfree (%)	18.3 / 23.1

The binding sites of Iron atom in the H109G Mutant of Uracil Dna Glycosylase X (pdb code 8iij). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the H109G Mutant of Uracil Dna Glycosylase X, PDB code: 8iij:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the H109G 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 H109G Mutant of Uracil Dna Glycosylase X within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe301 b:19.7 occ:1.00 FE1 A:SF4301 0.0 19.7 1.0 SG A:CYS120 2.2 17.0 1.0 S3 A:SF4301 2.3 19.5 1.0 S4 A:SF4301 2.3 22.2 1.0 S2 A:SF4301 2.3 18.4 1.0 FE4 A:SF4301 2.7 21.9 1.0 FE2 A:SF4301 2.7 22.3 1.0 FE3 A:SF4301 2.8 22.1 1.0 CB A:CYS120 3.2 19.4 1.0 CA A:CYS120 3.9 18.3 1.0 S1 A:SF4301 3.9 22.1 1.0 N A:LYS94 4.0 17.1 1.0 CD1 A:TRP123 4.1 22.1 1.0 CB A:LYS94 4.4 17.1 1.0 NE1 A:TRP123 4.5 21.1 1.0 CG A:LYS94 4.6 22.8 1.0 N A:CYS120 4.7 18.6 1.0 CA A:LYS94 4.7 17.9 1.0 SG A:CYS24 4.7 18.7 1.0 SG A:CYS27 4.7 23.6 1.0 N A:HIS95 4.8 17.1 1.0 CA A:VAL93 4.9 18.4 1.0 CB A:VAL93 4.9 20.8 1.0 ND1 A:HIS95 5.0 18.9 1.0 C A:VAL93 5.0 18.1 1.0 C A:CYS120 5.0 19.7 1.0

Iron binding site 2 out of 4 in the H109G 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 H109G Mutant of Uracil Dna Glycosylase X within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe301 b:22.3 occ:1.00 FE2 A:SF4301 0.0 22.3 1.0 S4 A:SF4301 2.3 22.2 1.0 S1 A:SF4301 2.3 22.1 1.0 S3 A:SF4301 2.3 19.5 1.0 SG A:CYS27 2.3 23.6 1.0 FE4 A:SF4301 2.7 21.9 1.0 FE1 A:SF4301 2.7 19.7 1.0 FE3 A:SF4301 2.8 22.1 1.0 N A:CYS27 3.3 24.8 1.0 CB A:CYS27 3.4 22.4 1.0 CA A:CYS27 3.8 24.4 1.0 S2 A:SF4301 3.9 18.4 1.0 C A:GLY26 4.1 24.1 1.0 C A:CYS27 4.2 23.7 1.0 O A:CYS27 4.3 27.2 1.0 CB A:LEU29 4.5 19.3 1.0 N A:GLY26 4.6 25.2 1.0 CA A:GLY26 4.6 23.6 1.0 N A:LEU29 4.7 22.3 1.0 SG A:CYS120 4.7 17.0 1.0 CB A:CYS120 4.9 19.4 1.0 SG A:CYS24 4.9 18.7 1.0 N A:GLY28 4.9 24.7 1.0 O A:GLY26 4.9 23.1 1.0 ND1 A:HIS95 5.0 18.9 1.0

Iron binding site 3 out of 4 in the H109G 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 H109G Mutant of Uracil Dna Glycosylase X within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe301 b:22.1 occ:1.00 FE3 A:SF4301 0.0 22.1 1.0 SG A:CYS24 2.3 18.7 1.0 S1 A:SF4301 2.3 22.1 1.0 S4 A:SF4301 2.3 22.2 1.0 S2 A:SF4301 2.3 18.4 1.0 FE4 A:SF4301 2.7 21.9 1.0 FE1 A:SF4301 2.8 19.7 1.0 FE2 A:SF4301 2.8 22.3 1.0 CB A:CYS24 3.1 19.5 1.0 N A:GLY26 3.6 25.2 1.0 S3 A:SF4301 3.9 19.5 1.0 NE1 A:TRP123 4.0 21.1 1.0 CA A:GLY26 4.0 23.6 1.0 C A:CYS24 4.2 24.1 1.0 CA A:CYS24 4.3 22.0 1.0 N A:CYS27 4.3 24.8 1.0 CB A:ALA4 4.4 20.9 1.0 O A:CYS24 4.4 21.9 1.0 N A:ARG25 4.5 23.3 1.0 CD1 A:TRP123 4.5 22.1 1.0 C A:GLY26 4.6 24.1 1.0 C A:ARG25 4.6 23.1 1.0 SG A:CYS120 4.7 17.0 1.0 ND1 A:HIS95 4.7 18.9 1.0 CA A:ARG25 4.9 23.9 1.0

Iron binding site 4 out of 4 in the H109G 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 H109G Mutant of Uracil Dna Glycosylase X within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe301 b:21.9 occ:1.00 FE4 A:SF4301 0.0 21.9 1.0 S2 A:SF4301 2.3 18.4 1.0 S3 A:SF4301 2.3 19.5 1.0 S1 A:SF4301 2.3 22.1 1.0 ND1 A:HIS95 2.5 18.9 1.0 FE1 A:SF4301 2.7 19.7 1.0 FE3 A:SF4301 2.7 22.1 1.0 FE2 A:SF4301 2.7 22.3 1.0 CG A:HIS95 3.4 19.5 1.0 CE1 A:HIS95 3.4 22.2 1.0 CB A:HIS95 3.5 18.9 1.0 S4 A:SF4301 3.8 22.2 1.0 N A:HIS95 4.0 17.1 1.0 CA A:HIS95 4.4 18.3 1.0 N A:TYR30 4.5 21.1 1.0 C A:LYS94 4.5 16.7 1.0 CD2 A:HIS95 4.5 18.4 1.0 NE2 A:HIS95 4.5 20.1 1.0 CB A:TYR30 4.6 23.9 1.0 SG A:CYS27 4.7 23.6 1.0 CB A:LYS94 4.7 17.1 1.0 CB A:CYS24 4.7 19.5 1.0 SG A:CYS24 4.7 18.7 1.0 SG A:CYS120 4.7 17.0 1.0 CA A:TYR30 4.8 21.9 1.0 CB A:LEU29 4.8 19.3 1.0 N A:LYS94 4.8 17.1 1.0 CA A:LYS94 4.9 17.9 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