Iron in the structure of T-to-T(High) Quaternary Transitions in Human Hemoglobin: BETAD99A Deoxy Low-Salt (10 Test Sets) (pdb 1y5k)

The binding sites of Iron atom in the structure of T-to-T(High) Quaternary Transitions in Human Hemoglobin: BETAD99A Deoxy Low-Salt (10 Test Sets) (pdb code 1y5k). This binding sites where shown with 5.0 Angstroms radius around Iron atom. The 1y5k structure was solved by J.S.KAVANAUGH, P.H.ROGERS, A.ARNONE, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 10.0-2.2 Space group P21212 a (A) 97.460 b (A) 99.880 c (A) 66.000 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 16.1 Rfree (%) 22.7 Iron Binding Sites: Iron binding site 1 out of 4 in 1y5k Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Iron in the PDB 1y5k. 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: Hoh219, conact list: Atom Atom Distance (A) Fe NE2 A:His58 4.70 Fe CE1 A:His58 4.63 Fe NE2 A:His87 2.19 Fe ND1 A:His87 4.22 Fe CD2 A:His87 3.30 Fe CE1 A:His87 3.03 Fe CG A:His87 4.38 Fe CD1 A:Leu91 4.79 Fe C2D A:Hem142 4.35 Fe NC A:Hem142 1.98 Fe CHB A:Hem142 3.43 Fe CHC A:Hem142 3.41 Fe C3D A:Hem142 4.32 Fe NA A:Hem142 2.08 Fe CHA A:Hem142 3.42 Fe C2A A:Hem142 4.29 Fe C1D A:Hem142 3.12 Fe C4A A:Hem142 3.11 Fe C4B A:Hem142 3.07 Fe C3A A:Hem142 4.31 Fe C4C A:Hem142 3.02 Fe C2B A:Hem142 4.23 Fe C1C A:Hem142 2.98 Fe C2C A:Hem142 4.19 Fe ND A:Hem142 2.08 Fe CHD A:Hem142 3.44 Fe C1B A:Hem142 3.04 Fe NB A:Hem142 2.04 Fe FE A:Hem142 0.00 Fe C3C A:Hem142 4.21 Fe C3B A:Hem142 4.29 Fe C4D A:Hem142 3.08 Fe C1A A:Hem142 3.07 Fe O A:Hoh219 3.32 interactive model: Iron binding site 2 out of 4 in 1y5k Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Iron in the PDB 1y5k. 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: Hem147, conact list: Atom Atom Distance (A) Fe NE2 B:His63 4.40 Fe CE1 B:His63 4.85 Fe CG2 B:Val67 4.20 Fe NE2 B:His92 2.11 Fe ND1 B:His92 4.10 Fe CD2 B:His92 3.25 Fe CE1 B:His92 2.90 Fe CG B:His92 4.30 Fe C2D B:Hem147 4.33 Fe NC B:Hem147 2.20 Fe CHB B:Hem147 3.37 Fe CHC B:Hem147 3.45 Fe C3D B:Hem147 4.31 Fe NA B:Hem147 2.05 Fe CHA B:Hem147 3.40 Fe C2A B:Hem147 4.26 Fe C1D B:Hem147 3.11 Fe C4A B:Hem147 3.02 Fe C4B B:Hem147 3.06 Fe C3A B:Hem147 4.24 Fe C4C B:Hem147 3.19 Fe C2B B:Hem147 4.29 Fe C1C B:Hem147 3.15 Fe C2C B:Hem147 4.38 Fe ND B:Hem147 2.07 Fe CHD B:Hem147 3.49 Fe C1B B:Hem147 3.05 Fe NB B:Hem147 2.06 Fe FE B:Hem147 0.00 Fe C3C B:Hem147 4.41 Fe C3B B:Hem147 4.26 Fe C4D B:Hem147 3.06 Fe C1A B:Hem147 3.05 interactive model: Iron binding site 3 out of 4 in 1y5k Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Iron in the PDB 1y5k. 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: Hoh256, conact list: Atom Atom Distance (A) Fe NE2 C:His58 4.85 Fe CE1 C:His58 4.85 Fe NE2 C:His87 2.18 Fe ND1 C:His87 4.16 Fe CD2 C:His87 3.35 Fe CE1 C:His87 2.95 Fe CG C:His87 4.38 Fe CD1 C:Leu91 4.72 Fe C2D C:Hem142 4.37 Fe NC C:Hem142 2.11 Fe CHB C:Hem142 3.47 Fe CHC C:Hem142 3.41 Fe C3D C:Hem142 4.27 Fe NA C:Hem142 2.04 Fe CHA C:Hem142 3.30 Fe C2A C:Hem142 4.25 Fe C1D C:Hem142 3.18 Fe C4A C:Hem142 3.10 Fe C4B C:Hem142 3.06 Fe C3A C:Hem142 4.29 Fe C4C C:Hem142 3.16 Fe C2B C:Hem142 4.26 Fe C1C C:Hem142 3.05 Fe C2C C:Hem142 4.29 Fe ND C:Hem142 2.10 Fe CHD C:Hem142 3.59 Fe C1B C:Hem142 3.10 Fe NB C:Hem142 2.10 Fe FE C:Hem142 0.00 Fe C3C C:Hem142 4.31 Fe C3B C:Hem142 4.26 Fe C4D C:Hem142 3.01 Fe C1A C:Hem142 3.00 Fe O C:Hoh256 3.39 interactive model: Iron binding site 4 out of 4 in 1y5k Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Iron in the PDB 1y5k. 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: Hem147, conact list: Atom Atom Distance (A) Fe NE2 D:His63 4.27 Fe CE1 D:His63 4.45 Fe CG2 D:Val67 3.81 Fe NE2 D:His92 2.33 Fe ND1 D:His92 4.33 Fe CD2 D:His92 3.45 Fe CE1 D:His92 3.13 Fe CG D:His92 4.51 Fe C2D D:Hem147 4.14 Fe NC D:Hem147 2.06 Fe CHB D:Hem147 3.32 Fe CHC D:Hem147 3.49 Fe C3D D:Hem147 4.22 Fe NA D:Hem147 2.12 Fe CHA D:Hem147 3.51 Fe C2A D:Hem147 4.36 Fe C1D D:Hem147 2.88 Fe C4A D:Hem147 3.04 Fe C4B D:Hem147 3.10 Fe C3A D:Hem147 4.30 Fe C4C D:Hem147 3.07 Fe C2B D:Hem147 4.16 Fe C1C D:Hem147 3.09 Fe C2C D:Hem147 4.28 Fe ND D:Hem147 1.92 Fe CHD D:Hem147 3.34 Fe C1B D:Hem147 2.95 Fe NB D:Hem147 2.02 Fe FE D:Hem147 0.00 Fe C3C D:Hem147 4.28 Fe C3B D:Hem147 4.28 Fe C4D D:Hem147 3.04 Fe C1A D:Hem147 3.17 interactive model: