Iron in the structure of Ribonucleotide Reductase R2 Soaked With Ferrous Ion At Neutral pH (pdb 1piy)

The binding sites of Iron atom in the structure of Ribonucleotide Reductase R2 Soaked With Ferrous Ion At Neutral pH (pdb code 1piy). This binding sites where shown with 5.0 Angstroms radius around Iron atom. The 1piy structure was solved by W.C.VOEGTLI, M.SOMMERHALTER, L.SALEH, J.BALDWIN, J.M.BOLLINGER JR., A.C.ROSENZWEIG, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 24.1-1.7 Space group P212121 a (A) 73.900 b (A) 84.600 c (A) 114.100 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 22.5 Rfree (%) 24.6 Iron Binding Sites: Iron binding site 1 out of 4 in 1piy Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Iron in the PDB 1piy. 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: His241, A: Fe377, conact list: Atom Atom Distance (A) Fe CB A:Asp84 4.22 Fe OD2 A:Asp84 3.02 Fe OD1 A:Asp84 1.94 Fe CG A:Asp84 2.81 Fe CA A:Asp84 4.83 Fe OE1 A:Glu115 2.14 Fe CB A:Glu115 4.34 Fe OE2 A:Glu115 3.47 Fe CD A:Glu115 3.04 Fe CG A:Glu115 4.24 Fe CA A:Glu115 4.28 Fe NE2 A:His118 4.03 Fe CB A:His118 3.84 Fe ND1 A:His118 2.10 Fe CD2 A:His118 4.27 Fe CE1 A:His118 2.80 Fe CG A:His118 3.29 Fe OH A:Tyr122 4.97 Fe CE2 A:Phe208 3.96 Fe CD2 A:Phe208 4.91 Fe CZ A:Phe208 3.45 Fe CE1 A:Phe208 4.07 Fe CG2 A:Ile234 4.28 Fe OE1 A:Glu238 4.10 Fe OE2 A:Glu238 2.17 Fe CD A:Glu238 3.29 Fe CG A:Glu238 4.17 Fe ND1 A:His241 4.84 Fe CE1 A:His241 4.76 Fe FE A:Fe377 3.64 interactive model: Iron binding site 2 out of 4 in 1piy Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Iron in the PDB 1piy. 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: Trp111, A: Glu115, A: His118, A: Glu204, A: Phe208, A: Glu238, A: His241, A: Fe376, conact list: Atom Atom Distance (A) Fe OD1 A:Asp84 4.88 Fe CD1 A:Trp111 4.32 Fe CE2 A:Trp111 4.92 Fe NE1 A:Trp111 3.76 Fe OE1 A:Glu115 3.02 Fe OE2 A:Glu115 2.09 Fe CD A:Glu115 2.86 Fe CG A:Glu115 4.24 Fe CE1 A:His118 4.89 Fe OE1 A:Glu204 2.92 Fe OE2 A:Glu204 2.58 Fe CD A:Glu204 3.11 Fe CG A:Glu204 4.61 Fe CE2 A:Phe208 3.82 Fe CD2 A:Phe208 4.38 Fe CZ A:Phe208 4.57 Fe N A:Glu238 4.98 Fe OE1 A:Glu238 1.73 Fe CB A:Glu238 4.47 Fe OE2 A:Glu238 2.36 Fe CD A:Glu238 2.33 Fe CG A:Glu238 3.82 Fe CA A:Glu238 4.33 Fe NE2 A:His241 4.30 Fe CB A:His241 3.64 Fe ND1 A:His241 2.25 Fe CD2 A:His241 4.39 Fe CE1 A:His241 3.14 Fe CG A:His241 3.29 Fe FE A:Fe376 3.64 interactive model: Iron binding site 3 out of 4 in 1piy Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Iron in the PDB 1piy. 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: Tyr122, B: Phe208, B: Ile234, B: Glu238, B: His241, B: Fe377, conact list: Atom Atom Distance (A) Fe CB B:Asp84 4.11 Fe OD2 B:Asp84 2.74 Fe OD1 B:Asp84 1.93 Fe CG B:Asp84 2.66 Fe CA B:Asp84 4.79 Fe OE1 B:Glu115 3.67 Fe CB B:Glu115 4.47 Fe OE2 B:Glu115 2.16 Fe CD B:Glu115 3.19 Fe CG B:Glu115 4.39 Fe CA B:Glu115 4.36 Fe NE2 B:His118 4.04 Fe CB B:His118 3.79 Fe ND1 B:His118 2.09 Fe CD2 B:His118 4.26 Fe CE1 B:His118 2.83 Fe CG B:His118 3.26 Fe OH B:Tyr122 4.88 Fe CE2 B:Phe208 3.96 Fe CZ B:Phe208 3.37 Fe CE1 B:Phe208 4.05 Fe CG2 B:Ile234 4.24 Fe OE1 B:Glu238 4.11 Fe OE2 B:Glu238 2.34 Fe CD B:Glu238 3.35 Fe CG B:Glu238 4.22 Fe ND1 B:His241 4.81 Fe CE1 B:His241 4.70 Fe FE B:Fe377 3.64 interactive model: Iron binding site 4 out of 4 in 1piy Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Iron in the PDB 1piy. 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: Trp111, B: Glu115, B: His118, B: Glu204, B: Phe208, B: Glu238, B: His241, B: Fe376, conact list: Atom Atom Distance (A) Fe OD1 B:Asp84 4.67 Fe CD1 B:Trp111 4.35 Fe CE2 B:Trp111 4.96 Fe NE1 B:Trp111 3.79 Fe OE1 B:Glu115 2.13 Fe OE2 B:Glu115 3.11 Fe CD B:Glu115 2.95 Fe CG B:Glu115 4.34 Fe CE1 B:His118 4.91 Fe OE1 B:Glu204 2.59 Fe OE2 B:Glu204 2.55 Fe CD B:Glu204 2.91 Fe CG B:Glu204 4.42 Fe CE2 B:Phe208 3.77 Fe CD2 B:Phe208 4.41 Fe CZ B:Phe208 4.47 Fe OE1 B:Glu238 1.79 Fe CB B:Glu238 4.51 Fe OE2 B:Glu238 2.35 Fe CD B:Glu238 2.35 Fe CG B:Glu238 3.84 Fe CA B:Glu238 4.38 Fe NE2 B:His241 4.25 Fe CB B:His241 3.62 Fe ND1 B:His241 2.20 Fe CD2 B:His241 4.35 Fe CE1 B:His241 3.09 Fe CG B:His241 3.26 Fe FE B:Fe376 3.64 interactive model: