Iron in the structure of Ribonucleoside-Diphosphate Reductase 1 Beta Chain (pdb 1pfr)

The binding sites of Iron atom in the structure of Ribonucleoside-Diphosphate Reductase 1 Beta Chain (pdb code 1pfr). This binding sites where shown with 5.0 Angstroms radius around Iron atom. The 1pfr structure was solved by D.T.LOGAN, X.D.SU, A.ABERG, K.REGNSTROM, J.HAJDU, H.EKLUND, P.NORDLUND, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 15.0-2.2 Space group P212121 a (A) 74.300 b (A) 85.500 c (A) 115.700 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 17.9 Rfree (%) n/a Iron Binding Sites: Iron binding site 1 out of 4 in 1pfr Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Iron in the PDB 1pfr. 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: Asp84, A: Glu115, A: His118, A: Tyr122, A: Phe208, A: Ile234, A: Glu238, A: Fe502, conact list: Atom Atom Distance (A) Fe CB A:Asp84 4.17 Fe OD2 A:Asp84 2.88 Fe OD1 A:Asp84 2.10 Fe CG A:Asp84 2.78 Fe CA A:Asp84 4.77 Fe O A:Glu115 4.77 Fe OE1 A:Glu115 2.19 Fe CB A:Glu115 4.31 Fe OE2 A:Glu115 3.67 Fe CD A:Glu115 3.16 Fe CG A:Glu115 4.30 Fe CA A:Glu115 4.25 Fe NE2 A:His118 4.41 Fe CB A:His118 3.72 Fe ND1 A:His118 2.35 Fe CD2 A:His118 4.49 Fe CE1 A:His118 3.25 Fe CG A:His118 3.38 Fe OH A:Tyr122 5.00 Fe CE2 A:Phe208 4.58 Fe CZ A:Phe208 3.95 Fe CE1 A:Phe208 4.56 Fe CG2 A:Ile234 4.86 Fe OE1 A:Glu238 3.49 Fe OE2 A:Glu238 2.27 Fe CD A:Glu238 3.19 Fe CG A:Glu238 4.46 Fe FE A:Fe502 3.87 interactive model: Iron binding site 2 out of 4 in 1pfr Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Iron in the PDB 1pfr. 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: Gln87, A: Trp111, A: Glu115, A: Glu204, A: Phe208, A: Glu238, A: His241, A: Fe501, conact list: Atom Atom Distance (A) Fe NE2 A:Gln87 4.92 Fe CD1 A:Trp111 4.39 Fe CE2 A:Trp111 4.98 Fe NE1 A:Trp111 3.84 Fe OE1 A:Glu115 2.95 Fe OE2 A:Glu115 2.16 Fe CD A:Glu115 2.91 Fe CG A:Glu115 4.33 Fe OE1 A:Glu204 2.51 Fe OE2 A:Glu204 2.48 Fe CD A:Glu204 2.85 Fe CG A:Glu204 4.36 Fe CE2 A:Phe208 4.59 Fe OE1 A:Glu238 1.90 Fe CB A:Glu238 4.54 Fe OE2 A:Glu238 3.35 Fe CD A:Glu238 2.95 Fe CG A:Glu238 4.27 Fe CA A:Glu238 4.38 Fe NE2 A:His241 4.49 Fe CB A:His241 3.68 Fe ND1 A:His241 2.40 Fe CD2 A:His241 4.52 Fe CE1 A:His241 3.35 Fe CG A:His241 3.38 Fe FE A:Fe501 3.87 interactive model: Iron binding site 3 out of 4 in 1pfr Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Iron in the PDB 1pfr. 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: B: Asp84, B: Glu115, B: His118, B: Phe208, B: Ile234, B: Glu238, B: His241, B: Fe504, B: Hoh663, conact list: Atom Atom Distance (A) Fe CB B:Asp84 4.16 Fe OD2 B:Asp84 2.12 Fe OD1 B:Asp84 2.58 Fe CG B:Asp84 2.67 Fe OE1 B:Glu115 2.13 Fe CB B:Glu115 4.40 Fe OE2 B:Glu115 3.84 Fe CD B:Glu115 3.28 Fe CG B:Glu115 4.42 Fe CA B:Glu115 4.50 Fe NE2 B:His118 4.12 Fe CB B:His118 3.59 Fe ND1 B:His118 2.08 Fe CD2 B:His118 4.24 Fe CE1 B:His118 2.96 Fe CG B:His118 3.15 Fe CE2 B:Phe208 4.62 Fe CZ B:Phe208 4.46 Fe CE1 B:Phe208 4.98 Fe CG2 B:Ile234 4.52 Fe OE1 B:Glu238 4.08 Fe OE2 B:Glu238 2.22 Fe CD B:Glu238 3.40 Fe CG B:Glu238 4.46 Fe ND1 B:His241 5.00 Fe CE1 B:His241 4.97 Fe FE B:Fe504 3.51 Fe O B:Hoh663 3.27 interactive model: Iron binding site 4 out of 4 in 1pfr Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Iron in the PDB 1pfr. 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: B: Asp84, B: Gln87, B: Trp111, B: Glu115, B: His118, B: Glu204, B: Glu238, B: His241, B: Fe503, B: Hoh663, conact list: Atom Atom Distance (A) Fe OD1 B:Asp84 4.42 Fe NE2 B:Gln87 4.89 Fe CD1 B:Trp111 4.65 Fe NE1 B:Trp111 4.12 Fe OE1 B:Glu115 2.91 Fe OE2 B:Glu115 2.23 Fe CD B:Glu115 2.91 Fe CG B:Glu115 4.34 Fe ND1 B:His118 4.78 Fe CE1 B:His118 4.78 Fe OE1 B:Glu204 3.06 Fe OE2 B:Glu204 2.49 Fe CD B:Glu204 3.12 Fe CG B:Glu204 4.54 Fe OE1 B:Glu238 1.52 Fe CB B:Glu238 4.63 Fe OE2 B:Glu238 2.44 Fe CD B:Glu238 2.24 Fe CG B:Glu238 3.70 Fe CA B:Glu238 4.50 Fe NE2 B:His241 4.48 Fe CB B:His241 3.84 Fe ND1 B:His241 2.44 Fe CD2 B:His241 4.60 Fe CE1 B:His241 3.30 Fe CG B:His241 3.51 Fe FE B:Fe503 3.51 Fe O B:Hoh663 2.45 interactive model: