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

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

Resolution Low / High (Å)	37.03 / 1.95
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	68.920, 150.170, 93.410, 90.00, 90.00, 90.00
R / Rfree (%)	20 / 22.5

The binding sites of Iron atom in the Crystal Structure of Uracil-Dna Glycosylase in Complex with Ap:A Containing Dna (pdb code 2dem). 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:A Containing Dna, PDB code: 2dem:
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:A 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:A Containing Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe220 b:22.8 occ:1.00 FE1 A:SF4220 0.0 22.8 1.0 S4 A:SF4220 2.2 20.3 1.0 S2 A:SF4220 2.3 20.5 1.0 S3 A:SF4220 2.3 22.8 1.0 SG A:CYS115 2.4 20.2 1.0 FE4 A:SF4220 2.7 24.4 1.0 FE2 A:SF4220 2.7 24.5 1.0 FE3 A:SF4220 2.7 23.0 1.0 CB A:CYS115 3.3 19.1 1.0 S1 A:SF4220 3.8 22.2 1.0 N A:CYS115 4.0 17.9 1.0 CA A:CYS115 4.3 18.3 1.0 CG A:PRO42 4.4 19.4 1.0 C A:ARG114 4.5 19.1 1.0 NH2 A:ARG23 4.5 23.8 1.0 CB A:PRO42 4.7 19.2 1.0 SG A:CYS13 4.8 24.2 1.0 SG A:CYS130 4.9 21.2 1.0 O A:ARG114 4.9 18.4 1.0 CB A:ARG114 5.0 16.4 1.0 CA A:ARG114 5.0 17.5 1.0 N A:ARG114 5.0 18.2 1.0 SG A:CYS16 5.0 25.5 1.0

Iron binding site 2 out of 4 in the Crystal Structure of Uracil-Dna Glycosylase in Complex with Ap:A 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:A Containing Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe220 b:24.5 occ:1.00 FE2 A:SF4220 0.0 24.5 1.0 S1 A:SF4220 2.2 22.2 1.0 S3 A:SF4220 2.3 22.8 1.0 S4 A:SF4220 2.3 20.3 1.0 SG A:CYS16 2.5 25.5 1.0 FE4 A:SF4220 2.7 24.4 1.0 FE1 A:SF4220 2.7 22.8 1.0 FE3 A:SF4220 2.7 23.0 1.0 CB A:CYS16 3.3 25.7 1.0 N A:CYS16 3.8 25.1 1.0 S2 A:SF4220 3.8 20.5 1.0 CA A:CYS16 4.2 24.7 1.0 CB A:LEU15 4.5 28.3 1.0 CD1 A:LEU19 4.5 17.7 1.0 C A:LEU15 4.6 27.1 1.0 CB A:CYS130 4.7 21.9 1.0 N A:LEU15 4.8 26.6 1.0 SG A:CYS13 4.8 24.2 1.0 SG A:CYS130 4.8 21.2 1.0 CA A:LEU15 4.8 27.2 1.0 CB A:ALA129 4.8 25.6 1.0 N A:CYS130 4.9 24.4 1.0 O A:GLU126 4.9 25.4 1.0 SG A:CYS115 4.9 20.2 1.0

Iron binding site 3 out of 4 in the Crystal Structure of Uracil-Dna Glycosylase in Complex with Ap:A 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:A Containing Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe220 b:23.0 occ:1.00 FE3 A:SF4220 0.0 23.0 1.0 S2 A:SF4220 2.2 20.5 1.0 S4 A:SF4220 2.3 20.3 1.0 S1 A:SF4220 2.3 22.2 1.0 SG A:CYS130 2.4 21.2 1.0 FE2 A:SF4220 2.7 24.5 1.0 FE1 A:SF4220 2.7 22.8 1.0 FE4 A:SF4220 2.7 24.4 1.0 CB A:CYS130 3.1 21.9 1.0 CA A:CYS130 3.8 23.6 1.0 S3 A:SF4220 3.9 22.8 1.0 CD1 A:TRP133 3.9 22.1 1.0 N A:ARG114 4.1 18.2 1.0 NE1 A:TRP133 4.4 23.0 1.0 CB A:ARG114 4.4 16.4 1.0 N A:CYS130 4.4 24.4 1.0 CA A:ARG114 4.7 17.5 1.0 SG A:CYS13 4.8 24.2 1.0 SG A:CYS115 4.9 20.2 1.0 N A:CYS115 4.9 17.9 1.0 SG A:CYS16 4.9 25.5 1.0 CG A:ARG114 5.0 15.9 1.0 C A:CYS130 5.0 23.0 1.0

Iron binding site 4 out of 4 in the Crystal Structure of Uracil-Dna Glycosylase in Complex with Ap:A 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:A Containing Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe220 b:24.4 occ:1.00 FE4 A:SF4220 0.0 24.4 1.0 S1 A:SF4220 2.2 22.2 1.0 S3 A:SF4220 2.3 22.8 1.0 S2 A:SF4220 2.3 20.5 1.0 SG A:CYS13 2.4 24.2 1.0 FE2 A:SF4220 2.7 24.5 1.0 FE1 A:SF4220 2.7 22.8 1.0 FE3 A:SF4220 2.7 23.0 1.0 CB A:CYS13 3.4 21.9 1.0 NE1 A:TRP133 3.8 23.0 1.0 S4 A:SF4220 3.8 20.3 1.0 N A:LEU15 4.1 26.6 1.0 CB A:LEU15 4.2 28.3 1.0 CD1 A:TRP133 4.3 22.1 1.0 C A:CYS13 4.3 24.8 1.0 CA A:CYS13 4.5 23.1 1.0 N A:ARG14 4.5 24.1 1.0 O A:CYS13 4.6 23.7 1.0 CG A:LEU15 4.6 31.1 1.0 CD1 A:LEU15 4.6 29.6 1.0 CA A:LEU15 4.7 27.2 1.0 N A:CYS16 4.9 25.1 1.0 SG A:CYS115 4.9 20.2 1.0 SG A:CYS16 4.9 25.5 1.0 CE2 A:TRP133 4.9 21.7 1.0 SG A:CYS130 4.9 21.2 1.0

H.Kosaka, J.Hoseki, N.Nakagawa, S.Kuramitsu, R.Masui. Crystal Structure of Family 5 Uracil-Dna Glycosylase Bound to Dna. J.Mol.Biol. V. 373 839 2007.
ISSN: ISSN 0022-2836
PubMed: 17870091
DOI: 10.1016/J.JMB.2007.08.022