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

The structure of Crystal Structure of Uracil-Dna Glycosylase in Complex with Ap:G Containing Dna, PDB code: 2ddg 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)	37.16 / 2.10
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	68.927, 150.174, 93.408, 90.00, 90.00, 90.00
R / Rfree (%)	21.8 / 24

The binding sites of Iron atom in the Crystal Structure of Uracil-Dna Glycosylase in Complex with Ap:G Containing Dna (pdb code 2ddg). 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:G Containing Dna, PDB code: 2ddg:
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:G 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:G Containing Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe220 b:28.4 occ:1.00 FE1 A:SF4220 0.0 28.4 1.0 S3 A:SF4220 2.3 26.8 1.0 S2 A:SF4220 2.3 25.4 1.0 S4 A:SF4220 2.3 25.5 1.0 SG A:CYS13 2.4 28.3 1.0 FE4 A:SF4220 2.7 29.4 1.0 FE2 A:SF4220 2.7 27.4 1.0 FE3 A:SF4220 2.7 29.0 1.0 CB A:CYS13 3.4 26.7 1.0 NE1 A:TRP133 3.8 27.8 1.0 S1 A:SF4220 3.8 28.2 1.0 N A:LEU15 4.1 32.2 1.0 CD1 A:TRP133 4.2 25.7 1.0 C A:CYS13 4.3 29.8 1.0 CB A:LEU15 4.3 33.4 1.0 CA A:CYS13 4.5 27.9 1.0 N A:ARG14 4.5 30.3 1.0 O A:CYS13 4.5 29.9 1.0 CG A:LEU15 4.7 34.8 1.0 CA A:LEU15 4.8 32.2 1.0 CD1 A:LEU15 4.8 34.0 1.0 N A:CYS16 4.9 30.3 1.0 SG A:CYS115 4.9 22.3 1.0 SG A:CYS16 4.9 26.9 1.0 SG A:CYS130 4.9 26.1 1.0 CE2 A:TRP133 5.0 26.1 1.0 CA A:ARG14 5.0 31.9 1.0

Iron binding site 2 out of 4 in the Crystal Structure of Uracil-Dna Glycosylase in Complex with Ap:G 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:G Containing Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe220 b:27.4 occ:1.00 FE2 A:SF4220 0.0 27.4 1.0 S4 A:SF4220 2.2 25.5 1.0 S3 A:SF4220 2.3 26.8 1.0 S1 A:SF4220 2.3 28.2 1.0 SG A:CYS130 2.4 26.1 1.0 FE1 A:SF4220 2.7 28.4 1.0 FE4 A:SF4220 2.7 29.4 1.0 FE3 A:SF4220 2.7 29.0 1.0 CB A:CYS130 3.2 26.9 1.0 CA A:CYS130 3.8 26.8 1.0 S2 A:SF4220 3.8 25.4 1.0 CD1 A:TRP133 3.9 25.7 1.0 N A:ARG114 4.2 22.7 1.0 NE1 A:TRP133 4.4 27.8 1.0 N A:CYS130 4.4 27.5 1.0 CB A:ARG114 4.4 23.2 1.0 CA A:ARG114 4.7 23.2 1.0 SG A:CYS13 4.8 28.3 1.0 SG A:CYS115 4.9 22.3 1.0 SG A:CYS16 4.9 26.9 1.0 N A:CYS115 5.0 21.4 1.0 CG A:ARG114 5.0 23.6 1.0

Iron binding site 3 out of 4 in the Crystal Structure of Uracil-Dna Glycosylase in Complex with Ap:G 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:G Containing Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe220 b:29.0 occ:1.00 FE3 A:SF4220 0.0 29.0 1.0 S1 A:SF4220 2.3 28.2 1.0 S2 A:SF4220 2.3 25.4 1.0 S4 A:SF4220 2.3 25.5 1.0 SG A:CYS115 2.5 22.3 1.0 FE1 A:SF4220 2.7 28.4 1.0 FE4 A:SF4220 2.7 29.4 1.0 FE2 A:SF4220 2.7 27.4 1.0 CB A:CYS115 3.2 21.5 1.0 S3 A:SF4220 3.8 26.8 1.0 N A:CYS115 4.1 21.4 1.0 CA A:CYS115 4.2 21.0 1.0 CG A:PRO42 4.5 23.7 1.0 C A:ARG114 4.5 23.0 1.0 NH2 A:ARG23 4.7 26.2 1.0 CB A:PRO42 4.8 22.6 1.0 SG A:CYS13 4.8 28.3 1.0 SG A:CYS130 4.9 26.1 1.0 O A:ARG114 4.9 21.8 1.0 N A:ARG114 5.0 22.7 1.0 SG A:CYS16 5.0 26.9 1.0 CD1 A:LEU19 5.0 22.4 1.0

Iron binding site 4 out of 4 in the Crystal Structure of Uracil-Dna Glycosylase in Complex with Ap:G 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:G Containing Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe220 b:29.4 occ:1.00 FE4 A:SF4220 0.0 29.4 1.0 S3 A:SF4220 2.3 26.8 1.0 S1 A:SF4220 2.3 28.2 1.0 S2 A:SF4220 2.3 25.4 1.0 SG A:CYS16 2.5 26.9 1.0 FE1 A:SF4220 2.7 28.4 1.0 FE2 A:SF4220 2.7 27.4 1.0 FE3 A:SF4220 2.7 29.0 1.0 CB A:CYS16 3.2 29.4 1.0 N A:CYS16 3.7 30.3 1.0 S4 A:SF4220 3.8 25.5 1.0 CA A:CYS16 4.1 28.6 1.0 CD1 A:LEU19 4.5 22.4 1.0 CB A:LEU15 4.5 33.4 1.0 C A:LEU15 4.6 32.0 1.0 CB A:CYS130 4.7 26.9 1.0 N A:LEU15 4.7 32.2 1.0 CB A:ALA129 4.7 27.6 1.0 SG A:CYS13 4.8 28.3 1.0 SG A:CYS130 4.8 26.1 1.0 CA A:LEU15 4.8 32.2 1.0 N A:CYS130 4.9 27.5 1.0 O A:GLU126 4.9 27.1 1.0 SG A:CYS115 5.0 22.3 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