Iron in PDB 6ail: Crystal Structure at 1.3 Angstroms Resolution of A Novel Udg, Udgx, From Mycobacterium Smegmatis

The structure of Crystal Structure at 1.3 Angstroms Resolution of A Novel Udg, Udgx, From Mycobacterium Smegmatis, PDB code: 6ail was solved by W.C.Ahn, S.Aroli, V.Varshney, E.J.Woo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	28.11 / 1.34
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	36.326, 51.638, 54.362, 90.00, 105.31, 90.00
R / Rfree (%)	13.3 / 15.6

The binding sites of Iron atom in the Crystal Structure at 1.3 Angstroms Resolution of A Novel Udg, Udgx, From Mycobacterium Smegmatis (pdb code 6ail). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Crystal Structure at 1.3 Angstroms Resolution of A Novel Udg, Udgx, From Mycobacterium Smegmatis, PDB code: 6ail:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the Crystal Structure at 1.3 Angstroms Resolution of A Novel Udg, Udgx, From Mycobacterium Smegmatis


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Crystal Structure at 1.3 Angstroms Resolution of A Novel Udg, Udgx, From Mycobacterium Smegmatis within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe301 b:7.8 occ:1.00 FE1 A:SF4301 0.0 7.8 1.0 ND1 A:HIS95 2.1 8.2 1.0 S3 A:SF4301 2.3 7.6 1.0 S4 A:SF4301 2.3 7.7 1.0 S2 A:SF4301 2.3 8.3 1.0 FE3 A:SF4301 2.7 8.2 1.0 FE2 A:SF4301 2.7 7.6 1.0 FE4 A:SF4301 2.7 8.0 1.0 CE1 A:HIS95 2.9 8.8 1.0 HE1 A:HIS95 3.0 10.6 1.0 HB2 A:HIS95 3.1 9.4 1.0 CG A:HIS95 3.2 7.8 1.0 CB A:HIS95 3.6 7.8 1.0 H A:HIS95 3.8 8.5 1.0 S1 A:SF4301 3.8 8.3 1.0 HB2 A:LEU29 3.9 11.0 1.0 HB3 A:TYR30 3.9 11.8 1.0 N A:HIS95 4.0 7.1 1.0 H A:LYS94 4.1 8.7 1.0 NE2 A:HIS95 4.1 9.2 1.0 HB3 A:CYS24 4.1 11.3 1.0 HB2 A:LYS94 4.2 11.4 1.0 CD2 A:HIS95 4.2 8.7 1.0 H A:TYR30 4.4 11.2 1.0 HB3 A:HIS95 4.4 9.4 1.0 C A:LYS94 4.4 7.3 1.0 CA A:HIS95 4.4 7.2 1.0 HA A:TYR30 4.5 11.5 1.0 N A:TYR30 4.5 9.3 1.0 HG13 A:VAL93 4.6 21.9 1.0 SG A:CYS27 4.6 9.2 1.0 CB A:TYR30 4.7 9.8 1.0 SG A:CYS24 4.7 8.7 1.0 N A:LYS94 4.7 7.2 1.0 CB A:LEU29 4.8 9.2 1.0 SG A:CYS120 4.8 7.7 1.0 H A:CYS27 4.8 11.1 1.0 CA A:TYR30 4.8 9.6 1.0 HE2 A:HIS95 4.9 11.1 1.0 CA A:LYS94 4.9 7.2 1.0 CB A:LYS94 4.9 9.5 1.0 HB3 A:LEU29 4.9 11.0 1.0 CB A:CYS24 4.9 9.4 1.0 O A:CYS24 4.9 11.2 1.0 HA A:HIS95 4.9 8.6 1.0 O A:LYS94 5.0 7.9 1.0

Iron binding site 2 out of 4 in the Crystal Structure at 1.3 Angstroms Resolution of A Novel Udg, Udgx, From Mycobacterium Smegmatis


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Crystal Structure at 1.3 Angstroms Resolution of A Novel Udg, Udgx, From Mycobacterium Smegmatis within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe301 b:7.6 occ:1.00 FE2 A:SF4301 0.0 7.6 1.0 SG A:CYS120 2.3 7.7 1.0 S4 A:SF4301 2.3 7.7 1.0 S3 A:SF4301 2.3 7.6 1.0 S1 A:SF4301 2.3 8.3 1.0 FE3 A:SF4301 2.7 8.2 1.0 FE1 A:SF4301 2.7 7.8 1.0 FE4 A:SF4301 2.7 8.0 1.0 HB2 A:CYS120 3.0 9.1 1.0 CB A:CYS120 3.1 7.6 1.0 H A:LYS94 3.2 8.7 1.0 HA A:CYS120 3.4 9.8 1.0 HD1 A:TRP123 3.5 10.4 1.0 HB2 A:LYS94 3.6 11.4 1.0 HG13 A:VAL93 3.8 21.9 1.0 CA A:CYS120 3.8 8.2 1.0 S2 A:SF4301 3.9 8.3 1.0 HB3 A:CYS120 4.0 9.1 1.0 N A:LYS94 4.0 7.2 1.0 HA A:VAL93 4.2 10.8 1.0 CD1 A:TRP123 4.2 8.7 1.0 HE1 A:TRP123 4.2 10.9 1.0 HB2 A:ALA4 4.4 12.0 1.0 H A:HIS95 4.5 8.5 1.0 CB A:LYS94 4.5 9.5 1.0 NE1 A:TRP123 4.6 9.1 1.0 ND1 A:HIS95 4.6 8.2 1.0 SG A:CYS24 4.7 8.7 1.0 N A:CYS120 4.7 7.8 1.0 CA A:LYS94 4.7 7.2 1.0 SG A:CYS27 4.7 9.2 1.0 CG1 A:VAL93 4.7 18.3 1.0 HG22 A:VAL93 4.8 15.5 1.0 HG3 A:LYS94 4.9 14.2 1.0 HD2 A:LYS94 4.9 15.6 1.0 CA A:VAL93 4.9 9.0 1.0 N A:HIS95 4.9 7.1 1.0 HG12 A:VAL93 4.9 21.9 1.0 H A:CYS120 4.9 9.4 1.0 HB2 A:HIS95 5.0 9.4 1.0 C A:VAL93 5.0 8.7 1.0 C A:CYS120 5.0 8.6 1.0

Iron binding site 3 out of 4 in the Crystal Structure at 1.3 Angstroms Resolution of A Novel Udg, Udgx, From Mycobacterium Smegmatis


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Crystal Structure at 1.3 Angstroms Resolution of A Novel Udg, Udgx, From Mycobacterium Smegmatis within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe301 b:8.2 occ:1.00 FE3 A:SF4301 0.0 8.2 1.0 S1 A:SF4301 2.3 8.3 1.0 S4 A:SF4301 2.3 7.7 1.0 S2 A:SF4301 2.3 8.3 1.0 SG A:CYS24 2.3 8.7 1.0 FE1 A:SF4301 2.7 7.8 1.0 FE2 A:SF4301 2.7 7.6 1.0 FE4 A:SF4301 2.8 8.0 1.0 H A:GLY26 2.9 11.2 1.0 HB3 A:CYS24 3.0 11.3 1.0 CB A:CYS24 3.3 9.4 1.0 HE1 A:TRP123 3.4 10.9 1.0 N A:GLY26 3.6 9.3 1.0 HA3 A:GLY26 3.6 12.3 1.0 HB2 A:ALA4 3.7 12.0 1.0 H A:CYS27 3.7 11.1 1.0 S3 A:SF4301 3.9 7.6 1.0 HB2 A:CYS24 3.9 11.3 1.0 CA A:GLY26 4.0 10.2 1.0 NE1 A:TRP123 4.1 9.1 1.0 HE1 A:HIS95 4.1 10.6 1.0 C A:CYS24 4.2 9.8 1.0 N A:CYS27 4.3 9.2 1.0 HD1 A:TRP123 4.3 10.4 1.0 O A:CYS24 4.3 11.2 1.0 HB1 A:ALA4 4.3 12.0 1.0 CA A:CYS24 4.3 9.1 1.0 ND1 A:HIS95 4.4 8.2 1.0 CB A:ALA4 4.4 10.0 1.0 N A:ARG25 4.5 9.9 1.0 C A:GLY26 4.5 9.7 1.0 C A:ARG25 4.5 9.7 1.0 CD1 A:TRP123 4.6 8.7 1.0 CE1 A:HIS95 4.6 8.8 1.0 HA A:ARG25 4.6 12.2 1.0 HA A:CYS120 4.6 9.8 1.0 SG A:CYS120 4.7 7.7 1.0 HB3 A:TYR30 4.8 11.8 1.0 H A:ARG25 4.8 11.9 1.0 HA A:CYS24 4.8 11.0 1.0 CA A:ARG25 4.8 10.2 1.0 HA A:ALA4 4.8 11.8 1.0 HA2 A:GLY26 4.9 12.3 1.0 SG A:CYS27 5.0 9.2 1.0

Iron binding site 4 out of 4 in the Crystal Structure at 1.3 Angstroms Resolution of A Novel Udg, Udgx, From Mycobacterium Smegmatis


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Crystal Structure at 1.3 Angstroms Resolution of A Novel Udg, Udgx, From Mycobacterium Smegmatis within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe301 b:8.0 occ:1.00 FE4 A:SF4301 0.0 8.0 1.0 S1 A:SF4301 2.3 8.3 1.0 SG A:CYS27 2.3 9.2 1.0 S2 A:SF4301 2.3 8.3 1.0 S3 A:SF4301 2.3 7.6 1.0 FE1 A:SF4301 2.7 7.8 1.0 FE2 A:SF4301 2.7 7.6 1.0 FE3 A:SF4301 2.8 8.2 1.0 H A:CYS27 2.9 11.1 1.0 CB A:CYS27 3.3 10.2 1.0 HB3 A:CYS27 3.3 12.3 1.0 N A:CYS27 3.3 9.2 1.0 HB2 A:LEU29 3.6 11.0 1.0 CA A:CYS27 3.7 8.4 1.0 H A:LEU29 3.9 10.4 1.0 S4 A:SF4301 3.9 7.7 1.0 C A:GLY26 4.1 9.7 1.0 HB2 A:CYS120 4.2 9.1 1.0 C A:CYS27 4.2 9.4 1.0 HB2 A:CYS27 4.2 12.3 1.0 HD12 A:LEU29 4.2 12.4 1.0 H A:GLY26 4.3 11.2 1.0 O A:CYS27 4.3 10.8 1.0 HG13 A:VAL93 4.4 21.9 1.0 HA3 A:GLY26 4.5 12.3 1.0 CB A:LEU29 4.5 9.2 1.0 H A:TYR30 4.5 11.2 1.0 ND1 A:HIS95 4.5 8.2 1.0 N A:GLY26 4.6 9.3 1.0 HB2 A:HIS95 4.6 9.4 1.0 CA A:GLY26 4.6 10.2 1.0 N A:LEU29 4.6 8.7 1.0 HG A:LEU29 4.6 11.8 1.0 HA A:CYS27 4.7 10.1 1.0 HB3 A:ALA119 4.7 11.0 1.0 SG A:CYS120 4.7 7.7 1.0 CB A:CYS120 4.8 7.6 1.0 HA A:CYS120 4.9 9.8 1.0 O A:GLY26 4.9 11.3 1.0 HB1 A:ALA119 4.9 11.0 1.0 HB3 A:TYR30 4.9 11.8 1.0 N A:GLY28 4.9 9.4 1.0 SG A:CYS24 5.0 8.7 1.0 CG A:LEU29 5.0 9.8 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