The binding sites of Iron atom in the structure of Direct Observation Of Photolysis-Induced Tertiary Structural Changes in Human Haemoglobin; Crystal Structure of Alpha(Ni)-Beta(Fe-Co) Hemoglobin (Laser Unphotolysed) (pdb code 1j40). This binding sites where shown with 5.0 Angstroms radius around Iron atom. The 1j40 structure was solved by S.ADACHI, S.-Y.PARK, J.R.H.TAME, Y.SHIRO, N.SHIBAYAMA, RIKENSTRUCTURAL GENOMICS/PROTEOMICS INITIATIVE (RSGI), with X-Ray Crystallography technique, brief refinement statistics is given in the table below:
Resolution (A) | 20.0-1.4 | Space group | P1211 | a (A) | 64.708 | b (A) | 94.860 | c (A) | 99.730 | alpha (°) | 90.00 | beta (°) | 101.97 | gamma (°) | 90.00 | Rfactor (%) | 16.5 | Rfree (%) | 19.7 |
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Iron binding site 1 out of 4 in 1j40
|  Click to enlarge |  Click to enlarge | Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Iron in the PDB 1j40. 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, B: Cmo148, | conact list:
Atom | Atom | Distance (A) | Fe | NE2 B:His63 | 4.29 | Fe | CG2 B:Val67 | 4.34 | Fe | NE2 B:His92 | 2.13 | Fe | ND1 B:His92 | 4.20 | Fe | CD2 B:His92 | 3.19 | Fe | CE1 B:His92 | 3.05 | Fe | CG B:His92 | 4.30 | Fe | C2D B:Hem147 | 4.31 | Fe | NC B:Hem147 | 2.04 | Fe | CHB B:Hem147 | 3.46 | Fe | CHC B:Hem147 | 3.40 | Fe | C3D B:Hem147 | 4.32 | Fe | NA B:Hem147 | 2.05 | Fe | CHA B:Hem147 | 3.45 | Fe | C2A B:Hem147 | 4.29 | Fe | C1D B:Hem147 | 3.07 | Fe | C4A B:Hem147 | 3.09 | Fe | C4B B:Hem147 | 3.04 | Fe | C3A B:Hem147 | 4.30 | Fe | C4C B:Hem147 | 3.08 | Fe | C2B B:Hem147 | 4.28 | Fe | C1C B:Hem147 | 3.04 | Fe | C2C B:Hem147 | 4.27 | Fe | ND B:Hem147 | 2.06 | Fe | CHD B:Hem147 | 3.46 | Fe | C1B B:Hem147 | 3.09 | Fe | NB B:Hem147 | 2.04 | Fe | FE B:Hem147 | 0.00 | Fe | C3C B:Hem147 | 4.28 | Fe | C3B B:Hem147 | 4.26 | Fe | C4D B:Hem147 | 3.09 | Fe | C1A B:Hem147 | 3.07 | Fe | O B:Cmo148 | 2.95 | Fe | C B:Cmo148 | 1.71 |
| interactive model:
| Iron binding site 2 out of 4 in 1j40
|  Click to enlarge |  Click to enlarge | Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Iron in the PDB 1j40. 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, D: Cmo148, | conact list:
Atom | Atom | Distance (A) | Fe | NE2 D:His63 | 4.40 | Fe | CG2 D:Val67 | 4.63 | Fe | NE2 D:His92 | 2.13 | Fe | ND1 D:His92 | 4.20 | Fe | CD2 D:His92 | 3.17 | Fe | CE1 D:His92 | 3.05 | Fe | CG D:His92 | 4.28 | Fe | C2D D:Hem147 | 4.28 | Fe | NC D:Hem147 | 1.99 | Fe | CHB D:Hem147 | 3.46 | Fe | CHC D:Hem147 | 3.43 | Fe | C3D D:Hem147 | 4.29 | Fe | NA D:Hem147 | 2.03 | Fe | CHA D:Hem147 | 3.43 | Fe | C2A D:Hem147 | 4.28 | Fe | C1D D:Hem147 | 3.05 | Fe | C4A D:Hem147 | 3.07 | Fe | C4B D:Hem147 | 3.08 | Fe | C3A D:Hem147 | 4.28 | Fe | C4C D:Hem147 | 3.02 | Fe | C2B D:Hem147 | 4.30 | Fe | C1C D:Hem147 | 3.02 | Fe | C2C D:Hem147 | 4.22 | Fe | ND D:Hem147 | 2.03 | Fe | CHD D:Hem147 | 3.41 | Fe | C1B D:Hem147 | 3.09 | Fe | NB D:Hem147 | 2.06 | Fe | FE D:Hem147 | 0.00 | Fe | C3C D:Hem147 | 4.23 | Fe | C3B D:Hem147 | 4.31 | Fe | C4D D:Hem147 | 3.06 | Fe | C1A D:Hem147 | 3.06 | Fe | O D:Cmo148 | 2.81 | Fe | C D:Cmo148 | 1.57 |
| interactive model:
| Iron binding site 3 out of 4 in 1j40
|  Click to enlarge |  Click to enlarge | Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Iron in the PDB 1j40. 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: F: His63, F: Val67, F: His92, F: Hem147, F: Cmo148, | conact list:
Atom | Atom | Distance (A) | Fe | NE2 F:His63 | 4.39 | Fe | CG2 F:Val67 | 4.53 | Fe | NE2 F:His92 | 2.13 | Fe | ND1 F:His92 | 4.20 | Fe | CD2 F:His92 | 3.18 | Fe | CE1 F:His92 | 3.05 | Fe | CG F:His92 | 4.29 | Fe | C2D F:Hem147 | 4.29 | Fe | NC F:Hem147 | 2.00 | Fe | CHB F:Hem147 | 3.47 | Fe | CHC F:Hem147 | 3.41 | Fe | C3D F:Hem147 | 4.31 | Fe | NA F:Hem147 | 2.06 | Fe | CHA F:Hem147 | 3.43 | Fe | C2A F:Hem147 | 4.31 | Fe | C1D F:Hem147 | 3.06 | Fe | C4A F:Hem147 | 3.11 | Fe | C4B F:Hem147 | 3.04 | Fe | C3A F:Hem147 | 4.32 | Fe | C4C F:Hem147 | 3.03 | Fe | C2B F:Hem147 | 4.28 | Fe | C1C F:Hem147 | 3.03 | Fe | C2C F:Hem147 | 4.25 | Fe | ND F:Hem147 | 2.05 | Fe | CHD F:Hem147 | 3.43 | Fe | C1B F:Hem147 | 3.08 | Fe | NB F:Hem147 | 2.04 | Fe | FE F:Hem147 | 0.00 | Fe | C3C F:Hem147 | 4.24 | Fe | C3B F:Hem147 | 4.27 | Fe | C4D F:Hem147 | 3.08 | Fe | C1A F:Hem147 | 3.07 | Fe | O F:Cmo148 | 2.94 | Fe | C F:Cmo148 | 1.72 |
| interactive model:
| Iron binding site 4 out of 4 in 1j40
|  Click to enlarge |  Click to enlarge | Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Iron in the PDB 1j40. 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: H: His63, H: Val67, H: His92, H: Hem147, H: Cmo148, | conact list:
Atom | Atom | Distance (A) | Fe | NE2 H:His63 | 4.40 | Fe | CG2 H:Val67 | 4.56 | Fe | NE2 H:His92 | 2.11 | Fe | ND1 H:His92 | 4.18 | Fe | CD2 H:His92 | 3.16 | Fe | CE1 H:His92 | 3.04 | Fe | CG H:His92 | 4.27 | Fe | C2D H:Hem147 | 4.30 | Fe | NC H:Hem147 | 2.04 | Fe | CHB H:Hem147 | 3.42 | Fe | CHC H:Hem147 | 3.45 | Fe | C3D H:Hem147 | 4.31 | Fe | NA H:Hem147 | 2.04 | Fe | CHA H:Hem147 | 3.45 | Fe | C2A H:Hem147 | 4.29 | Fe | C1D H:Hem147 | 3.05 | Fe | C4A H:Hem147 | 3.06 | Fe | C4B H:Hem147 | 3.08 | Fe | C3A H:Hem147 | 4.28 | Fe | C4C H:Hem147 | 3.06 | Fe | C2B H:Hem147 | 4.28 | Fe | C1C H:Hem147 | 3.07 | Fe | C2C H:Hem147 | 4.27 | Fe | ND H:Hem147 | 2.05 | Fe | CHD H:Hem147 | 3.42 | Fe | C1B H:Hem147 | 3.05 | Fe | NB H:Hem147 | 2.03 | Fe | FE H:Hem147 | 0.00 | Fe | C3C H:Hem147 | 4.28 | Fe | C3B H:Hem147 | 4.28 | Fe | C4D H:Hem147 | 3.08 | Fe | C1A H:Hem147 | 3.07 | Fe | O H:Cmo148 | 2.94 | Fe | C H:Cmo148 | 1.70 |
| interactive model:
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