Iron in the structure of 1.25A Resolution Crystal Structure of Human Hemoglobin in the Deoxy Form (pdb 2dn2)

The binding sites of Iron atom in the structure of 1.25A Resolution Crystal Structure of Human Hemoglobin in the Deoxy Form (pdb code 2dn2). This binding sites where shown with 5.0 Angstroms radius around Iron atom. The 2dn2 structure was solved by S.-Y.PARK, T.YOKOYAMA, N.SHIBAYAMA, Y.SHIRO, J.R.TAME, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 20.0-1.2 Space group P1211 a (A) 63.105 b (A) 82.914 c (A) 53.650 alpha (°) 90.00 beta (°) 99.29 gamma (°) 90.00 Rfactor (%) 17.9 Rfree (%) n/a Iron Binding Sites: Iron binding site 1 out of 4 in 2dn2 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Iron in the PDB 2dn2. 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: His58, A: His87, A: Leu91, A: Hem142, A: Hoh156, conact list: Atom Atom Distance (A) Fe NE2 A:His58 4.50 Fe CE1 A:His58 4.60 Fe NE2 A:His87 2.20 Fe ND1 A:His87 4.27 Fe CD2 A:His87 3.31 Fe CE1 A:His87 3.10 Fe CG A:His87 4.41 Fe CD1 A:Leu91 4.48 Fe C2D A:Hem142 4.37 Fe NC A:Hem142 2.12 Fe CHB A:Hem142 3.51 Fe CHC A:Hem142 3.48 Fe C3D A:Hem142 4.39 Fe NA A:Hem142 2.11 Fe CHA A:Hem142 3.41 Fe C2A A:Hem142 4.33 Fe C1D A:Hem142 3.14 Fe C4A A:Hem142 3.12 Fe C4B A:Hem142 3.19 Fe C3A A:Hem142 4.40 Fe C4C A:Hem142 3.13 Fe C2B A:Hem142 4.38 Fe C1C A:Hem142 3.17 Fe C2C A:Hem142 4.36 Fe ND A:Hem142 2.08 Fe CHD A:Hem142 3.50 Fe C1B A:Hem142 3.16 Fe NB A:Hem142 2.12 Fe FE A:Hem142 0.00 Fe C3C A:Hem142 4.36 Fe C3B A:Hem142 4.38 Fe C4D A:Hem142 3.14 Fe C1A A:Hem142 3.19 Fe O A:Hoh156 3.30 interactive model: Iron binding site 2 out of 4 in 2dn2 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Iron in the PDB 2dn2. 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: Leu96, B: Hem147, conact list: Atom Atom Distance (A) Fe NE2 B:His63 4.21 Fe CE1 B:His63 4.50 Fe CG2 B:Val67 4.16 Fe NE2 B:His92 2.19 Fe ND1 B:His92 4.25 Fe CD2 B:His92 3.27 Fe CE1 B:His92 3.07 Fe CG B:His92 4.37 Fe CD1 B:Leu96 4.97 Fe C2D B:Hem147 4.29 Fe NC B:Hem147 2.09 Fe CHB B:Hem147 3.55 Fe CHC B:Hem147 3.52 Fe C3D B:Hem147 4.27 Fe NA B:Hem147 2.10 Fe CHA B:Hem147 3.41 Fe C2A B:Hem147 4.29 Fe C1D B:Hem147 3.11 Fe C4A B:Hem147 3.08 Fe C4B B:Hem147 3.19 Fe C3A B:Hem147 4.36 Fe C4C B:Hem147 3.15 Fe C2B B:Hem147 4.38 Fe C1C B:Hem147 3.14 Fe C2C B:Hem147 4.27 Fe ND B:Hem147 2.08 Fe CHD B:Hem147 3.43 Fe C1B B:Hem147 3.12 Fe NB B:Hem147 2.12 Fe FE B:Hem147 0.00 Fe C3C B:Hem147 4.34 Fe C3B B:Hem147 4.35 Fe C4D B:Hem147 3.18 Fe C1A B:Hem147 3.12 interactive model: Iron binding site 3 out of 4 in 2dn2 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Iron in the PDB 2dn2. 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: His58, C: His87, C: Leu91, C: Hem142, C: Hoh174, conact list: Atom Atom Distance (A) Fe NE2 C:His58 4.39 Fe CE1 C:His58 4.57 Fe NE2 C:His87 2.21 Fe ND1 C:His87 4.25 Fe CD2 C:His87 3.29 Fe CE1 C:His87 3.08 Fe CG C:His87 4.39 Fe CD1 C:Leu91 4.57 Fe C2D C:Hem142 4.33 Fe NC C:Hem142 2.10 Fe CHB C:Hem142 3.45 Fe CHC C:Hem142 3.50 Fe C3D C:Hem142 4.30 Fe NA C:Hem142 2.08 Fe CHA C:Hem142 3.46 Fe C2A C:Hem142 4.31 Fe C1D C:Hem142 3.15 Fe C4A C:Hem142 3.11 Fe C4B C:Hem142 3.17 Fe C3A C:Hem142 4.31 Fe C4C C:Hem142 3.12 Fe C2B C:Hem142 4.38 Fe C1C C:Hem142 3.11 Fe C2C C:Hem142 4.28 Fe ND C:Hem142 2.02 Fe CHD C:Hem142 3.43 Fe C1B C:Hem142 3.15 Fe NB C:Hem142 2.10 Fe FE C:Hem142 0.00 Fe C3C C:Hem142 4.29 Fe C3B C:Hem142 4.30 Fe C4D C:Hem142 3.14 Fe C1A C:Hem142 3.09 Fe O C:Hoh174 3.48 interactive model: Iron binding site 4 out of 4 in 2dn2 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Iron in the PDB 2dn2. 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: Leu96, D: Hem147, conact list: Atom Atom Distance (A) Fe NE2 D:His63 4.28 Fe CE1 D:His63 4.79 Fe CG2 D:Val67 4.27 Fe NE2 D:His92 2.16 Fe ND1 D:His92 4.23 Fe CD2 D:His92 3.24 Fe CE1 D:His92 3.05 Fe CG D:His92 4.35 Fe CD1 D:Leu96 4.93 Fe C2D D:Hem147 4.31 Fe NC D:Hem147 2.07 Fe CHB D:Hem147 3.51 Fe CHC D:Hem147 3.46 Fe C3D D:Hem147 4.27 Fe NA D:Hem147 2.06 Fe CHA D:Hem147 3.42 Fe C2A D:Hem147 4.33 Fe C1D D:Hem147 3.05 Fe C4A D:Hem147 3.03 Fe C4B D:Hem147 3.06 Fe C3A D:Hem147 4.36 Fe C4C D:Hem147 3.14 Fe C2B D:Hem147 4.37 Fe C1C D:Hem147 3.10 Fe C2C D:Hem147 4.35 Fe ND D:Hem147 2.08 Fe CHD D:Hem147 3.51 Fe C1B D:Hem147 3.06 Fe NB D:Hem147 2.04 Fe FE D:Hem147 0.00 Fe C3C D:Hem147 4.34 Fe C3B D:Hem147 4.33 Fe C4D D:Hem147 3.04 Fe C1A D:Hem147 3.09 interactive model: