Iron in the structure of Cytoglobin Cavities (pdb 1ury)

The binding sites of Iron atom in the structure of Cytoglobin Cavities (pdb code 1ury). This binding sites where shown with 5.0 Angstroms radius around Iron atom. The 1ury structure was solved by D.DE SANCTIS, S.DEWILDE, A.PESCE, L.MOENS, P.ASCENZI, T.HANKELN, T.BURMESTER, M.BOLOGNESI, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 29.9-2.4 Space group P212121 a (A) 47.848 b (A) 70.524 c (A) 98.728 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 19.702 Rfree (%) 25.442 Iron Binding Sites: Iron binding site 1 out of 4 in 1ury Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Iron in the PDB 1ury. 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: His81, A: Val85, A: His113, A: Hem700, conact list: Atom Atom Distance (A) Fe NE2 A:His81 2.10 Fe ND1 A:His81 3.83 Fe CD2 A:His81 3.27 Fe CE1 A:His81 2.65 Fe CG A:His81 4.16 Fe CG2 A:Val85 4.72 Fe NE2 A:His113 2.13 Fe ND1 A:His113 4.03 Fe CD2 A:His113 3.24 Fe CE1 A:His113 2.88 Fe CG A:His113 4.23 Fe C2D A:Hem700 4.39 Fe NC A:Hem700 2.07 Fe CHB A:Hem700 3.35 Fe CHC A:Hem700 3.46 Fe C3D A:Hem700 4.38 Fe NA A:Hem700 2.02 Fe CHA A:Hem700 3.49 Fe C2A A:Hem700 4.25 Fe C1D A:Hem700 3.14 Fe C4A A:Hem700 3.00 Fe C4B A:Hem700 3.04 Fe C3A A:Hem700 4.23 Fe C4C A:Hem700 3.09 Fe C2B A:Hem700 4.23 Fe C1C A:Hem700 3.10 Fe C2C A:Hem700 4.33 Fe ND A:Hem700 2.16 Fe CHD A:Hem700 3.47 Fe C1B A:Hem700 2.99 Fe NB A:Hem700 1.98 Fe FE A:Hem700 0.00 Fe C3C A:Hem700 4.32 Fe C3B A:Hem700 4.25 Fe C4D A:Hem700 3.16 Fe C1A A:Hem700 3.07 interactive model: Iron binding site 2 out of 4 in 1ury Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Iron in the PDB 1ury. 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: Lys125, A: Arg155, A: Tyr159, B: Ser55, A: Fc61175, conact list: Atom Atom Distance (A) Fe CD A:Lys125 4.26 Fe NZ A:Lys125 4.85 Fe CD A:Arg155 4.58 Fe CZ A:Arg155 4.95 Fe NE A:Arg155 4.47 Fe CD2 A:Tyr159 4.69 Fe N B:Ser55 4.85 Fe CB B:Ser55 4.45 Fe OG B:Ser55 4.73 Fe N24 A:Fc61175 3.01 Fe N23 A:Fc61175 2.99 Fe N22 A:Fc61175 2.99 Fe C24 A:Fc61175 1.83 Fe FE2 A:Fc61175 0.00 Fe C11 A:Fc61175 1.83 Fe N11 A:Fc61175 2.98 Fe C23 A:Fc61175 1.83 Fe N25 A:Fc61175 3.00 Fe C22 A:Fc61175 1.83 Fe C26 A:Fc61175 1.83 Fe C21 A:Fc61175 1.83 Fe N21 A:Fc61175 3.01 interactive model: Iron binding site 3 out of 4 in 1ury Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Iron in the PDB 1ury. 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: His81, B: Val85, B: His113, B: His117, B: Hem700, conact list: Atom Atom Distance (A) Fe NE2 B:His81 2.11 Fe ND1 B:His81 4.04 Fe CD2 B:His81 3.25 Fe CE1 B:His81 2.86 Fe CG B:His81 4.25 Fe CG2 B:Val85 4.68 Fe NE2 B:His113 1.98 Fe ND1 B:His113 4.05 Fe CD2 B:His113 3.02 Fe CE1 B:His113 2.93 Fe CG B:His113 4.13 Fe CD2 B:His117 4.92 Fe C2D B:Hem700 4.25 Fe NC B:Hem700 1.92 Fe CHB B:Hem700 3.41 Fe CHC B:Hem700 3.41 Fe C3D B:Hem700 4.29 Fe NA B:Hem700 2.01 Fe CHA B:Hem700 3.46 Fe C2A B:Hem700 4.27 Fe C1D B:Hem700 2.98 Fe C4A B:Hem700 3.04 Fe C4B B:Hem700 3.06 Fe C3A B:Hem700 4.27 Fe C4C B:Hem700 2.93 Fe C2B B:Hem700 4.30 Fe C1C B:Hem700 2.99 Fe C2C B:Hem700 4.18 Fe ND B:Hem700 2.02 Fe CHD B:Hem700 3.30 Fe C1B B:Hem700 3.06 Fe NB B:Hem700 2.03 Fe FE B:Hem700 0.00 Fe C3C B:Hem700 4.16 Fe C3B B:Hem700 4.30 Fe C4D B:Hem700 3.09 Fe C1A B:Hem700 3.05 interactive model: Iron binding site 4 out of 4 in 1ury Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Iron in the PDB 1ury. 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: Pro54, A: Ser55, B: Lys125, B: Arg155, B: Tyr159, B: Fc61175, conact list: Atom Atom Distance (A) Fe CG A:Pro54 4.92 Fe N A:Ser55 4.80 Fe CB A:Ser55 4.37 Fe OG A:Ser55 4.61 Fe CE B:Lys125 4.31 Fe CD B:Arg155 4.56 Fe CZ B:Arg155 4.82 Fe NE B:Arg155 4.33 Fe CD1 B:Tyr159 4.52 Fe N24 B:Fc61175 3.02 Fe N23 B:Fc61175 3.00 Fe N22 B:Fc61175 3.01 Fe C24 B:Fc61175 1.84 Fe FE2 B:Fc61175 0.00 Fe C11 B:Fc61175 1.83 Fe N11 B:Fc61175 3.01 Fe C23 B:Fc61175 1.83 Fe N25 B:Fc61175 2.99 Fe C22 B:Fc61175 1.83 Fe C26 B:Fc61175 1.83 Fe C21 B:Fc61175 1.83 Fe N21 B:Fc61175 3.00 interactive model: