Iron in the structure of Crystal Structure of Uracil-Dna Glycosylase in Complex With Ap:C Containing Dna (pdb 2dp6)

The binding sites of Iron atom in the structure of Crystal Structure of Uracil-Dna Glycosylase in Complex With Ap:C Containing Dna (pdb code 2dp6). This binding sites where shown with 5.0 Angstroms radius around Iron atom. The 2dp6 structure was solved by H.KOSAKA, N.NAKAGAWA, R.MASUI, S.KURAMITSU, J.HOSEKI, RIKEN STRUCTURALGENOMICS/PROTEOMICS INITIATIVE (RSGI), with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 31.2-1.8 Space group C2221 a (A) 68.868 b (A) 148.754 c (A) 93.086 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 20.4 Rfree (%) 21.7 Iron Binding Sites: Iron binding site 1 out of 4 in 2dp6 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Iron in the PDB 2dp6. 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: Arg23, A: Pro42, A: Arg114, A: Cys115, A: Cys130, A: Sf4220, conact list: Atom Atom Distance (A) Fe O A:Cys13 4.89 Fe SG A:Cys13 4.82 Fe SG A:Cys16 4.94 Fe NH2 A:Arg23 4.49 Fe CB A:Pro42 4.67 Fe CG A:Pro42 4.32 Fe O A:Arg114 4.93 Fe N A:Arg114 4.96 Fe CB A:Arg114 4.95 Fe C A:Arg114 4.45 Fe CA A:Arg114 4.96 Fe N A:Cys115 4.04 Fe CB A:Cys115 3.25 Fe SG A:Cys115 2.39 Fe CA A:Cys115 4.25 Fe SG A:Cys130 4.83 Fe S1 A:Sf4220 3.83 Fe FE1 A:Sf4220 0.00 Fe FE3 A:Sf4220 2.69 Fe S4 A:Sf4220 2.24 Fe FE2 A:Sf4220 2.69 Fe S2 A:Sf4220 2.24 Fe FE4 A:Sf4220 2.68 Fe S3 A:Sf4220 2.26 interactive model: Iron binding site 2 out of 4 in 2dp6 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Iron in the PDB 2dp6. 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 4.80 Fe N A:Leu15 4.77 Fe CB A:Leu15 4.49 Fe C A:Leu15 4.62 Fe CA A:Leu15 4.85 Fe N A:Cys16 3.78 Fe CB A:Cys16 3.33 Fe SG A:Cys16 2.46 Fe CA A:Cys16 4.20 Fe CD1 A:Leu19 4.42 Fe SG A:Cys115 4.89 Fe O A:Glu126 4.94 Fe CB A:Ala129 4.77 Fe N A:Cys130 4.92 Fe CB A:Cys130 4.68 Fe SG A:Cys130 4.74 Fe S1 A:Sf4220 2.25 Fe FE1 A:Sf4220 2.69 Fe FE3 A:Sf4220 2.67 Fe S4 A:Sf4220 2.26 Fe FE2 A:Sf4220 0.00 Fe S2 A:Sf4220 3.80 Fe FE4 A:Sf4220 2.66 Fe S3 A:Sf4220 2.25 interactive model: Iron binding site 3 out of 4 in 2dp6 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Iron in the PDB 2dp6. 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 4.87 Fe N A:Arg114 4.15 Fe CB A:Arg114 4.33 Fe CG A:Arg114 4.99 Fe CA A:Arg114 4.66 Fe N A:Cys115 4.90 Fe SG A:Cys115 4.81 Fe N A:Cys130 4.43 Fe CB A:Cys130 3.17 Fe SG A:Cys130 2.39 Fe CA A:Cys130 3.78 Fe CD1 A:Trp133 3.89 Fe NE1 A:Trp133 4.35 Fe S1 A:Sf4220 2.26 Fe FE1 A:Sf4220 2.69 Fe FE3 A:Sf4220 0.00 Fe S4 A:Sf4220 2.24 Fe FE2 A:Sf4220 2.67 Fe S2 A:Sf4220 2.24 Fe FE4 A:Sf4220 2.69 Fe S3 A:Sf4220 3.83 interactive model: Iron binding site 4 out of 4 in 2dp6 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Iron in the PDB 2dp6. 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: Cys115, A: Cys130, A: Trp133, A: Sf4220, conact list: Atom Atom Distance (A) Fe O A:Cys13 4.40 Fe CB A:Cys13 3.32 Fe SG A:Cys13 2.36 Fe C A:Cys13 4.22 Fe CA A:Cys13 4.40 Fe N A:Arg14 4.48 Fe CA A:Arg14 5.00 Fe N A:Leu15 4.10 Fe CB A:Leu15 4.25 Fe CD1 A:Leu15 4.61 Fe CG A:Leu15 4.51 Fe CA A:Leu15 4.73 Fe N A:Cys16 4.84 Fe SG A:Cys16 4.84 Fe SG A:Cys115 4.82 Fe SG A:Cys130 4.90 Fe CD1 A:Trp133 4.24 Fe CE2 A:Trp133 4.95 Fe NE1 A:Trp133 3.79 Fe S1 A:Sf4220 2.24 Fe FE1 A:Sf4220 2.68 Fe FE3 A:Sf4220 2.69 Fe S4 A:Sf4220 3.81 Fe FE2 A:Sf4220 2.66 Fe S2 A:Sf4220 2.25 Fe FE4 A:Sf4220 0.00 Fe S3 A:Sf4220 2.25 interactive model: