Iron in the structure of Crystal Structure of Uracil-Dna Glycosylase From Thermus Thermophilus HB8 (pdb 2d3y)

The binding sites of Iron atom in the structure of Crystal Structure of Uracil-Dna Glycosylase From Thermus Thermophilus HB8 (pdb code 2d3y). This binding sites where shown with 5.0 Angstroms radius around Iron atom. The 2d3y structure was solved by H.KOSAKA, N.NAKAGAWA, R.MASUI, S.KURAMITSU, RIKEN STRUCTURALGENOMICS/PROTEOMICS INITIATIVE (RSGI), with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 50.0-1.6 Space group P212121 a (A) 48.180 b (A) 62.350 c (A) 63.040 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 18.6 Rfree (%) 21 Iron Binding Sites: Iron binding site 1 out of 4 in 2d3y Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Iron in the PDB 2d3y. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Iron atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: A: Cys13, A: Arg14, A: Leu15, A: Cys16, A: Pro42, A: Cys115, A: Cys130, A: Trp133, A: Sf4220, conact list: Atom Atom Distance (A) Fe O A:Cys13 4.54 Fe CB A:Cys13 3.28 Fe SG A:Cys13 2.35 Fe C A:Cys13 4.32 Fe CA A:Cys13 4.42 Fe N A:Arg14 4.58 Fe N A:Leu15 4.16 Fe CB A:Leu15 4.15 Fe CD1 A:Leu15 4.51 Fe CG A:Leu15 4.49 Fe CA A:Leu15 4.72 Fe N A:Cys16 4.84 Fe SG A:Cys16 4.76 Fe CG A:Pro42 5.00 Fe SG A:Cys115 4.79 Fe SG A:Cys130 4.89 Fe CD1 A:Trp133 4.19 Fe NE1 A:Trp133 3.81 Fe S1 A:Sf4220 3.83 Fe FE1 A:Sf4220 0.00 Fe FE3 A:Sf4220 2.69 Fe S4 A:Sf4220 2.26 Fe FE2 A:Sf4220 2.70 Fe S2 A:Sf4220 2.25 Fe FE4 A:Sf4220 2.69 Fe S3 A:Sf4220 2.26 interactive model: Iron binding site 2 out of 4 in 2d3y Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Iron in the PDB 2d3y. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Iron atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: A: Cys13, A: Cys16, A: Leu19, A: Arg23, A: Pro42, A: Arg114, A: Cys115, A: Cys130, A: Sf4220, conact list: Atom Atom Distance (A) Fe SG A:Cys13 4.82 Fe SG A:Cys16 4.87 Fe CD1 A:Leu19 4.95 Fe NH2 A:Arg23 4.12 Fe CB A:Pro42 4.56 Fe CG A:Pro42 4.24 Fe O A:Arg114 4.92 Fe N A:Arg114 4.92 Fe C A:Arg114 4.45 Fe CA A:Arg114 4.97 Fe N A:Cys115 4.03 Fe CB A:Cys115 3.23 Fe SG A:Cys115 2.35 Fe CA A:Cys115 4.22 Fe SG A:Cys130 4.78 Fe S1 A:Sf4220 2.25 Fe FE1 A:Sf4220 2.70 Fe FE3 A:Sf4220 2.71 Fe S4 A:Sf4220 2.26 Fe FE2 A:Sf4220 0.00 Fe S2 A:Sf4220 3.83 Fe FE4 A:Sf4220 2.68 Fe S3 A:Sf4220 2.26 interactive model: Iron binding site 3 out of 4 in 2d3y Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Iron in the PDB 2d3y. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Iron atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: A: Cys13, A: Leu15, A: Cys16, A: Leu19, A: Cys115, A: Glu126, A: Ala129, A: Cys130, A: Sf4220, conact list: Atom Atom Distance (A) Fe SG A:Cys13 4.81 Fe N A:Leu15 4.88 Fe CB A:Leu15 4.44 Fe C A:Leu15 4.66 Fe CA A:Leu15 4.88 Fe N A:Cys16 3.78 Fe CB A:Cys16 3.29 Fe SG A:Cys16 2.36 Fe CA A:Cys16 4.19 Fe CD1 A:Leu19 4.50 Fe SG A:Cys115 4.86 Fe O A:Glu126 4.96 Fe CB A:Ala129 4.73 Fe N A:Cys130 4.98 Fe CB A:Cys130 4.85 Fe SG A:Cys130 4.78 Fe S1 A:Sf4220 2.26 Fe FE1 A:Sf4220 2.69 Fe FE3 A:Sf4220 0.00 Fe S4 A:Sf4220 2.26 Fe FE2 A:Sf4220 2.71 Fe S2 A:Sf4220 2.26 Fe FE4 A:Sf4220 2.69 Fe S3 A:Sf4220 3.84 interactive model: Iron binding site 4 out of 4 in 2d3y Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Iron in the PDB 2d3y. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Iron atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: A: Cys13, A: Cys16, A: Arg114, A: Cys115, A: Cys130, A: Trp133, A: Sf4220, conact list: Atom Atom Distance (A) Fe SG A:Cys13 4.79 Fe SG A:Cys16 4.81 Fe N A:Arg114 4.18 Fe CB A:Arg114 4.47 Fe CA A:Arg114 4.75 Fe N A:Cys115 4.94 Fe SG A:Cys115 4.76 Fe N A:Cys130 4.41 Fe CB A:Cys130 3.24 Fe SG A:Cys130 2.37 Fe CA A:Cys130 3.78 Fe CD1 A:Trp133 3.88 Fe NE1 A:Trp133 4.40 Fe S1 A:Sf4220 2.25 Fe FE1 A:Sf4220 2.69 Fe FE3 A:Sf4220 2.69 Fe S4 A:Sf4220 3.83 Fe FE2 A:Sf4220 2.68 Fe S2 A:Sf4220 2.24 Fe FE4 A:Sf4220 0.00 Fe S3 A:Sf4220 2.25 interactive model: