Iron in the structure of Crystal Structure of Isph:Dmapp-Complex (pdb 3kef)

The binding sites of Iron atom in the structure of Crystal Structure of Isph:Dmapp-Complex (pdb code 3kef). This binding sites where shown with 5.0 Angstroms radius around Iron atom. The 3kef structure was solved by M.GROLL, T.GRAEWERT, I.SPAN, W.EISENREICH, A.BACHER, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 10.0-1.7 Space group P212121 a (A) 70.120 b (A) 80.380 c (A) 110.840 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 21.6 Rfree (%) 23.7 Iron Binding Sites: Iron binding site 1 out of 6 in 3kef Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Iron in the PDB 3kef. 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: Cys12, A: Cys96, A: Leu98, A: Thr167, A: Cys197, A: Ala199, A: Thr200, A: F3s997, A: Dma998, A: Hoh341, conact list: Atom Atom Distance (A) Fe SG A:Cys12 4.74 Fe SG A:Cys96 4.88 Fe CD1 A:Leu98 4.59 Fe CB A:Thr167 4.69 Fe OG1 A:Thr167 4.54 Fe CB A:Cys197 3.23 Fe SG A:Cys197 2.30 Fe CA A:Cys197 4.67 Fe CB A:Ala199 4.26 Fe OG1 A:Thr200 4.53 Fe S1 A:F3s997 2.17 Fe FE1 A:F3s997 0.00 Fe FE3 A:F3s997 2.68 Fe S4 A:F3s997 3.87 Fe S2 A:F3s997 2.18 Fe FE4 A:F3s997 2.75 Fe S3 A:F3s997 2.13 Fe C2 A:Dma998 4.68 Fe C4 A:Dma998 4.02 Fe C3 A:Dma998 4.61 Fe O A:Hoh341 4.77 interactive model: Iron binding site 2 out of 6 in 3kef Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Iron in the PDB 3kef. 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: Cys12, A: Ala13, A: Gly14, A: Val15, A: Cys96, A: Cys197, A: Ala199, A: Ala268, A: F3s997, A: Dma998, conact list: Atom Atom Distance (A) Fe CB A:Cys12 3.29 Fe SG A:Cys12 2.28 Fe C A:Cys12 4.91 Fe CA A:Cys12 4.66 Fe N A:Ala13 4.99 Fe N A:Gly14 4.22 Fe C A:Gly14 4.78 Fe CA A:Gly14 4.37 Fe N A:Val15 4.35 Fe CG2 A:Val15 4.46 Fe SG A:Cys96 4.79 Fe SG A:Cys197 4.71 Fe CB A:Ala199 4.61 Fe CB A:Ala268 4.34 Fe S1 A:F3s997 2.22 Fe FE1 A:F3s997 2.68 Fe FE3 A:F3s997 0.00 Fe S4 A:F3s997 2.18 Fe S2 A:F3s997 4.01 Fe FE4 A:F3s997 2.83 Fe S3 A:F3s997 2.20 Fe C1 A:Dma998 4.14 Fe C2 A:Dma998 3.71 Fe C5 A:Dma998 4.89 Fe C4 A:Dma998 4.42 Fe C3 A:Dma998 4.08 interactive model: Iron binding site 3 out of 6 in 3kef Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Iron in the PDB 3kef. 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: Cys12, A: Gly14, A: Cys96, A: Leu98, A: Cys197, A: F3s997, A: Dma998, conact list: Atom Atom Distance (A) Fe SG A:Cys12 4.74 Fe N A:Gly14 4.43 Fe CA A:Gly14 4.10 Fe CB A:Cys96 3.13 Fe SG A:Cys96 2.26 Fe CA A:Cys96 4.58 Fe N A:Leu98 4.97 Fe CB A:Leu98 4.27 Fe CD1 A:Leu98 4.41 Fe CG A:Leu98 4.60 Fe SG A:Cys197 4.86 Fe S1 A:F3s997 4.08 Fe FE1 A:F3s997 2.75 Fe FE3 A:F3s997 2.83 Fe S4 A:F3s997 2.20 Fe S2 A:F3s997 2.23 Fe FE4 A:F3s997 0.00 Fe S3 A:F3s997 2.10 Fe C2 A:Dma998 4.84 Fe C5 A:Dma998 4.67 Fe C4 A:Dma998 4.14 Fe C3 A:Dma998 4.34 interactive model: Iron binding site 4 out of 6 in 3kef Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Iron in the PDB 3kef. 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: Cys12, B: Cys96, B: Leu98, B: Thr167, B: Cys197, B: Ala199, B: Thr200, B: F3s997, B: Dma998, B: Hoh333, conact list: Atom Atom Distance (A) Fe SG B:Cys12 4.76 Fe SG B:Cys96 4.87 Fe CD1 B:Leu98 4.70 Fe CB B:Thr167 4.69 Fe OG1 B:Thr167 4.53 Fe CB B:Cys197 3.23 Fe SG B:Cys197 2.31 Fe CA B:Cys197 4.67 Fe CB B:Ala199 4.21 Fe OG1 B:Thr200 4.52 Fe S1 B:F3s997 2.17 Fe FE1 B:F3s997 0.00 Fe FE3 B:F3s997 2.70 Fe S4 B:F3s997 3.88 Fe S2 B:F3s997 2.19 Fe FE4 B:F3s997 2.75 Fe S3 B:F3s997 2.14 Fe C2 B:Dma998 4.75 Fe C4 B:Dma998 4.26 Fe C3 B:Dma998 4.73 Fe O B:Hoh333 4.81 interactive model: Iron binding site 5 out of 6 in 3kef Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Iron in the PDB 3kef. 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: Cys12, B: Gly14, B: Val15, B: Cys96, B: Cys197, B: Ala199, B: Ala268, B: F3s997, B: Dma998, conact list: Atom Atom Distance (A) Fe CB B:Cys12 3.26 Fe SG B:Cys12 2.27 Fe C B:Cys12 4.89 Fe CA B:Cys12 4.63 Fe N B:Gly14 4.21 Fe C B:Gly14 4.78 Fe CA B:Gly14 4.33 Fe N B:Val15 4.35 Fe CG2 B:Val15 4.53 Fe SG B:Cys96 4.78 Fe SG B:Cys197 4.72 Fe CB B:Ala199 4.57 Fe CB B:Ala268 4.31 Fe S1 B:F3s997 2.22 Fe FE1 B:F3s997 2.70 Fe FE3 B:F3s997 0.00 Fe S4 B:F3s997 2.18 Fe S2 B:F3s997 4.01 Fe FE4 B:F3s997 2.82 Fe S3 B:F3s997 2.21 Fe C1 B:Dma998 4.15 Fe C2 B:Dma998 3.83 Fe C5 B:Dma998 4.95 Fe C4 B:Dma998 4.66 Fe C3 B:Dma998 4.23 interactive model: Iron binding site 6 out of 6 in 3kef Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 6 of Iron in the PDB 3kef. 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: Cys12, B: Gly14, B: Cys96, B: Leu98, B: Cys197, B: F3s997, B: Dma998, conact list: Atom Atom Distance (A) Fe SG B:Cys12 4.71 Fe N B:Gly14 4.42 Fe CA B:Gly14 4.06 Fe CB B:Cys96 3.12 Fe SG B:Cys96 2.25 Fe CA B:Cys96 4.56 Fe N B:Leu98 4.97 Fe CB B:Leu98 4.26 Fe CD1 B:Leu98 4.53 Fe CG B:Leu98 4.63 Fe SG B:Cys197 4.89 Fe S1 B:F3s997 4.07 Fe FE1 B:F3s997 2.75 Fe FE3 B:F3s997 2.82 Fe S4 B:F3s997 2.20 Fe S2 B:F3s997 2.24 Fe FE4 B:F3s997 0.00 Fe S3 B:F3s997 2.10 Fe C2 B:Dma998 4.92 Fe C5 B:Dma998 4.72 Fe C4 B:Dma998 4.35 Fe C3 B:Dma998 4.46 interactive model: