Iron in PDB 6ajo: Complex Form of Uracil Dna Glycosylase X and Uracil-Dna.

The structure of Complex Form of Uracil Dna Glycosylase X and Uracil-Dna., PDB code: 6ajo was solved by W.C.Ahn, S.Aroli, U.Varshney, E.J.Woo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	31.98 / 2.27
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	36.829, 64.450, 82.900, 90.00, 90.00, 90.00
R / Rfree (%)	19.2 / 25.7

The binding sites of Iron atom in the Complex Form of Uracil Dna Glycosylase X and Uracil-Dna. (pdb code 6ajo). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Complex Form of Uracil Dna Glycosylase X and Uracil-Dna., PDB code: 6ajo:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the Complex Form of Uracil Dna Glycosylase X and Uracil-Dna.


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Complex Form of Uracil Dna Glycosylase X and Uracil-Dna. within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe301 b:37.1 occ:1.00 FE1 A:SF4301 0.0 37.1 1.0 S3 A:SF4301 2.1 36.4 1.0 S4 A:SF4301 2.1 37.9 1.0 SG A:CYS24 2.1 34.8 1.0 S2 A:SF4301 2.2 35.5 1.0 H A:GLY26 2.6 35.9 1.0 HB3 A:CYS24 2.8 36.6 1.0 FE3 A:SF4301 2.9 43.3 1.0 FE2 A:SF4301 3.0 36.8 1.0 FE4 A:SF4301 3.0 37.0 1.0 CB A:CYS24 3.1 38.7 1.0 HA3 A:GLY26 3.1 39.1 1.0 N A:GLY26 3.3 41.1 1.0 HE1 A:TRP123 3.4 35.3 1.0 H A:CYS27 3.5 37.3 1.0 HB2 A:ALA4 3.6 31.0 1.0 CA A:GLY26 3.7 44.1 1.0 S1 A:SF4301 3.7 38.1 1.0 HB2 A:CYS24 3.7 36.6 1.0 HD2 A:HIS95 3.9 32.8 1.0 C A:CYS24 4.1 40.4 1.0 NE1 A:TRP123 4.1 37.2 1.0 CA A:CYS24 4.1 41.3 1.0 N A:CYS27 4.2 40.6 1.0 O A:CYS24 4.3 49.9 1.0 N A:ARG25 4.3 39.0 1.0 HA A:ALA4 4.4 34.8 1.0 C A:GLY26 4.4 45.2 1.0 HA2 A:GLY26 4.4 39.1 1.0 HD1 A:TRP123 4.5 35.5 1.0 C A:ARG25 4.5 45.2 1.0 CB A:ALA4 4.5 30.4 1.0 HA A:CYS24 4.6 38.7 1.0 H A:ARG25 4.6 38.1 1.0 HB3 A:TYR30 4.6 46.3 1.0 HA A:ARG25 4.6 40.1 1.0 HB1 A:ALA4 4.6 31.0 1.0 CD2 A:HIS95 4.6 35.6 1.0 CD1 A:TRP123 4.7 37.1 1.0 HA A:CYS120 4.8 31.0 1.0 HE2 A:HIS95 4.8 31.4 1.0 CA A:ARG25 4.8 41.1 1.0 SG A:CYS27 4.9 40.6 1.0 SG A:CYS120 5.0 35.6 1.0 CA A:ALA4 5.0 33.5 1.0 HB2 A:LYS94 5.0 47.1 1.0

Iron binding site 2 out of 4 in the Complex Form of Uracil Dna Glycosylase X and Uracil-Dna.


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Complex Form of Uracil Dna Glycosylase X and Uracil-Dna. within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe301 b:36.8 occ:1.00 FE2 A:SF4301 0.0 36.8 1.0 SG A:CYS27 2.0 40.6 1.0 S3 A:SF4301 2.0 36.4 1.0 S4 A:SF4301 2.1 37.9 1.0 S1 A:SF4301 2.2 38.1 1.0 HG A:CYS27 2.6 38.1 1.0 H A:CYS27 2.6 37.3 1.0 FE1 A:SF4301 3.0 37.1 1.0 FE3 A:SF4301 3.0 43.3 1.0 FE4 A:SF4301 3.1 37.0 1.0 N A:CYS27 3.1 40.6 1.0 CB A:CYS27 3.2 39.5 1.0 HB3 A:CYS27 3.4 36.7 1.0 HB2 A:LEU29 3.4 36.7 1.0 CA A:CYS27 3.6 38.5 1.0 H A:LEU29 3.7 35.3 1.0 S2 A:SF4301 3.9 35.5 1.0 HB2 A:CYS27 4.0 36.7 1.0 C A:CYS27 4.0 44.0 1.0 HA3 A:GLY26 4.0 39.1 1.0 C A:GLY26 4.0 45.2 1.0 O A:CYS27 4.1 45.9 1.0 HD2 A:HIS95 4.2 32.8 1.0 HB2 A:CYS120 4.2 32.9 1.0 H A:GLY26 4.2 35.9 1.0 H A:TYR30 4.2 40.2 1.0 CB A:LEU29 4.3 39.3 1.0 HD12 A:LEU29 4.3 37.3 1.0 HG A:LEU29 4.4 36.5 1.0 CA A:GLY26 4.4 44.1 1.0 N A:LEU29 4.4 38.6 1.0 N A:GLY26 4.5 41.1 1.0 HA A:CYS27 4.5 35.2 1.0 HB3 A:ALA119 4.6 32.7 1.0 HG2 A:GLU116 4.7 41.5 1.0 HB2 A:HIS95 4.7 36.4 1.0 HB1 A:ALA119 4.7 32.7 1.0 HG13 A:VAL93 4.7 45.2 1.0 CG A:LEU29 4.8 39.0 1.0 N A:GLY28 4.8 50.8 1.0 CA A:LEU29 4.9 38.8 1.0 CD2 A:HIS95 4.9 35.6 1.0 N A:TYR30 4.9 39.9 1.0 HB3 A:TYR30 4.9 46.3 1.0 HA A:CYS120 4.9 31.0 1.0 HD2 A:TYR30 4.9 45.0 1.0 CB A:CYS120 4.9 33.5 1.0 O A:GLY26 5.0 43.2 1.0 HB3 A:LEU29 5.0 36.7 1.0

Iron binding site 3 out of 4 in the Complex Form of Uracil Dna Glycosylase X and Uracil-Dna.


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Complex Form of Uracil Dna Glycosylase X and Uracil-Dna. within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe301 b:43.3 occ:1.00 FE3 A:SF4301 0.0 43.3 1.0 HD2 A:HIS95 1.4 32.8 1.0 S2 A:SF4301 2.1 35.5 1.0 S1 A:SF4301 2.1 38.1 1.0 S4 A:SF4301 2.2 37.9 1.0 CD2 A:HIS95 2.2 35.6 1.0 FE4 A:SF4301 2.8 37.0 1.0 FE1 A:SF4301 2.9 37.1 1.0 FE2 A:SF4301 3.0 36.8 1.0 HB2 A:HIS95 3.2 36.4 1.0 CG A:HIS95 3.2 35.8 1.0 NE2 A:HIS95 3.2 34.5 1.0 HB2 A:LYS94 3.4 47.1 1.0 HE2 A:HIS95 3.4 31.4 1.0 S3 A:SF4301 3.5 36.4 1.0 H A:HIS95 3.7 40.1 1.0 CB A:HIS95 3.7 38.9 1.0 HB3 A:TYR30 3.8 46.3 1.0 HB2 A:LEU29 3.8 36.7 1.0 HB3 A:CYS24 4.0 36.6 1.0 N A:HIS95 4.0 42.0 1.0 H A:TYR30 4.1 40.2 1.0 H A:LYS94 4.1 39.8 1.0 CB A:LYS94 4.3 50.0 1.0 ND1 A:HIS95 4.3 36.9 1.0 CE1 A:HIS95 4.3 34.6 1.0 N A:TYR30 4.4 39.9 1.0 CA A:HIS95 4.4 39.7 1.0 HB3 A:HIS95 4.5 36.4 1.0 C A:LYS94 4.5 45.9 1.0 HA A:TYR30 4.6 46.0 1.0 HB3 A:LYS94 4.6 47.1 1.0 SG A:CYS27 4.6 40.6 1.0 CB A:TYR30 4.6 46.5 1.0 CB A:LEU29 4.7 39.3 1.0 SG A:CYS24 4.7 34.8 1.0 CB A:CYS24 4.8 38.7 1.0 H A:CYS27 4.8 37.3 1.0 SG A:CYS120 4.8 35.6 1.0 CA A:LYS94 4.8 45.8 1.0 N A:LYS94 4.8 42.4 1.0 CA A:TYR30 4.8 45.9 1.0 HB3 A:LEU29 4.8 36.7 1.0 HG13 A:VAL93 4.9 45.2 1.0 HB2 A:ALA36 4.9 41.8 1.0 HA A:HIS95 4.9 37.6 1.0 HB2 A:TYR30 4.9 46.3 1.0 H A:GLY26 5.0 35.9 1.0

Iron binding site 4 out of 4 in the Complex Form of Uracil Dna Glycosylase X and Uracil-Dna.


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Complex Form of Uracil Dna Glycosylase X and Uracil-Dna. within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe301 b:37.0 occ:1.00 FE4 A:SF4301 0.0 37.0 1.0 S1 A:SF4301 2.1 38.1 1.0 S2 A:SF4301 2.1 35.5 1.0 SG A:CYS120 2.2 35.6 1.0 S3 A:SF4301 2.2 36.4 1.0 HB2 A:CYS120 2.8 32.9 1.0 FE3 A:SF4301 2.8 43.3 1.0 CB A:CYS120 3.0 33.5 1.0 FE1 A:SF4301 3.0 37.1 1.0 FE2 A:SF4301 3.1 36.8 1.0 HB2 A:LYS94 3.2 47.1 1.0 H A:LYS94 3.2 39.8 1.0 HA A:CYS120 3.2 31.0 1.0 HD1 A:TRP123 3.5 35.5 1.0 CA A:CYS120 3.7 31.8 1.0 S4 A:SF4301 3.7 37.9 1.0 HG2 A:LYS94 3.8 47.7 1.0 HB3 A:CYS120 3.8 32.9 1.0 HG13 A:VAL93 3.9 45.2 1.0 CB A:LYS94 4.0 50.0 1.0 N A:LYS94 4.0 42.4 1.0 HD2 A:HIS95 4.1 32.8 1.0 CD1 A:TRP123 4.2 37.1 1.0 CG A:LYS94 4.2 50.5 1.0 HB2 A:ALA4 4.2 31.0 1.0 HG3 A:LYS94 4.2 47.7 1.0 HE1 A:TRP123 4.2 35.3 1.0 HA A:VAL93 4.3 42.3 1.0 H A:HIS95 4.3 40.1 1.0 N A:CYS120 4.5 32.0 1.0 NE1 A:TRP123 4.5 37.2 1.0 CA A:LYS94 4.6 45.8 1.0 HG A:CYS27 4.6 38.1 1.0 SG A:CYS24 4.7 34.8 1.0 SG A:CYS27 4.7 40.6 1.0 O A:CYS120 4.7 37.5 1.0 H A:CYS120 4.7 31.1 1.0 HB3 A:LYS94 4.8 47.1 1.0 C A:CYS120 4.8 32.6 1.0 CG1 A:VAL93 4.8 45.8 1.0 CD2 A:HIS95 4.9 35.6 1.0 N A:HIS95 4.9 42.0 1.0

W.C.Ahn, S.Aroli, J.H.Kim, J.H.Moon, G.S.Lee, M.H.Lee, P.B.Sang, B.H.Oh, U.Varshney, E.J.Woo. Covalent Binding of Uracil Dna Glycosylase Udgx to Abasic Dna Upon Uracil Excision. Nat.Chem.Biol. V. 15 607 2019.
ISSN: ESSN 1552-4469
PubMed: 31101917
DOI: 10.1038/S41589-019-0289-3