Iron in the structure of Crystal Structure of Deoxy Hemoglobin From Trematomus Bernacchii At pH 8.4 (pdb 2h8d)

The binding sites of Iron atom in the structure of Crystal Structure of Deoxy Hemoglobin From Trematomus Bernacchii At pH 8.4 (pdb code 2h8d). This binding sites where shown with 5.0 Angstroms radius around Iron atom. The 2h8d structure was solved by L.MAZZARELLA, A.VERGARA, L.VITAGLIANO, A.MERLINO, G.BONOMI, S.SCALA, C.VERDE, G.DI PRISCO, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 20.0-1.8 Space group P1211 a (A) 61.800 b (A) 94.630 c (A) 61.860 alpha (°) 90.00 beta (°) 90.19 gamma (°) 90.00 Rfactor (%) 18 Rfree (%) 22.4 Iron Binding Sites: Iron binding site 1 out of 4 in 2h8d Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Iron in the PDB 2h8d. 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: His59, A: Val63, A: His88, A: Leu92, A: Hem200, conact list: Atom Atom Distance (A) Fe NE2 A:His59 4.16 Fe CE1 A:His59 4.46 Fe CG2 A:Val63 4.51 Fe NE2 A:His88 2.16 Fe ND1 A:His88 4.19 Fe CD2 A:His88 3.26 Fe CE1 A:His88 3.00 Fe CG A:His88 4.35 Fe CD1 A:Leu92 4.85 Fe C2D A:Hem200 4.30 Fe NC A:Hem200 2.09 Fe CHB A:Hem200 3.40 Fe CHC A:Hem200 3.48 Fe C3D A:Hem200 4.29 Fe NA A:Hem200 2.05 Fe CHA A:Hem200 3.43 Fe C2A A:Hem200 4.29 Fe C1D A:Hem200 3.09 Fe C4A A:Hem200 3.08 Fe C4B A:Hem200 3.06 Fe C3A A:Hem200 4.30 Fe C4C A:Hem200 3.12 Fe C2B A:Hem200 4.26 Fe C1C A:Hem200 3.10 Fe C2C A:Hem200 4.35 Fe ND A:Hem200 2.03 Fe CHD A:Hem200 3.46 Fe C1B A:Hem200 3.03 Fe NB A:Hem200 1.99 Fe FE A:Hem200 0.00 Fe C3C A:Hem200 4.36 Fe C3B A:Hem200 4.27 Fe C4D A:Hem200 3.06 Fe C1A A:Hem200 3.08 interactive model: Iron binding site 2 out of 4 in 2h8d Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Iron in the PDB 2h8d. 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: His63, B: Val67, B: His92, B: Hem400, conact list: Atom Atom Distance (A) Fe NE2 B:His63 4.14 Fe CE1 B:His63 4.83 Fe CG2 B:Val67 4.06 Fe NE2 B:His92 2.24 Fe ND1 B:His92 4.31 Fe CD2 B:His92 3.24 Fe CE1 B:His92 3.18 Fe CG B:His92 4.38 Fe C2D B:Hem400 4.28 Fe NC B:Hem400 2.01 Fe CHB B:Hem400 3.42 Fe CHC B:Hem400 3.37 Fe C3D B:Hem400 4.30 Fe NA B:Hem400 2.09 Fe CHA B:Hem400 3.49 Fe C2A B:Hem400 4.36 Fe C1D B:Hem400 3.07 Fe C4A B:Hem400 3.09 Fe C4B B:Hem400 2.98 Fe C3A B:Hem400 4.34 Fe C4C B:Hem400 3.05 Fe C2B B:Hem400 4.23 Fe C1C B:Hem400 3.03 Fe C2C B:Hem400 4.26 Fe ND B:Hem400 2.03 Fe CHD B:Hem400 3.42 Fe C1B B:Hem400 3.03 Fe NB B:Hem400 1.95 Fe FE B:Hem400 0.00 Fe C3C B:Hem400 4.27 Fe C3B B:Hem400 4.22 Fe C4D B:Hem400 3.11 Fe C1A B:Hem400 3.15 interactive model: Iron binding site 3 out of 4 in 2h8d Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Iron in the PDB 2h8d. 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: His59, C: Val63, C: His88, C: Leu92, C: Hem600, conact list: Atom Atom Distance (A) Fe NE2 C:His59 4.16 Fe CE1 C:His59 4.36 Fe CG2 C:Val63 4.69 Fe NE2 C:His88 2.25 Fe ND1 C:His88 4.33 Fe CD2 C:His88 3.29 Fe CE1 C:His88 3.18 Fe CG C:His88 4.42 Fe CD1 C:Leu92 4.68 Fe C2D C:Hem600 4.17 Fe NC C:Hem600 1.98 Fe CHB C:Hem600 3.55 Fe CHC C:Hem600 3.49 Fe C3D C:Hem600 4.18 Fe NA C:Hem600 2.12 Fe CHA C:Hem600 3.43 Fe C2A C:Hem600 4.37 Fe C1D C:Hem600 2.95 Fe C4A C:Hem600 3.19 Fe C4B C:Hem600 3.13 Fe C3A C:Hem600 4.40 Fe C4C C:Hem600 2.97 Fe C2B C:Hem600 4.39 Fe C1C C:Hem600 3.03 Fe C2C C:Hem600 4.26 Fe ND C:Hem600 1.92 Fe CHD C:Hem600 3.31 Fe C1B C:Hem600 3.20 Fe NB C:Hem600 2.12 Fe FE C:Hem600 0.00 Fe C3C C:Hem600 4.22 Fe C3B C:Hem600 4.39 Fe C4D C:Hem600 2.97 Fe C1A C:Hem600 3.12 interactive model: Iron binding site 4 out of 4 in 2h8d Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Iron in the PDB 2h8d. 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: D: His63, D: Val67, D: His92, D: Hem800, conact list: Atom Atom Distance (A) Fe NE2 D:His63 3.94 Fe CE1 D:His63 4.46 Fe CG2 D:Val67 3.98 Fe NE2 D:His92 2.26 Fe ND1 D:His92 4.33 Fe CD2 D:His92 3.32 Fe CE1 D:His92 3.17 Fe CG D:His92 4.44 Fe C2D D:Hem800 4.17 Fe NC D:Hem800 2.01 Fe CHB D:Hem800 3.47 Fe CHC D:Hem800 3.47 Fe C3D D:Hem800 4.17 Fe NA D:Hem800 2.14 Fe CHA D:Hem800 3.37 Fe C2A D:Hem800 4.34 Fe C1D D:Hem800 2.96 Fe C4A D:Hem800 3.12 Fe C4B D:Hem800 3.10 Fe C3A D:Hem800 4.35 Fe C4C D:Hem800 3.00 Fe C2B D:Hem800 4.36 Fe C1C D:Hem800 3.08 Fe C2C D:Hem800 4.28 Fe ND D:Hem800 1.91 Fe CHD D:Hem800 3.34 Fe C1B D:Hem800 3.15 Fe NB D:Hem800 2.10 Fe FE D:Hem800 0.00 Fe C3C D:Hem800 4.26 Fe C3B D:Hem800 4.36 Fe C4D D:Hem800 2.96 Fe C1A D:Hem800 3.10 interactive model: