Iron in the structure of Crystal Structure of A Gemcitabine-Diphosphate Inhibited E. Coli Class Ia Ribonucleotide Reductase Complex (pdb 4erp)

The binding sites of Iron atom in the structure of Crystal Structure of A Gemcitabine-Diphosphate Inhibited E. Coli Class Ia Ribonucleotide Reductase Complex (pdb code 4erp). This binding sites where shown with 5.0 Angstroms radius around Iron atom. The 4erp structure was solved by C.M.ZIMANYI, C.L.DRENNAN, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 50.0-4.5 Space group C2221 a (A) 128.669 b (A) 398.906 c (A) 319.437 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 23.3 Rfree (%) 26.7 Iron Binding Sites: Iron binding site 1 out of 8 in 4erp Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Iron in the PDB 4erp. 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: E: Asp84, E: Glu115, E: His118, E: Tyr122, E: Phe208, E: Ile234, E: Glu238, E: Feo501, E: Hoh601, E: Hoh602, conact list: Atom Atom Distance (A) Fe CB E:Asp84 3.66 Fe OD2 E:Asp84 2.04 Fe OD1 E:Asp84 2.57 Fe CG E:Asp84 2.43 Fe CA E:Asp84 4.75 Fe O E:Glu115 4.73 Fe OE1 E:Glu115 1.79 Fe CB E:Glu115 4.26 Fe OE2 E:Glu115 3.48 Fe CD E:Glu115 2.94 Fe C E:Glu115 4.96 Fe CG E:Glu115 4.16 Fe CA E:Glu115 4.13 Fe NE2 E:His118 4.03 Fe CB E:His118 3.66 Fe ND1 E:His118 2.14 Fe CD2 E:His118 4.18 Fe CE1 E:His118 2.91 Fe CG E:His118 3.18 Fe OH E:Tyr122 4.57 Fe CE2 E:Phe208 4.21 Fe CD2 E:Phe208 4.96 Fe CZ E:Phe208 4.45 Fe CG2 E:Ile234 4.51 Fe OE1 E:Glu238 4.46 Fe OE2 E:Glu238 4.30 Fe CD E:Glu238 4.68 Fe O E:Feo501 2.03 Fe FE1 E:Feo501 0.00 Fe FE2 E:Feo501 3.43 Fe O E:Hoh601 2.59 Fe O E:Hoh602 3.44 interactive model: Iron binding site 2 out of 8 in 4erp Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Iron in the PDB 4erp. 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: E: Asp84, E: Trp111, E: Glu115, E: His118, E: Glu204, E: Glu238, E: His241, E: Feo501, E: Hoh601, E: Hoh602, conact list: Atom Atom Distance (A) Fe OD1 E:Asp84 4.30 Fe CD1 E:Trp111 4.78 Fe NE1 E:Trp111 4.20 Fe OE1 E:Glu115 2.99 Fe OE2 E:Glu115 1.78 Fe CD E:Glu115 2.68 Fe CG E:Glu115 4.05 Fe ND1 E:His118 4.83 Fe CE1 E:His118 4.64 Fe OE1 E:Glu204 2.04 Fe CB E:Glu204 4.63 Fe OE2 E:Glu204 4.08 Fe CD E:Glu204 2.90 Fe CG E:Glu204 3.11 Fe OE1 E:Glu238 1.93 Fe CB E:Glu238 4.73 Fe OE2 E:Glu238 3.23 Fe CD E:Glu238 2.90 Fe CG E:Glu238 4.26 Fe CA E:Glu238 4.54 Fe NE2 E:His241 4.06 Fe CB E:His241 4.05 Fe ND1 E:His241 2.20 Fe CD2 E:His241 4.38 Fe CE1 E:His241 2.81 Fe CG E:His241 3.44 Fe O E:Feo501 2.03 Fe FE1 E:Feo501 3.43 Fe FE2 E:Feo501 0.00 Fe O E:Hoh601 4.20 Fe O E:Hoh602 2.40 interactive model: Iron binding site 3 out of 8 in 4erp Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Iron in the PDB 4erp. 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: F: Asp84, F: Glu115, F: His118, F: Tyr122, F: Phe208, F: Ile234, F: Glu238, F: Feo501, F: Hoh601, F: Hoh602, conact list: Atom Atom Distance (A) Fe CB F:Asp84 3.63 Fe OD2 F:Asp84 1.99 Fe OD1 F:Asp84 2.52 Fe CG F:Asp84 2.38 Fe CA F:Asp84 4.71 Fe O F:Glu115 4.72 Fe OE1 F:Glu115 2.08 Fe CB F:Glu115 4.27 Fe OE2 F:Glu115 3.46 Fe CD F:Glu115 3.01 Fe C F:Glu115 4.96 Fe CG F:Glu115 4.20 Fe CA F:Glu115 4.13 Fe NE2 F:His118 4.06 Fe CB F:His118 3.67 Fe ND1 F:His118 2.17 Fe CD2 F:His118 4.21 Fe CE1 F:His118 2.95 Fe CG F:His118 3.21 Fe OH F:Tyr122 4.60 Fe CE2 F:Phe208 4.24 Fe CD2 F:Phe208 4.97 Fe CZ F:Phe208 4.47 Fe CG2 F:Ile234 4.55 Fe OE1 F:Glu238 4.48 Fe OE2 F:Glu238 4.31 Fe CD F:Glu238 4.70 Fe O F:Feo501 2.03 Fe FE1 F:Feo501 0.00 Fe FE2 F:Feo501 3.43 Fe O F:Hoh601 2.51 Fe O F:Hoh602 3.55 interactive model: Iron binding site 4 out of 8 in 4erp Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Iron in the PDB 4erp. 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: F: Asp84, F: Trp111, F: Glu115, F: His118, F: Glu204, F: Glu238, F: His241, F: Feo501, F: Hoh601, F: Hoh602, conact list: Atom Atom Distance (A) Fe OD1 F:Asp84 4.27 Fe CD1 F:Trp111 4.74 Fe NE1 F:Trp111 4.12 Fe OE1 F:Glu115 2.98 Fe OE2 F:Glu115 1.77 Fe CD F:Glu115 2.69 Fe CG F:Glu115 4.08 Fe ND1 F:His118 4.85 Fe CE1 F:His118 4.67 Fe OE1 F:Glu204 1.99 Fe CB F:Glu204 4.61 Fe OE2 F:Glu204 4.03 Fe CD F:Glu204 2.86 Fe CG F:Glu204 3.09 Fe OE1 F:Glu238 1.97 Fe CB F:Glu238 4.78 Fe OE2 F:Glu238 3.25 Fe CD F:Glu238 2.94 Fe CG F:Glu238 4.30 Fe CA F:Glu238 4.59 Fe NE2 F:His241 4.07 Fe CB F:His241 4.06 Fe ND1 F:His241 2.21 Fe CD2 F:His241 4.39 Fe CE1 F:His241 2.81 Fe CG F:His241 3.46 Fe O F:Feo501 2.03 Fe FE1 F:Feo501 3.43 Fe FE2 F:Feo501 0.00 Fe O F:Hoh601 4.15 Fe O F:Hoh602 2.58 interactive model: Iron binding site 5 out of 8 in 4erp Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Iron in the PDB 4erp. 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: G: Asp84, G: Glu115, G: His118, G: Tyr122, G: Phe208, G: Ile234, G: Glu238, G: His241, G: Feo501, G: Hoh601, G: Hoh602, conact list: Atom Atom Distance (A) Fe CB G:Asp84 3.61 Fe OD2 G:Asp84 2.00 Fe OD1 G:Asp84 2.53 Fe CG G:Asp84 2.37 Fe CA G:Asp84 4.69 Fe O G:Glu115 4.67 Fe N G:Glu115 4.97 Fe OE1 G:Glu115 1.79 Fe CB G:Glu115 4.17 Fe OE2 G:Glu115 3.66 Fe CD G:Glu115 2.98 Fe C G:Glu115 4.89 Fe CG G:Glu115 4.08 Fe CA G:Glu115 4.04 Fe NE2 G:His118 4.06 Fe CB G:His118 3.65 Fe ND1 G:His118 2.18 Fe CD2 G:His118 4.19 Fe CE1 G:His118 2.95 Fe CG G:His118 3.20 Fe OH G:Tyr122 4.68 Fe CE2 G:Phe208 4.27 Fe CZ G:Phe208 4.50 Fe CG2 G:Ile234 4.63 Fe OE1 G:Glu238 4.50 Fe OE2 G:Glu238 4.37 Fe CD G:Glu238 4.74 Fe CE1 G:His241 4.98 Fe O G:Feo501 2.03 Fe FE1 G:Feo501 0.00 Fe FE2 G:Feo501 3.43 Fe O G:Hoh601 3.47 Fe O G:Hoh602 2.69 interactive model: Iron binding site 6 out of 8 in 4erp Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 6 of Iron in the PDB 4erp. 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: G: Asp84, G: Trp111, G: Glu115, G: His118, G: Glu204, G: Glu238, G: His241, G: Feo501, G: Hoh601, G: Hoh602, conact list: Atom Atom Distance (A) Fe OD1 G:Asp84 4.28 Fe CD1 G:Trp111 4.70 Fe NE1 G:Trp111 4.12 Fe OE1 G:Glu115 2.94 Fe OE2 G:Glu115 2.15 Fe CD G:Glu115 2.74 Fe CG G:Glu115 3.99 Fe ND1 G:His118 4.85 Fe CE1 G:His118 4.67 Fe OE1 G:Glu204 1.96 Fe CB G:Glu204 4.67 Fe OE2 G:Glu204 4.06 Fe CD G:Glu204 2.89 Fe CG G:Glu204 3.15 Fe OE1 G:Glu238 2.04 Fe CB G:Glu238 4.84 Fe OE2 G:Glu238 3.34 Fe CD G:Glu238 3.02 Fe CG G:Glu238 4.38 Fe CA G:Glu238 4.64 Fe NE2 G:His241 4.02 Fe CB G:His241 4.06 Fe ND1 G:His241 2.18 Fe CD2 G:His241 4.36 Fe CE1 G:His241 2.76 Fe CG G:His241 3.44 Fe O G:Feo501 2.03 Fe FE1 G:Feo501 3.43 Fe FE2 G:Feo501 0.00 Fe O G:Hoh601 2.42 Fe O G:Hoh602 4.22 interactive model: Iron binding site 7 out of 8 in 4erp Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 7 of Iron in the PDB 4erp. 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: H: Asp84, H: Glu115, H: His118, H: Tyr122, H: Phe208, H: Ile234, H: Glu238, H: His241, H: Feo501, H: Hoh601, H: Hoh602, conact list: Atom Atom Distance (A) Fe CB H:Asp84 3.61 Fe OD2 H:Asp84 2.03 Fe OD1 H:Asp84 2.54 Fe CG H:Asp84 2.39 Fe CA H:Asp84 4.69 Fe O H:Glu115 4.65 Fe N H:Glu115 4.96 Fe OE1 H:Glu115 1.76 Fe CB H:Glu115 4.14 Fe OE2 H:Glu115 3.42 Fe CD H:Glu115 2.87 Fe C H:Glu115 4.88 Fe CG H:Glu115 4.07 Fe CA H:Glu115 4.03 Fe NE2 H:His118 4.06 Fe CB H:His118 3.65 Fe ND1 H:His118 2.18 Fe CD2 H:His118 4.19 Fe CE1 H:His118 2.95 Fe CG H:His118 3.20 Fe OH H:Tyr122 4.67 Fe CE2 H:Phe208 4.28 Fe CZ H:Phe208 4.52 Fe CG2 H:Ile234 4.60 Fe OE1 H:Glu238 4.50 Fe OE2 H:Glu238 4.39 Fe CD H:Glu238 4.75 Fe CE1 H:His241 4.98 Fe O H:Feo501 2.03 Fe FE1 H:Feo501 0.00 Fe FE2 H:Feo501 3.43 Fe O H:Hoh601 3.49 Fe O H:Hoh602 2.71 interactive model: Iron binding site 8 out of 8 in 4erp Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 8 of Iron in the PDB 4erp. 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: H: Asp84, H: Trp111, H: Glu115, H: His118, H: Glu204, H: Glu238, H: His241, H: Feo501, H: Hoh601, H: Hoh602, conact list: Atom Atom Distance (A) Fe OD1 H:Asp84 4.28 Fe CD1 H:Trp111 4.59 Fe NE1 H:Trp111 3.94 Fe OE1 H:Glu115 2.89 Fe OE2 H:Glu115 1.72 Fe CD H:Glu115 2.59 Fe CG H:Glu115 3.96 Fe ND1 H:His118 4.85 Fe CE1 H:His118 4.67 Fe OE1 H:Glu204 2.01 Fe CB H:Glu204 4.68 Fe OE2 H:Glu204 3.94 Fe CD H:Glu204 3.13 Fe CG H:Glu204 4.00 Fe OE1 H:Glu238 2.04 Fe CB H:Glu238 4.85 Fe OE2 H:Glu238 3.34 Fe CD H:Glu238 3.02 Fe CG H:Glu238 4.38 Fe CA H:Glu238 4.66 Fe NE2 H:His241 4.02 Fe CB H:His241 4.06 Fe ND1 H:His241 2.18 Fe CD2 H:His241 4.36 Fe CE1 H:His241 2.76 Fe CG H:His241 3.44 Fe O H:Feo501 2.03 Fe FE1 H:Feo501 3.43 Fe FE2 H:Feo501 0.00 Fe O H:Hoh601 2.43 Fe O H:Hoh602 4.24 interactive model: