Iron in PDB 8iih: H109C Mutant of Uracil Dna Glycosylase X

All present enzymatic activity of H109C Mutant of Uracil Dna Glycosylase X:
3.2.2.27;

The structure of H109C Mutant of Uracil Dna Glycosylase X, PDB code: 8iih was solved by S.Aroli, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	26.56 / 2.13
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	36.38, 51.51, 54.9, 90, 104.67, 90
R / Rfree (%)	17.2 / 22.2

The binding sites of Iron atom in the H109C Mutant of Uracil Dna Glycosylase X (pdb code 8iih). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the H109C Mutant of Uracil Dna Glycosylase X, PDB code: 8iih:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the H109C 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 H109C Mutant of Uracil Dna Glycosylase X within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe301 b:14.5 occ:1.00 FE1 A:SF4301 0.0 14.5 1.0 SG A:CYS120 2.3 13.8 1.0 S3 A:SF4301 2.3 12.6 1.0 S2 A:SF4301 2.3 13.0 1.0 S4 A:SF4301 2.3 12.4 1.0 FE3 A:SF4301 2.7 15.6 1.0 FE2 A:SF4301 2.7 15.1 1.0 FE4 A:SF4301 2.7 17.1 1.0 CB A:CYS120 3.1 12.1 1.0 CA A:CYS120 3.9 16.5 1.0 S1 A:SF4301 3.9 12.8 1.0 N A:LYS94 4.1 14.1 1.0 CD1 A:TRP123 4.1 12.5 1.0 NE1 A:TRP123 4.4 12.7 1.0 SG A:CYS24 4.5 14.1 1.0 SG A:CYS27 4.6 14.6 1.0 CB A:LYS94 4.7 15.5 1.0 N A:CYS120 4.7 16.7 1.0 CG A:LYS94 4.7 17.0 1.0 CA A:VAL93 4.8 16.1 1.0 CB A:VAL93 4.8 17.4 1.0 CA A:LYS94 4.9 15.3 1.0 N A:HIS95 4.9 12.4 1.0 ND1 A:HIS95 4.9 15.6 1.0 C A:CYS120 5.0 16.4 1.0 C A:VAL93 5.0 17.0 1.0

Iron binding site 2 out of 4 in the H109C 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 H109C Mutant of Uracil Dna Glycosylase X within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe301 b:15.1 occ:1.00 FE2 A:SF4301 0.0 15.1 1.0 SG A:CYS27 2.3 14.6 1.0 S4 A:SF4301 2.3 12.4 1.0 S1 A:SF4301 2.3 12.8 1.0 S3 A:SF4301 2.3 12.6 1.0 FE4 A:SF4301 2.7 17.1 1.0 FE1 A:SF4301 2.7 14.5 1.0 FE3 A:SF4301 2.7 15.6 1.0 N A:CYS27 3.4 14.3 1.0 CB A:CYS27 3.4 14.3 1.0 CA A:CYS27 3.8 17.4 1.0 S2 A:SF4301 3.9 13.0 1.0 C A:CYS27 4.2 14.8 1.0 C A:GLY26 4.2 16.8 1.0 O A:CYS27 4.3 16.3 1.0 CB A:LEU29 4.4 13.7 1.0 N A:LEU29 4.5 17.3 1.0 N A:GLY26 4.6 16.1 1.0 CA A:GLY26 4.6 14.2 1.0 SG A:CYS120 4.7 13.8 1.0 CB A:CYS120 4.8 12.1 1.0 SG A:CYS24 4.8 14.1 1.0 CG A:LEU29 4.9 16.1 1.0 ND1 A:HIS95 4.9 15.6 1.0 CA A:LEU29 5.0 15.6 1.0

Iron binding site 3 out of 4 in the H109C 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 H109C Mutant of Uracil Dna Glycosylase X within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe301 b:15.6 occ:1.00 FE3 A:SF4301 0.0 15.6 1.0 SG A:CYS24 2.2 14.1 1.0 S1 A:SF4301 2.3 12.8 1.0 S2 A:SF4301 2.3 13.0 1.0 S4 A:SF4301 2.3 12.4 1.0 FE4 A:SF4301 2.7 17.1 1.0 FE1 A:SF4301 2.7 14.5 1.0 FE2 A:SF4301 2.7 15.1 1.0 CB A:CYS24 3.2 16.0 1.0 N A:GLY26 3.5 16.1 1.0 S3 A:SF4301 3.9 12.6 1.0 CA A:GLY26 3.9 14.2 1.0 NE1 A:TRP123 4.1 12.7 1.0 C A:CYS24 4.1 16.9 1.0 N A:CYS27 4.2 14.3 1.0 CA A:CYS24 4.3 15.1 1.0 O A:CYS24 4.3 17.9 1.0 CB A:ALA4 4.4 14.8 1.0 N A:ARG25 4.4 16.5 1.0 C A:ARG25 4.5 16.2 1.0 C A:GLY26 4.5 16.8 1.0 CD1 A:TRP123 4.6 12.5 1.0 ND1 A:HIS95 4.6 15.6 1.0 SG A:CYS120 4.7 13.8 1.0 CA A:ARG25 4.8 18.0 1.0 SG A:CYS27 4.9 14.6 1.0

Iron binding site 4 out of 4 in the H109C 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 H109C Mutant of Uracil Dna Glycosylase X within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe301 b:17.1 occ:1.00 FE4 A:SF4301 0.0 17.1 1.0 S1 A:SF4301 2.3 12.8 1.0 S2 A:SF4301 2.3 13.0 1.0 S3 A:SF4301 2.3 12.6 1.0 ND1 A:HIS95 2.4 15.6 1.0 FE3 A:SF4301 2.7 15.6 1.0 FE2 A:SF4301 2.7 15.1 1.0 FE1 A:SF4301 2.7 14.5 1.0 CG A:HIS95 3.3 15.5 1.0 CE1 A:HIS95 3.4 15.3 1.0 CB A:HIS95 3.4 13.7 1.0 S4 A:SF4301 3.9 12.4 1.0 N A:HIS95 4.0 12.4 1.0 CA A:HIS95 4.3 14.9 1.0 CD2 A:HIS95 4.4 17.4 1.0 NE2 A:HIS95 4.5 16.4 1.0 N A:TYR30 4.5 13.8 1.0 C A:LYS94 4.6 15.6 1.0 SG A:CYS27 4.6 14.6 1.0 CB A:LEU29 4.6 13.7 1.0 SG A:CYS24 4.7 14.1 1.0 CB A:TYR30 4.7 15.2 1.0 SG A:CYS120 4.8 13.8 1.0 CA A:TYR30 4.8 15.9 1.0 N A:LYS94 4.8 14.1 1.0 CB A:CYS24 4.9 16.0 1.0 C A:LEU29 4.9 15.6 1.0 CB A:LYS94 5.0 15.5 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