Iron in the structure of F110A Variant of Human Ferrochelatase With Protoheme Bound (pdb 2qd2)

The binding sites of Iron atom in the structure of F110A Variant of Human Ferrochelatase With Protoheme Bound (pdb code 2qd2). This binding sites where shown with 5.0 Angstroms radius around Iron atom. The 2qd2 structure was solved by A.E.MEDLOCK, T.A.DAILEY, T.A.ROSS, H.A.DAILEY, W.N.LANZILOTA, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 47.0-2.2 Space group P212121 a (A) 86.203 b (A) 92.644 c (A) 109.030 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 22 Rfree (%) 26.1 Iron Binding Sites: Iron binding site 1 out of 6 in 2qd2 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Iron in the PDB 2qd2. 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: Cys196, A: Ser402, A: Cys403, A: Cys406, A: Asn408, A: Cys411, A: Fes424, A: Hoh630, A: Hoh644, A: Hoh713, conact list: Atom Atom Distance (A) Fe CB A:Cys196 4.87 Fe SG A:Cys196 4.42 Fe CB A:Ser402 4.95 Fe OG A:Ser402 4.99 Fe N A:Cys403 4.78 Fe CB A:Cys403 4.78 Fe SG A:Cys403 4.61 Fe CB A:Cys406 3.37 Fe SG A:Cys406 2.31 Fe C A:Cys406 4.99 Fe CA A:Cys406 4.26 Fe O A:Asn408 4.43 Fe N A:Asn408 4.85 Fe CB A:Asn408 4.38 Fe CB A:Cys411 3.24 Fe SG A:Cys411 2.30 Fe CA A:Cys411 4.65 Fe S1 A:Fes424 2.24 Fe S2 A:Fes424 2.22 Fe FE1 A:Fes424 0.00 Fe FE2 A:Fes424 2.70 Fe O A:Hoh630 4.32 Fe O A:Hoh644 4.27 Fe O A:Hoh713 3.84 interactive model: Iron binding site 2 out of 6 in 2qd2 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Iron in the PDB 2qd2. 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: Cys196, A: Ser402, A: Cys403, A: Cys406, A: Cys411, A: Fes424, A: Hoh616, A: Hoh713, A: Hoh797, conact list: Atom Atom Distance (A) Fe CB A:Cys196 3.38 Fe SG A:Cys196 2.31 Fe CA A:Cys196 4.77 Fe C A:Ser402 4.99 Fe N A:Cys403 3.86 Fe CB A:Cys403 3.40 Fe SG A:Cys403 2.33 Fe CA A:Cys403 4.21 Fe CB A:Cys406 4.54 Fe SG A:Cys406 4.48 Fe SG A:Cys411 4.45 Fe S1 A:Fes424 2.22 Fe S2 A:Fes424 2.26 Fe FE1 A:Fes424 2.70 Fe FE2 A:Fes424 0.00 Fe O A:Hoh616 3.66 Fe O A:Hoh713 3.62 Fe O A:Hoh797 4.25 interactive model: Iron binding site 3 out of 6 in 2qd2 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Iron in the PDB 2qd2. 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: Imd425, A: Bct1, A: Hem602, conact list: Atom Atom Distance (A) Fe N1 A:Imd425 4.47 Fe C5 A:Imd425 4.51 Fe N3 A:Imd425 2.39 Fe C4 A:Imd425 3.37 Fe C2 A:Imd425 3.33 Fe O1 A:Bct1 2.57 Fe O2 A:Bct1 4.70 Fe C A:Bct1 3.64 Fe O3 A:Bct1 4.02 Fe C2D A:Hem602 4.29 Fe NC A:Hem602 1.99 Fe CHB A:Hem602 3.34 Fe CHC A:Hem602 3.42 Fe C3D A:Hem602 4.30 Fe NA A:Hem602 1.98 Fe CHA A:Hem602 3.42 Fe C2A A:Hem602 4.27 Fe C1D A:Hem602 2.98 Fe C4A A:Hem602 3.02 Fe C4B A:Hem602 3.08 Fe C3A A:Hem602 4.23 Fe C4C A:Hem602 2.99 Fe C2B A:Hem602 4.30 Fe C1C A:Hem602 3.02 Fe C2C A:Hem602 4.29 Fe ND A:Hem602 2.00 Fe CHD A:Hem602 3.33 Fe C1B A:Hem602 3.03 Fe NB A:Hem602 2.01 Fe FE A:Hem602 0.00 Fe C3C A:Hem602 4.31 Fe C3B A:Hem602 4.30 Fe C4D A:Hem602 3.05 Fe C1A A:Hem602 3.06 interactive model: Iron binding site 4 out of 6 in 2qd2 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Iron in the PDB 2qd2. 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: Cys196, B: Ser402, B: Cys403, B: Cys406, B: Asn408, B: Cys411, B: Fes424, B: Hoh620, B: Hoh665, B: Hoh713, conact list: Atom Atom Distance (A) Fe CB B:Cys196 4.83 Fe SG B:Cys196 4.40 Fe CB B:Ser402 4.98 Fe OG B:Ser402 4.96 Fe N B:Cys403 4.80 Fe CB B:Cys403 4.75 Fe SG B:Cys403 4.61 Fe CB B:Cys406 3.40 Fe SG B:Cys406 2.34 Fe CA B:Cys406 4.30 Fe O B:Asn408 4.48 Fe N B:Asn408 4.87 Fe CB B:Asn408 4.32 Fe CB B:Cys411 3.23 Fe SG B:Cys411 2.31 Fe CA B:Cys411 4.65 Fe S1 B:Fes424 2.24 Fe S2 B:Fes424 2.23 Fe FE1 B:Fes424 0.00 Fe FE2 B:Fes424 2.69 Fe O B:Hoh620 4.30 Fe O B:Hoh665 4.28 Fe O B:Hoh713 4.41 interactive model: Iron binding site 5 out of 6 in 2qd2 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Iron in the PDB 2qd2. 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: Cys196, B: Arg272, B: Cys403, B: Cys406, B: Cys411, B: Fes424, B: Hoh612, B: Hoh713, conact list: Atom Atom Distance (A) Fe CB B:Cys196 3.38 Fe SG B:Cys196 2.29 Fe CA B:Cys196 4.75 Fe CD B:Arg272 4.77 Fe NH1 B:Arg272 4.95 Fe N B:Cys403 3.92 Fe CB B:Cys403 3.40 Fe SG B:Cys403 2.34 Fe CA B:Cys403 4.25 Fe CB B:Cys406 4.60 Fe SG B:Cys406 4.51 Fe SG B:Cys411 4.45 Fe S1 B:Fes424 2.22 Fe S2 B:Fes424 2.25 Fe FE1 B:Fes424 2.69 Fe FE2 B:Fes424 0.00 Fe O B:Hoh612 3.72 Fe O B:Hoh713 4.03 interactive model: Iron binding site 6 out of 6 in 2qd2 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 6 of Iron in the PDB 2qd2. 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: Imd425, B: Bct2, B: Hem601, conact list: Atom Atom Distance (A) Fe N1 B:Imd425 4.51 Fe C5 B:Imd425 4.51 Fe N3 B:Imd425 2.44 Fe C4 B:Imd425 3.36 Fe C2 B:Imd425 3.41 Fe O1 B:Bct2 2.84 Fe O2 B:Bct2 4.88 Fe C B:Bct2 4.09 Fe O3 B:Bct2 4.87 Fe C2D B:Hem601 4.29 Fe NC B:Hem601 1.99 Fe CHB B:Hem601 3.35 Fe CHC B:Hem601 3.42 Fe C3D B:Hem601 4.30 Fe NA B:Hem601 1.98 Fe CHA B:Hem601 3.41 Fe C2A B:Hem601 4.26 Fe C1D B:Hem601 2.98 Fe C4A B:Hem601 3.02 Fe C4B B:Hem601 3.08 Fe C3A B:Hem601 4.23 Fe C4C B:Hem601 2.99 Fe C2B B:Hem601 4.31 Fe C1C B:Hem601 3.02 Fe C2C B:Hem601 4.29 Fe ND B:Hem601 2.00 Fe CHD B:Hem601 3.34 Fe C1B B:Hem601 3.04 Fe NB B:Hem601 2.01 Fe FE B:Hem601 0.00 Fe C3C B:Hem601 4.32 Fe C3B B:Hem601 4.31 Fe C4D B:Hem601 3.04 Fe C1A B:Hem601 3.06 interactive model: