Iron in PDB 2dp6: Crystal Structure of Uracil-Dna Glycosylase in Complex with Ap:C Containing Dna

The structure of Crystal Structure of Uracil-Dna Glycosylase in Complex with Ap:C Containing Dna, PDB code: 2dp6 was solved by H.Kosaka, N.Nakagawa, R.Masui, S.Kuramitsu, J.Hoseki, Riken Structuralgenomics/Proteomics Initiative (Rsgi), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	31.25 / 1.80
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	68.868, 148.754, 93.086, 90.00, 90.00, 90.00
R / Rfree (%)	20.4 / 21.7

The binding sites of Iron atom in the Crystal Structure of Uracil-Dna Glycosylase in Complex with Ap:C Containing Dna (pdb code 2dp6). 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 of Uracil-Dna Glycosylase in Complex with Ap:C Containing Dna, PDB code: 2dp6:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the Crystal Structure of Uracil-Dna Glycosylase in Complex with Ap:C Containing Dna


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Crystal Structure of Uracil-Dna Glycosylase in Complex with Ap:C Containing Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe220 b:17.5 occ:1.00 FE1 A:SF4220 0.0 17.5 1.0 S2 A:SF4220 2.2 15.7 1.0 S4 A:SF4220 2.2 16.9 1.0 S3 A:SF4220 2.3 17.1 1.0 SG A:CYS115 2.4 16.5 1.0 FE4 A:SF4220 2.7 17.7 1.0 FE3 A:SF4220 2.7 16.7 1.0 FE2 A:SF4220 2.7 18.9 1.0 CB A:CYS115 3.3 16.8 1.0 S1 A:SF4220 3.8 17.6 1.0 N A:CYS115 4.0 14.8 1.0 CA A:CYS115 4.2 14.3 1.0 CG A:PRO42 4.3 16.2 1.0 C A:ARG114 4.4 14.8 1.0 NH2 A:ARG23 4.5 19.8 1.0 CB A:PRO42 4.7 14.6 1.0 SG A:CYS13 4.8 20.6 1.0 SG A:CYS130 4.8 17.8 1.0 O A:CYS13 4.9 21.2 1.0 O A:ARG114 4.9 14.3 1.0 SG A:CYS16 4.9 21.1 1.0 CB A:ARG114 5.0 12.9 1.0 N A:ARG114 5.0 14.2 1.0 CA A:ARG114 5.0 14.2 1.0

Iron binding site 2 out of 4 in the Crystal Structure of Uracil-Dna Glycosylase in Complex with Ap:C Containing Dna


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Crystal Structure of Uracil-Dna Glycosylase in Complex with Ap:C Containing Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe220 b:18.9 occ:1.00 FE2 A:SF4220 0.0 18.9 1.0 S1 A:SF4220 2.2 17.6 1.0 S3 A:SF4220 2.2 17.1 1.0 S4 A:SF4220 2.3 16.9 1.0 SG A:CYS16 2.5 21.1 1.0 FE4 A:SF4220 2.7 17.7 1.0 FE3 A:SF4220 2.7 16.7 1.0 FE1 A:SF4220 2.7 17.5 1.0 CB A:CYS16 3.3 20.4 1.0 N A:CYS16 3.8 22.1 1.0 S2 A:SF4220 3.8 15.7 1.0 CA A:CYS16 4.2 21.3 1.0 CD1 A:LEU19 4.4 16.0 1.0 CB A:LEU15 4.5 24.2 1.0 C A:LEU15 4.6 23.8 1.0 CB A:CYS130 4.7 18.5 1.0 SG A:CYS130 4.7 17.8 1.0 CB A:ALA129 4.8 21.6 1.0 N A:LEU15 4.8 22.8 1.0 SG A:CYS13 4.8 20.6 1.0 CA A:LEU15 4.8 23.4 1.0 SG A:CYS115 4.9 16.5 1.0 N A:CYS130 4.9 20.0 1.0 O A:GLU126 4.9 21.2 1.0

Iron binding site 3 out of 4 in the Crystal Structure of Uracil-Dna Glycosylase in Complex with Ap:C Containing Dna


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Crystal Structure of Uracil-Dna Glycosylase in Complex with Ap:C Containing Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe220 b:16.7 occ:1.00 FE3 A:SF4220 0.0 16.7 1.0 S4 A:SF4220 2.2 16.9 1.0 S2 A:SF4220 2.2 15.7 1.0 S1 A:SF4220 2.3 17.6 1.0 SG A:CYS130 2.4 17.8 1.0 FE2 A:SF4220 2.7 18.9 1.0 FE1 A:SF4220 2.7 17.5 1.0 FE4 A:SF4220 2.7 17.7 1.0 CB A:CYS130 3.2 18.5 1.0 CA A:CYS130 3.8 18.9 1.0 S3 A:SF4220 3.8 17.1 1.0 CD1 A:TRP133 3.9 17.0 1.0 N A:ARG114 4.1 14.2 1.0 CB A:ARG114 4.3 12.9 1.0 NE1 A:TRP133 4.4 18.5 1.0 N A:CYS130 4.4 20.0 1.0 CA A:ARG114 4.7 14.2 1.0 SG A:CYS13 4.8 20.6 1.0 SG A:CYS115 4.8 16.5 1.0 SG A:CYS16 4.9 21.1 1.0 N A:CYS115 4.9 14.8 1.0 CG A:ARG114 5.0 13.3 1.0

Iron binding site 4 out of 4 in the Crystal Structure of Uracil-Dna Glycosylase in Complex with Ap:C Containing Dna


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Crystal Structure of Uracil-Dna Glycosylase in Complex with Ap:C Containing Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe220 b:17.7 occ:1.00 FE4 A:SF4220 0.0 17.7 1.0 S1 A:SF4220 2.2 17.6 1.0 S2 A:SF4220 2.2 15.7 1.0 S3 A:SF4220 2.3 17.1 1.0 SG A:CYS13 2.4 20.6 1.0 FE2 A:SF4220 2.7 18.9 1.0 FE1 A:SF4220 2.7 17.5 1.0 FE3 A:SF4220 2.7 16.7 1.0 CB A:CYS13 3.3 20.8 1.0 NE1 A:TRP133 3.8 18.5 1.0 S4 A:SF4220 3.8 16.9 1.0 N A:LEU15 4.1 22.8 1.0 C A:CYS13 4.2 21.7 1.0 CD1 A:TRP133 4.2 17.0 1.0 CB A:LEU15 4.3 24.2 1.0 O A:CYS13 4.4 21.2 1.0 CA A:CYS13 4.4 21.1 1.0 N A:ARG14 4.5 21.8 1.0 CG A:LEU15 4.5 25.8 1.0 CD1 A:LEU15 4.6 25.6 1.0 CA A:LEU15 4.7 23.4 1.0 SG A:CYS115 4.8 16.5 1.0 SG A:CYS16 4.8 21.1 1.0 N A:CYS16 4.8 22.1 1.0 SG A:CYS130 4.9 17.8 1.0 CE2 A:TRP133 5.0 18.6 1.0 CA A:ARG14 5.0 22.4 1.0

H.Kosaka, N.Nakagawa, R.Masui, S.Kuramitsu. Structure of Family 5 Uracil-Dna Glycosylase Bound to Dna Reveals Insights Into the Mechanism For Substrate Recognition and Catalysis To Be Published.