Iron in PDB 2d3y: Crystal Structure of Uracil-Dna Glycosylase From Thermus Thermophilus HB8

The structure of Crystal Structure of Uracil-Dna Glycosylase From Thermus Thermophilus HB8, PDB code: 2d3y was solved by H.Kosaka, N.Nakagawa, R.Masui, 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)	50.00 / 1.55
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	48.180, 62.350, 63.040, 90.00, 90.00, 90.00
R / Rfree (%)	18.6 / 21

The binding sites of Iron atom in the Crystal Structure of Uracil-Dna Glycosylase From Thermus Thermophilus HB8 (pdb code 2d3y). 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 From Thermus Thermophilus HB8, PDB code: 2d3y:
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 From Thermus Thermophilus HB8


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 From Thermus Thermophilus HB8 within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe220 b:4.8 occ:1.00 FE1 A:SF4220 0.0 4.8 1.0 S2 A:SF4220 2.3 4.6 1.0 S4 A:SF4220 2.3 5.1 1.0 S3 A:SF4220 2.3 4.7 1.0 SG A:CYS13 2.3 5.4 1.0 FE4 A:SF4220 2.7 5.2 1.0 FE3 A:SF4220 2.7 5.3 1.0 FE2 A:SF4220 2.7 4.7 1.0 CB A:CYS13 3.3 6.1 1.0 NE1 A:TRP133 3.8 4.8 1.0 S1 A:SF4220 3.8 4.3 1.0 CB A:LEU15 4.2 7.6 1.0 N A:LEU15 4.2 6.2 1.0 CD1 A:TRP133 4.2 3.5 1.0 C A:CYS13 4.3 5.8 1.0 CA A:CYS13 4.4 5.7 1.0 CG A:LEU15 4.5 8.7 1.0 CD1 A:LEU15 4.5 10.7 1.0 O A:CYS13 4.5 5.6 1.0 N A:ARG14 4.6 5.8 1.0 CA A:LEU15 4.7 6.9 1.0 SG A:CYS16 4.8 5.7 1.0 SG A:CYS115 4.8 5.0 1.0 N A:CYS16 4.8 5.9 1.0 SG A:CYS130 4.9 3.0 1.0 CG A:PRO42 5.0 3.2 1.0

Iron binding site 2 out of 4 in the Crystal Structure of Uracil-Dna Glycosylase From Thermus Thermophilus HB8


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 From Thermus Thermophilus HB8 within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe220 b:4.7 occ:1.00 FE2 A:SF4220 0.0 4.7 1.0 S1 A:SF4220 2.3 4.3 1.0 S4 A:SF4220 2.3 5.1 1.0 S3 A:SF4220 2.3 4.7 1.0 SG A:CYS115 2.3 5.0 1.0 FE4 A:SF4220 2.7 5.2 1.0 FE1 A:SF4220 2.7 4.8 1.0 FE3 A:SF4220 2.7 5.3 1.0 CB A:CYS115 3.2 4.5 1.0 S2 A:SF4220 3.8 4.6 1.0 N A:CYS115 4.0 4.4 1.0 NH2 A:ARG23 4.1 7.2 1.0 CA A:CYS115 4.2 4.4 1.0 CG A:PRO42 4.2 3.2 1.0 C A:ARG114 4.4 4.0 1.0 CB A:PRO42 4.6 3.3 1.0 SG A:CYS130 4.8 3.0 1.0 SG A:CYS13 4.8 5.4 1.0 SG A:CYS16 4.9 5.7 1.0 O A:ARG114 4.9 3.2 1.0 N A:ARG114 4.9 3.3 1.0 CD1 A:LEU19 5.0 6.0 1.0 CA A:ARG114 5.0 3.2 1.0

Iron binding site 3 out of 4 in the Crystal Structure of Uracil-Dna Glycosylase From Thermus Thermophilus HB8


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 From Thermus Thermophilus HB8 within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe220 b:5.3 occ:1.00 FE3 A:SF4220 0.0 5.3 1.0 S1 A:SF4220 2.3 4.3 1.0 S4 A:SF4220 2.3 5.1 1.0 S2 A:SF4220 2.3 4.6 1.0 SG A:CYS16 2.4 5.7 1.0 FE4 A:SF4220 2.7 5.2 1.0 FE1 A:SF4220 2.7 4.8 1.0 FE2 A:SF4220 2.7 4.7 1.0 CB A:CYS16 3.3 6.1 1.0 N A:CYS16 3.8 5.9 1.0 S3 A:SF4220 3.8 4.7 1.0 CA A:CYS16 4.2 7.2 1.0 CB A:LEU15 4.4 7.6 1.0 CD1 A:LEU19 4.5 6.0 1.0 C A:LEU15 4.7 6.3 1.0 CB A:ALA129 4.7 6.8 1.0 SG A:CYS130 4.8 3.0 1.0 SG A:CYS13 4.8 5.4 1.0 CB A:CYS130 4.8 2.7 1.0 SG A:CYS115 4.9 5.0 1.0 N A:LEU15 4.9 6.2 1.0 CA A:LEU15 4.9 6.9 1.0 O A:GLU126 5.0 5.9 1.0 N A:CYS130 5.0 5.1 1.0

Iron binding site 4 out of 4 in the Crystal Structure of Uracil-Dna Glycosylase From Thermus Thermophilus HB8


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 From Thermus Thermophilus HB8 within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe220 b:5.2 occ:1.00 FE4 A:SF4220 0.0 5.2 1.0 S2 A:SF4220 2.2 4.6 1.0 S1 A:SF4220 2.2 4.3 1.0 S3 A:SF4220 2.3 4.7 1.0 SG A:CYS130 2.4 3.0 1.0 FE2 A:SF4220 2.7 4.7 1.0 FE3 A:SF4220 2.7 5.3 1.0 FE1 A:SF4220 2.7 4.8 1.0 CB A:CYS130 3.2 2.7 1.0 CA A:CYS130 3.8 4.5 1.0 S4 A:SF4220 3.8 5.1 1.0 CD1 A:TRP133 3.9 3.5 1.0 N A:ARG114 4.2 3.3 1.0 NE1 A:TRP133 4.4 4.8 1.0 N A:CYS130 4.4 5.1 1.0 CB A:ARG114 4.5 3.2 1.0 CA A:ARG114 4.7 3.2 1.0 SG A:CYS115 4.8 5.0 1.0 SG A:CYS13 4.8 5.4 1.0 SG A:CYS16 4.8 5.7 1.0 N A:CYS115 4.9 4.4 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