Iron in the structure of Crystal Structure of the Dioxygen-Bound Heme Oxygenase From Corynebacterium Diphtheriae (pdb 1v8x)

The binding sites of Iron atom in the structure of Crystal Structure of the Dioxygen-Bound Heme Oxygenase From Corynebacterium Diphtheriae (pdb code 1v8x). This binding sites where shown with 5.0 Angstroms radius around Iron atom. The 1v8x structure was solved by M.UNNO, T.MATSUI, G.C.CHU, M.COUTURE, T.YOSHIDA, D.L.ROUSSEAU, J.S.OLSON, M.IKEDA-SAITO, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 40.0-1.9 Space group P1211 a (A) 54.003 b (A) 62.969 c (A) 107.490 alpha (°) 90.00 beta (°) 100.96 gamma (°) 90.00 Rfactor (%) 15.3 Rfree (%) 19.3 Iron Binding Sites: Iron binding site 1 out of 3 in 1v8x Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Iron in the PDB 1v8x. 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: His20, A: Gly135, A: Ser138, A: Gly139, A: Hem901, A: Oxy5001, A: Hoh5064, conact list: Atom Atom Distance (A) Fe NE2 A:His20 2.20 Fe ND1 A:His20 4.30 Fe CD2 A:His20 3.16 Fe CE1 A:His20 3.19 Fe CG A:His20 4.32 Fe O A:Gly135 4.92 Fe CA A:Gly135 4.60 Fe CB A:Ser138 5.00 Fe N A:Gly139 4.19 Fe CA A:Gly139 4.30 Fe C2D A:Hem901 4.27 Fe NC A:Hem901 2.05 Fe CHB A:Hem901 3.42 Fe CHC A:Hem901 3.40 Fe C3D A:Hem901 4.28 Fe NA A:Hem901 2.03 Fe CHA A:Hem901 3.44 Fe C2A A:Hem901 4.30 Fe C1D A:Hem901 3.06 Fe C4A A:Hem901 3.03 Fe C4B A:Hem901 3.04 Fe C3A A:Hem901 4.25 Fe C4C A:Hem901 3.09 Fe C2B A:Hem901 4.28 Fe C1C A:Hem901 3.06 Fe C2C A:Hem901 4.29 Fe ND A:Hem901 2.03 Fe CHD A:Hem901 3.47 Fe C1B A:Hem901 3.07 Fe NB A:Hem901 2.06 Fe FE A:Hem901 0.00 Fe C3C A:Hem901 4.28 Fe C3B A:Hem901 4.27 Fe C4D A:Hem901 3.04 Fe C1A A:Hem901 3.07 Fe O1 A:Oxy5001 1.85 Fe O2 A:Oxy5001 2.61 Fe O A:Hoh5064 4.94 interactive model: Iron binding site 2 out of 3 in 1v8x Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Iron in the PDB 1v8x. 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: His320, B: Gly435, B: Gly439, B: Hem902, B: Oxy5002, B: Hoh5083, conact list: Atom Atom Distance (A) Fe NE2 B:His320 2.13 Fe ND1 B:His320 4.25 Fe CD2 B:His320 3.05 Fe CE1 B:His320 3.16 Fe CG B:His320 4.23 Fe O B:Gly435 4.82 Fe CA B:Gly435 4.57 Fe N B:Gly439 4.36 Fe CA B:Gly439 4.29 Fe C2D B:Hem902 4.25 Fe NC B:Hem902 2.12 Fe CHB B:Hem902 3.49 Fe CHC B:Hem902 3.37 Fe C3D B:Hem902 4.23 Fe NA B:Hem902 2.05 Fe CHA B:Hem902 3.36 Fe C2A B:Hem902 4.29 Fe C1D B:Hem902 3.03 Fe C4A B:Hem902 3.09 Fe C4B B:Hem902 2.98 Fe C3A B:Hem902 4.29 Fe C4C B:Hem902 3.19 Fe C2B B:Hem902 4.22 Fe C1C B:Hem902 3.09 Fe C2C B:Hem902 4.35 Fe ND B:Hem902 2.00 Fe CHD B:Hem902 3.49 Fe C1B B:Hem902 3.06 Fe NB B:Hem902 2.02 Fe FE B:Hem902 0.00 Fe C3C B:Hem902 4.39 Fe C3B B:Hem902 4.19 Fe C4D B:Hem902 2.98 Fe C1A B:Hem902 3.04 Fe O1 B:Oxy5002 1.97 Fe O2 B:Oxy5002 2.61 Fe O B:Hoh5083 4.59 interactive model: Iron binding site 3 out of 3 in 1v8x Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Iron in the PDB 1v8x. 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: C: His620, C: Gly735, C: Hem903, C: Oxy5003, C: Hoh218, conact list: Atom Atom Distance (A) Fe NE2 C:His620 2.04 Fe ND1 C:His620 4.18 Fe CD2 C:His620 2.90 Fe CE1 C:His620 3.13 Fe CG C:His620 4.10 Fe O C:Gly735 4.70 Fe C C:Gly735 4.96 Fe CA C:Gly735 4.39 Fe C2D C:Hem903 4.23 Fe NC C:Hem903 2.11 Fe CHB C:Hem903 3.38 Fe CHC C:Hem903 3.51 Fe C3D C:Hem903 4.29 Fe NA C:Hem903 2.04 Fe CHA C:Hem903 3.52 Fe C2A C:Hem903 4.29 Fe C1D C:Hem903 2.99 Fe C4A C:Hem903 2.99 Fe C4B C:Hem903 3.09 Fe C3A C:Hem903 4.23 Fe C4C C:Hem903 3.11 Fe C2B C:Hem903 4.25 Fe C1C C:Hem903 3.16 Fe C2C C:Hem903 4.40 Fe ND C:Hem903 2.04 Fe CHD C:Hem903 3.39 Fe C1B C:Hem903 3.04 Fe NB C:Hem903 2.05 Fe FE C:Hem903 0.00 Fe C3C C:Hem903 4.36 Fe C3B C:Hem903 4.28 Fe C4D C:Hem903 3.10 Fe C1A C:Hem903 3.12 Fe O1 C:Oxy5003 1.97 Fe O2 C:Oxy5003 2.48 Fe O C:Hoh218 4.47 interactive model: