Iron in PDB 6ajp: Complex Form of Uracil Dna Glycosylase X and Deoxyuridine Monophosphate.

The structure of Complex Form of Uracil Dna Glycosylase X and Deoxyuridine Monophosphate., PDB code: 6ajp 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)	18.88 / 1.33
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	36.436, 51.209, 54.533, 90.00, 104.98, 90.00
R / Rfree (%)	16.3 / 18.7

The binding sites of Iron atom in the Complex Form of Uracil Dna Glycosylase X and Deoxyuridine Monophosphate. (pdb code 6ajp). 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 Deoxyuridine Monophosphate., PDB code: 6ajp:
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 Deoxyuridine Monophosphate.


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 Deoxyuridine Monophosphate. within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe302 b:11.5 occ:1.00 FE1 A:SF4302 0.0 11.5 1.0 S3 A:SF4302 2.3 11.4 1.0 S4 A:SF4302 2.3 12.1 1.0 SG A:CYS27 2.3 12.6 1.0 S2 A:SF4302 2.3 11.2 1.0 FE3 A:SF4302 2.7 11.3 1.0 FE4 A:SF4302 2.7 10.8 1.0 FE2 A:SF4302 2.8 11.7 1.0 H A:CYS27 2.9 15.7 1.0 N A:CYS27 3.4 13.1 1.0 CB A:CYS27 3.4 13.0 1.0 HB3 A:CYS27 3.4 15.7 1.0 HB2 A:LEU29 3.5 15.0 1.0 CA A:CYS27 3.8 13.4 1.0 H A:LEU29 3.9 16.2 1.0 S1 A:SF4302 4.0 11.4 1.0 HB2 A:CYS120 4.1 13.3 1.0 C A:CYS27 4.2 14.3 1.0 C A:GLY26 4.2 14.0 1.0 HB2 A:CYS27 4.2 15.7 1.0 HD12 A:LEU29 4.3 18.4 1.0 H A:GLY26 4.4 15.6 1.0 O A:CYS27 4.4 16.1 1.0 HA3 A:GLY26 4.4 18.4 1.0 CB A:LEU29 4.5 12.5 1.0 H A:TYR30 4.5 15.5 1.0 HB2 A:HIS95 4.5 13.2 1.0 ND1 A:HIS95 4.5 11.5 1.0 N A:GLY26 4.6 13.0 1.0 HG13 A:VAL93 4.6 23.2 1.0 N A:LEU29 4.6 13.5 1.0 HG A:LEU29 4.6 15.2 1.0 CA A:GLY26 4.6 15.3 1.0 HA A:CYS27 4.7 16.1 1.0 HB3 A:ALA119 4.7 16.0 1.0 SG A:CYS120 4.7 10.5 1.0 CB A:CYS120 4.8 11.1 1.0 HA A:CYS120 4.8 13.8 1.0 HB1 A:ALA119 4.9 16.0 1.0 N A:GLY28 4.9 14.5 1.0 CG A:LEU29 5.0 12.7 1.0 SG A:CYS24 5.0 12.2 1.0 HB3 A:TYR30 5.0 16.3 1.0

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


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 Deoxyuridine Monophosphate. within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe302 b:11.7 occ:1.00 FE2 A:SF4302 0.0 11.7 1.0 S1 A:SF4302 2.3 11.4 1.0 S3 A:SF4302 2.3 11.4 1.0 SG A:CYS24 2.3 12.2 1.0 S4 A:SF4302 2.3 12.1 1.0 FE3 A:SF4302 2.6 11.3 1.0 FE4 A:SF4302 2.7 10.8 1.0 FE1 A:SF4302 2.8 11.5 1.0 H A:GLY26 2.9 15.6 1.0 HB3 A:CYS24 3.0 17.5 1.0 CB A:CYS24 3.3 14.6 1.0 HE1 A:TRP123 3.3 14.7 1.0 HA3 A:GLY26 3.6 18.4 1.0 N A:GLY26 3.6 13.0 1.0 H A:CYS27 3.6 15.7 1.0 HB2 A:ALA4 3.7 16.1 1.0 HB2 A:CYS24 3.9 17.5 1.0 S2 A:SF4302 3.9 11.2 1.0 CA A:GLY26 4.0 15.3 1.0 NE1 A:TRP123 4.1 12.2 1.0 HE1 A:HIS95 4.1 14.5 1.0 C A:CYS24 4.2 12.4 1.0 N A:CYS27 4.3 13.1 1.0 HD1 A:TRP123 4.3 14.1 1.0 CA A:CYS24 4.3 12.6 1.0 ND1 A:HIS95 4.4 11.5 1.0 O A:CYS24 4.4 13.9 1.0 HB1 A:ALA4 4.4 16.1 1.0 N A:ARG25 4.5 11.7 1.0 CB A:ALA4 4.5 13.4 1.0 C A:GLY26 4.6 14.0 1.0 C A:ARG25 4.6 15.8 1.0 CD1 A:TRP123 4.6 11.8 1.0 CE1 A:HIS95 4.6 12.1 1.0 HA A:CYS120 4.6 13.8 1.0 HA A:ARG25 4.6 16.7 1.0 SG A:CYS120 4.7 10.5 1.0 H A:ARG25 4.8 14.0 1.0 HB3 A:TYR30 4.8 16.3 1.0 HA A:ALA4 4.8 17.6 1.0 HA A:CYS24 4.8 15.1 1.0 CA A:ARG25 4.8 13.9 1.0 HA2 A:GLY26 4.9 18.4 1.0

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


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 Deoxyuridine Monophosphate. within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe302 b:11.3 occ:1.00 FE3 A:SF4302 0.0 11.3 1.0 ND1 A:HIS95 2.1 11.5 1.0 S2 A:SF4302 2.3 11.2 1.0 S4 A:SF4302 2.3 12.1 1.0 S1 A:SF4302 2.3 11.4 1.0 FE2 A:SF4302 2.6 11.7 1.0 FE4 A:SF4302 2.7 10.8 1.0 FE1 A:SF4302 2.7 11.5 1.0 CE1 A:HIS95 2.9 12.1 1.0 HE1 A:HIS95 3.0 14.5 1.0 HB2 A:HIS95 3.1 13.2 1.0 CG A:HIS95 3.2 11.7 1.0 CB A:HIS95 3.6 11.0 1.0 H A:HIS95 3.8 11.8 1.0 S3 A:SF4302 3.8 11.4 1.0 HB2 A:LEU29 3.9 15.0 1.0 HB3 A:TYR30 3.9 16.3 1.0 N A:HIS95 4.0 9.8 1.0 HB3 A:CYS24 4.1 17.5 1.0 HB2 A:LYS94 4.1 16.6 1.0 NE2 A:HIS95 4.1 12.7 1.0 H A:LYS94 4.2 12.6 1.0 CD2 A:HIS95 4.2 11.5 1.0 H A:TYR30 4.3 15.5 1.0 HB3 A:LYS94 4.4 16.6 1.0 HB3 A:HIS95 4.4 13.2 1.0 CA A:HIS95 4.4 11.4 1.0 N A:TYR30 4.5 12.9 1.0 HA A:TYR30 4.5 16.2 1.0 C A:LYS94 4.5 11.1 1.0 CB A:LYS94 4.6 13.8 1.0 SG A:CYS27 4.6 12.6 1.0 H A:CYS27 4.7 15.7 1.0 CB A:TYR30 4.7 13.6 1.0 SG A:CYS24 4.7 12.2 1.0 SG A:CYS120 4.8 10.5 1.0 CB A:LEU29 4.8 12.5 1.0 HG13 A:VAL93 4.8 23.2 1.0 CA A:TYR30 4.8 13.5 1.0 N A:LYS94 4.8 10.5 1.0 HE2 A:HIS95 4.9 15.3 1.0 CB A:CYS24 4.9 14.6 1.0 CA A:LYS94 4.9 10.8 1.0 HB3 A:LEU29 4.9 15.0 1.0 HA A:HIS95 5.0 13.7 1.0 O A:CYS24 5.0 13.9 1.0 C A:LEU29 5.0 13.5 1.0

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


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 Deoxyuridine Monophosphate. within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe302 b:10.8 occ:1.00 FE4 A:SF4302 0.0 10.8 1.0 SG A:CYS120 2.3 10.5 1.0 S1 A:SF4302 2.3 11.4 1.0 S2 A:SF4302 2.3 11.2 1.0 S3 A:SF4302 2.3 11.4 1.0 FE3 A:SF4302 2.7 11.3 1.0 FE2 A:SF4302 2.7 11.7 1.0 FE1 A:SF4302 2.7 11.5 1.0 HB2 A:CYS120 3.0 13.3 1.0 CB A:CYS120 3.2 11.1 1.0 H A:LYS94 3.2 12.6 1.0 HA A:CYS120 3.4 13.8 1.0 HB2 A:LYS94 3.4 16.6 1.0 HD1 A:TRP123 3.5 14.1 1.0 CA A:CYS120 3.8 11.5 1.0 S4 A:SF4302 3.9 12.1 1.0 HB3 A:CYS120 4.0 13.3 1.0 N A:LYS94 4.0 10.5 1.0 HG13 A:VAL93 4.1 23.2 1.0 HE1 A:TRP123 4.2 14.7 1.0 CD1 A:TRP123 4.2 11.8 1.0 HA A:VAL93 4.2 13.2 1.0 CB A:LYS94 4.3 13.8 1.0 H A:HIS95 4.4 11.8 1.0 HB2 A:ALA4 4.4 16.1 1.0 HB3 A:LYS94 4.5 16.6 1.0 NE1 A:TRP123 4.5 12.2 1.0 ND1 A:HIS95 4.6 11.5 1.0 SG A:CYS24 4.7 12.2 1.0 N A:CYS120 4.7 11.7 1.0 CA A:LYS94 4.7 10.8 1.0 SG A:CYS27 4.7 12.6 1.0 HD3 A:LYS94 4.7 25.1 1.0 N A:HIS95 4.9 9.8 1.0 HB2 A:HIS95 4.9 13.2 1.0 C A:CYS120 5.0 11.1 1.0 H A:CYS120 5.0 14.1 1.0 CA A:VAL93 5.0 11.0 1.0 CG1 A:VAL93 5.0 19.4 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