Iron in the structure of Structure Of (E)-4-Hydroxy-3-Methyl-But-2-Enyl Diphosphate Reductase, The Terminal Enzyme of the Non-Mevalonate Pathway (pdb 3dnf)

The binding sites of Iron atom in the structure of Structure Of (E)-4-Hydroxy-3-Methyl-But-2-Enyl Diphosphate Reductase, The Terminal Enzyme of the Non-Mevalonate Pathway (pdb code 3dnf). This binding sites where shown with 5.0 Angstroms radius around Iron atom. The 3dnf structure was solved by I.REKITTKE, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 9.9-1.6 Space group P1211 a (A) 60.370 b (A) 87.760 c (A) 72.400 alpha (°) 90.00 beta (°) 95.13 gamma (°) 90.00 Rfactor (%) 19.3 Rfree (%) 22.6 Iron Binding Sites: Iron binding site 1 out of 6 in 3dnf Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Iron in the PDB 3dnf. 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: Cys96, A: Tyr98, A: Thr165, A: Cys193, A: Ala195, A: F3s2302, A: Hoh3762, A: Hoh3892, A: Hoh3970, conact list: Atom Atom Distance (A) Fe CB A:Cys13 4.81 Fe SG A:Cys13 4.72 Fe SG A:Cys96 4.72 Fe CB A:Tyr98 4.83 Fe CD2 A:Tyr98 4.84 Fe CG A:Tyr98 4.94 Fe CB A:Thr165 4.78 Fe OG1 A:Thr165 4.71 Fe CB A:Cys193 3.24 Fe CB A:Cys193 3.16 Fe SG A:Cys193 2.40 Fe SG A:Cys193 2.52 Fe CA A:Cys193 4.69 Fe CA A:Cys193 4.64 Fe N A:Ala195 4.96 Fe CB A:Ala195 3.99 Fe S1 A:F3s2302 2.27 Fe FE1 A:F3s2302 0.00 Fe FE3 A:F3s2302 2.67 Fe S4 A:F3s2302 3.93 Fe S2 A:F3s2302 2.28 Fe FE4 A:F3s2302 2.44 Fe S3 A:F3s2302 2.29 Fe O A:Hoh3762 4.72 Fe O A:Hoh3892 4.60 Fe O A:Hoh3970 4.30 interactive model: Iron binding site 2 out of 6 in 3dnf Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Iron in the PDB 3dnf. 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: Gly15, A: Cys96, A: Tyr98, A: Cys193, A: F3s2302, A: Hoh3970, conact list: Atom Atom Distance (A) Fe SG A:Cys13 4.60 Fe N A:Gly15 3.94 Fe C A:Gly15 4.89 Fe CA A:Gly15 3.81 Fe CB A:Cys96 3.16 Fe SG A:Cys96 2.31 Fe CA A:Cys96 4.60 Fe CB A:Tyr98 4.34 Fe CD2 A:Tyr98 4.45 Fe CG A:Tyr98 4.80 Fe SG A:Cys193 4.91 Fe SG A:Cys193 4.47 Fe S1 A:F3s2302 2.21 Fe FE1 A:F3s2302 2.67 Fe FE3 A:F3s2302 0.00 Fe S4 A:F3s2302 2.25 Fe S2 A:F3s2302 3.97 Fe FE4 A:F3s2302 2.41 Fe S3 A:F3s2302 2.26 Fe O A:Hoh3970 4.15 interactive model: Iron binding site 3 out of 6 in 3dnf Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Iron in the PDB 3dnf. 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: Phe14, A: Gly15, A: Val16, A: Cys96, A: Cys193, A: Ala195, A: F3s2302, A: Hoh3865, A: Hoh3891, A: Hoh3970, conact list: Atom Atom Distance (A) Fe CB A:Cys13 3.29 Fe SG A:Cys13 2.52 Fe C A:Cys13 4.72 Fe CA A:Cys13 4.63 Fe N A:Phe14 4.79 Fe N A:Gly15 4.00 Fe C A:Gly15 4.92 Fe CA A:Gly15 4.27 Fe N A:Val16 4.65 Fe CG2 A:Val16 4.93 Fe SG A:Cys96 4.59 Fe SG A:Cys193 4.70 Fe SG A:Cys193 4.65 Fe CB A:Ala195 4.64 Fe S1 A:F3s2302 3.51 Fe FE1 A:F3s2302 2.44 Fe FE3 A:F3s2302 2.41 Fe S4 A:F3s2302 2.14 Fe S2 A:F3s2302 2.14 Fe FE4 A:F3s2302 0.00 Fe S3 A:F3s2302 2.15 Fe O A:Hoh3865 4.42 Fe O A:Hoh3891 4.94 Fe O A:Hoh3970 4.36 interactive model: Iron binding site 4 out of 6 in 3dnf Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Iron in the PDB 3dnf. 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: Cys13, B: Cys96, B: Tyr98, B: Thr165, B: Cys193, B: Ala195, B: F3s3302, B: Hoh3961, B: Hoh3998, B: Hoh4163, conact list: Atom Atom Distance (A) Fe CB B:Cys13 4.58 Fe SG B:Cys13 4.67 Fe SG B:Cys96 4.66 Fe CD2 B:Tyr98 4.30 Fe CB B:Thr165 4.98 Fe CB B:Cys193 3.15 Fe SG B:Cys193 2.35 Fe CA B:Cys193 4.62 Fe CB B:Ala195 4.04 Fe S1 B:F3s3302 2.26 Fe FE1 B:F3s3302 0.00 Fe FE3 B:F3s3302 2.71 Fe S4 B:F3s3302 4.00 Fe S2 B:F3s3302 2.28 Fe FE4 B:F3s3302 2.42 Fe S3 B:F3s3302 2.28 Fe O B:Hoh3961 4.32 Fe O B:Hoh3998 4.48 Fe O B:Hoh4163 4.39 interactive model: Iron binding site 5 out of 6 in 3dnf Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Iron in the PDB 3dnf. 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: Cys13, B: Gly15, B: Cys96, B: Tyr98, B: Cys193, B: F3s3302, B: Hoh3961, conact list: Atom Atom Distance (A) Fe SG B:Cys13 4.64 Fe N B:Gly15 4.09 Fe C B:Gly15 4.99 Fe CA B:Gly15 3.95 Fe CB B:Cys96 3.15 Fe SG B:Cys96 2.17 Fe CA B:Cys96 4.59 Fe CB B:Tyr98 4.38 Fe CE2 B:Tyr98 4.90 Fe CD2 B:Tyr98 3.98 Fe CG B:Tyr98 4.64 Fe SG B:Cys193 4.69 Fe S1 B:F3s3302 2.28 Fe FE1 B:F3s3302 2.71 Fe FE3 B:F3s3302 0.00 Fe S4 B:F3s3302 2.30 Fe S2 B:F3s3302 4.07 Fe FE4 B:F3s3302 2.46 Fe S3 B:F3s3302 2.28 Fe O B:Hoh3961 4.18 interactive model: Iron binding site 6 out of 6 in 3dnf Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 6 of Iron in the PDB 3dnf. 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: Cys13, B: Phe14, B: Gly15, B: Val16, B: Cys96, B: Cys193, B: Ala195, B: F3s3302, B: Hoh3961, B: Hoh3977, conact list: Atom Atom Distance (A) Fe CB B:Cys13 3.23 Fe SG B:Cys13 2.54 Fe C B:Cys13 4.75 Fe CA B:Cys13 4.58 Fe N B:Phe14 4.82 Fe N B:Gly15 4.13 Fe C B:Gly15 4.98 Fe CA B:Gly15 4.40 Fe N B:Val16 4.62 Fe CG2 B:Val16 4.97 Fe SG B:Cys96 4.46 Fe SG B:Cys193 4.66 Fe CB B:Ala195 4.81 Fe S1 B:F3s3302 3.51 Fe FE1 B:F3s3302 2.42 Fe FE3 B:F3s3302 2.46 Fe S4 B:F3s3302 2.18 Fe S2 B:F3s3302 2.17 Fe FE4 B:F3s3302 0.00 Fe S3 B:F3s3302 2.17 Fe O B:Hoh3961 4.08 Fe O B:Hoh3977 4.42 interactive model: