Iron in the structure of Y122F Mutant of Ribonucleotide Reductase From Escherichia Coli (pdb 2av8)

The binding sites of Iron atom in the structure of Y122F Mutant of Ribonucleotide Reductase From Escherichia Coli (pdb code 2av8). This binding sites where shown with 5.0 Angstroms radius around Iron atom. The 2av8 structure was solved by S.HAN, A.ARVAI, J.A.TAINER, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 7.0-2.5 Space group P61 a (A) 136.500 b (A) 136.500 c (A) 109.600 alpha (°) 90.00 beta (°) 90.00 gamma (°) 120.00 Rfactor (%) 18.1 Rfree (%) 23.7 Iron Binding Sites: Iron binding site 1 out of 5 in 2av8 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Iron in the PDB 2av8. 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: Pro66, A: His68, A: Glu69, A: Arg221, A: Ser295, A: Met296, A: Ile297, A: Hoh1243, A: Hoh1276, A: Hoh1338, conact list: Atom Atom Distance (A) Fe CG A:Pro66 4.68 Fe NE2 A:His68 4.63 Fe CE1 A:His68 4.96 Fe OE1 A:Glu69 3.47 Fe OE2 A:Glu69 1.96 Fe CD A:Glu69 3.03 Fe CG A:Glu69 4.29 Fe CZ A:Arg221 4.09 Fe NE A:Arg221 4.93 Fe NH2 A:Arg221 3.38 Fe NH1 A:Arg221 4.41 Fe O A:Ser295 4.70 Fe CB A:Met296 4.35 Fe CA A:Met296 4.40 Fe N A:Ile297 4.75 Fe O A:Hoh1243 2.10 Fe O A:Hoh1276 2.41 Fe O A:Hoh1338 2.52 interactive model: Iron binding site 2 out of 5 in 2av8 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Iron in the PDB 2av8. 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: Phe208, A: Ile234, A: Glu238, A: His241, A: Feo401, A: Hoh1201, A: Hoh1202, conact list: Atom Atom Distance (A) Fe CB A:Asp84 4.25 Fe OD2 A:Asp84 3.04 Fe OD1 A:Asp84 2.09 Fe CG A:Asp84 2.86 Fe CA A:Asp84 4.93 Fe OE1 A:Glu115 2.01 Fe CB A:Glu115 4.63 Fe OE2 A:Glu115 3.57 Fe CD A:Glu115 3.12 Fe CG A:Glu115 4.40 Fe CA A:Glu115 4.43 Fe NE2 A:His118 4.08 Fe CB A:His118 3.67 Fe ND1 A:His118 2.02 Fe CD2 A:His118 4.24 Fe CE1 A:His118 2.85 Fe CG A:His118 3.18 Fe CE2 A:Phe208 4.34 Fe CD2 A:Phe208 4.97 Fe CZ A:Phe208 4.35 Fe CE1 A:Phe208 4.99 Fe CG2 A:Ile234 4.38 Fe OE1 A:Glu238 3.82 Fe OE2 A:Glu238 4.16 Fe CD A:Glu238 4.39 Fe ND1 A:His241 4.60 Fe CE1 A:His241 4.51 Fe O A:Feo401 1.99 Fe FE1 A:Feo401 0.00 Fe FE2 A:Feo401 3.39 Fe O A:Hoh1201 3.22 Fe O A:Hoh1202 1.98 interactive model: Iron binding site 3 out of 5 in 2av8 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Iron in the PDB 2av8. 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: Gln87, A: Trp111, A: Glu115, A: His118, A: Glu204, A: Glu238, A: His241, A: Feo401, A: Hoh1201, A: Hoh1202, conact list: Atom Atom Distance (A) Fe OD1 A:Asp84 4.51 Fe NE2 A:Gln87 4.43 Fe CG A:Gln87 4.84 Fe CD1 A:Trp111 4.65 Fe NE1 A:Trp111 4.02 Fe OE1 A:Glu115 3.22 Fe OE2 A:Glu115 2.13 Fe CD A:Glu115 3.01 Fe CG A:Glu115 4.38 Fe ND1 A:His118 4.80 Fe CE1 A:His118 4.79 Fe OE1 A:Glu204 3.87 Fe CB A:Glu204 4.49 Fe OE2 A:Glu204 2.00 Fe CD A:Glu204 2.97 Fe CG A:Glu204 3.68 Fe OE1 A:Glu238 3.65 Fe OE2 A:Glu238 2.08 Fe CD A:Glu238 3.19 Fe CG A:Glu238 4.46 Fe CA A:Glu238 4.74 Fe NE2 A:His241 4.35 Fe CB A:His241 3.74 Fe ND1 A:His241 2.25 Fe CD2 A:His241 4.46 Fe CE1 A:His241 3.13 Fe CG A:His241 3.36 Fe O A:Feo401 2.13 Fe FE1 A:Feo401 3.39 Fe FE2 A:Feo401 0.00 Fe O A:Hoh1201 2.50 Fe O A:Hoh1202 4.54 interactive model: Iron binding site 4 out of 5 in 2av8 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Iron in the PDB 2av8. 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: Feo403, B: Hoh1203, B: Hoh1204, conact list: Atom Atom Distance (A) Fe CB B:Asp84 4.13 Fe OD2 B:Asp84 2.66 Fe OD1 B:Asp84 2.20 Fe CG B:Asp84 2.71 Fe CA B:Asp84 4.84 Fe OE1 B:Glu115 1.98 Fe CB B:Glu115 4.42 Fe OE2 B:Glu115 3.64 Fe CD B:Glu115 3.10 Fe CG B:Glu115 4.31 Fe CA B:Glu115 4.27 Fe NE2 B:His118 4.18 Fe CB B:His118 3.66 Fe ND1 B:His118 2.10 Fe CD2 B:His118 4.30 Fe CE1 B:His118 2.97 Fe CG B:His118 3.22 Fe CE2 B:Phe208 4.34 Fe CZ B:Phe208 4.35 Fe CG2 B:Ile234 4.59 Fe OE1 B:Glu238 4.37 Fe OE2 B:Glu238 4.19 Fe CD B:Glu238 4.61 Fe ND1 B:His241 4.62 Fe CE1 B:His241 4.55 Fe O B:Feo403 2.49 Fe FE1 B:Feo403 0.00 Fe FE2 B:Feo403 3.48 Fe O B:Hoh1203 3.20 Fe O B:Hoh1204 1.94 interactive model: Iron binding site 5 out of 5 in 2av8 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Iron in the PDB 2av8. 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: Feo403, B: Hoh1203, B: Hoh1204, conact list: Atom Atom Distance (A) Fe OD1 B:Asp84 4.52 Fe NE2 B:Gln87 4.59 Fe CG B:Gln87 4.87 Fe CD1 B:Trp111 4.53 Fe CE2 B:Trp111 4.99 Fe NE1 B:Trp111 3.86 Fe OE1 B:Glu115 3.13 Fe OE2 B:Glu115 2.23 Fe CD B:Glu115 3.04 Fe CG B:Glu115 4.48 Fe ND1 B:His118 4.84 Fe CE1 B:His118 4.85 Fe OE1 B:Glu204 3.99 Fe CB B:Glu204 4.50 Fe OE2 B:Glu204 2.28 Fe CD B:Glu204 3.11 Fe CG B:Glu204 3.70 Fe OE1 B:Glu238 2.13 Fe OE2 B:Glu238 3.24 Fe CD B:Glu238 3.04 Fe CG B:Glu238 4.46 Fe CA B:Glu238 4.69 Fe NE2 B:His241 4.44 Fe CB B:His241 3.66 Fe ND1 B:His241 2.32 Fe CD2 B:His241 4.50 Fe CE1 B:His241 3.26 Fe CG B:His241 3.36 Fe O B:Feo403 2.16 Fe FE1 B:Feo403 3.48 Fe FE2 B:Feo403 0.00 Fe O B:Hoh1203 2.66 Fe O B:Hoh1204 4.45 interactive model: