The binding sites of Iron atom in the structure of Crystal Structure of A Zinc Mediated Dimer For the Phenanthroline- Modified Cytochrome CB562 Variant, Mbp-PHEN2 (pdb code 3nmk). This binding sites where shown with 5.0 Angstroms radius around Iron atom. The 3nmk structure was solved by R.J.RADFORD, F.A.TEZCAN, with X-Ray Crystallography technique, brief refinement statistics is given in the table below:
Resolution (A) | 86.1-2.8 | Space group | P65 | a (A) | 99.467 | b (A) | 99.467 | c (A) | 109.544 | alpha (°) | 90.00 | beta (°) | 90.00 | gamma (°) | 120.00 | Rfactor (%) | 18.8 | Rfree (%) | 23.3 |
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Iron binding site 1 out of 4 in 3nmk
|  Click to enlarge |  Click to enlarge | Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Iron in the PDB 3nmk. 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: Met7, A: His102, A: Hem150, | conact list:
Atom | Atom | Distance (A) | Fe | CB A:Met7 | 4.22 | Fe | CE A:Met7 | 3.30 | Fe | CG A:Met7 | 3.47 | Fe | SD A:Met7 | 2.28 | Fe | NE2 A:His102 | 1.94 | Fe | ND1 A:His102 | 3.96 | Fe | CD2 A:His102 | 3.04 | Fe | CE1 A:His102 | 2.81 | Fe | CG A:His102 | 4.10 | Fe | C2D A:Hem150 | 4.38 | Fe | NC A:Hem150 | 1.99 | Fe | CHB A:Hem150 | 3.43 | Fe | CHC A:Hem150 | 3.40 | Fe | C3D A:Hem150 | 4.39 | Fe | NA A:Hem150 | 2.08 | Fe | CHA A:Hem150 | 3.49 | Fe | C2A A:Hem150 | 4.33 | Fe | C1D A:Hem150 | 3.11 | Fe | C4A A:Hem150 | 3.09 | Fe | C4B A:Hem150 | 3.04 | Fe | C3A A:Hem150 | 4.32 | Fe | C4C A:Hem150 | 3.02 | Fe | C2B A:Hem150 | 4.26 | Fe | C1C A:Hem150 | 3.01 | Fe | C2C A:Hem150 | 4.23 | Fe | ND A:Hem150 | 2.13 | Fe | CHD A:Hem150 | 3.42 | Fe | C1B A:Hem150 | 3.05 | Fe | NB A:Hem150 | 2.03 | Fe | FE A:Hem150 | 0.00 | Fe | C3C A:Hem150 | 4.23 | Fe | C3B A:Hem150 | 4.26 | Fe | C4D A:Hem150 | 3.15 | Fe | C1A A:Hem150 | 3.11 |
| interactive model:
| Iron binding site 2 out of 4 in 3nmk
|  Click to enlarge |  Click to enlarge | Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Iron in the PDB 3nmk. 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: Met7, B: His102, B: Hem150, | conact list:
Atom | Atom | Distance (A) | Fe | CB B:Met7 | 4.24 | Fe | CE B:Met7 | 3.35 | Fe | CG B:Met7 | 3.52 | Fe | SD B:Met7 | 2.29 | Fe | NE2 B:His102 | 1.94 | Fe | ND1 B:His102 | 3.98 | Fe | CD2 B:His102 | 3.02 | Fe | CE1 B:His102 | 2.83 | Fe | CG B:His102 | 4.10 | Fe | C2D B:Hem150 | 4.33 | Fe | NC B:Hem150 | 2.03 | Fe | CHB B:Hem150 | 3.43 | Fe | CHC B:Hem150 | 3.46 | Fe | C3D B:Hem150 | 4.33 | Fe | NA B:Hem150 | 2.04 | Fe | CHA B:Hem150 | 3.44 | Fe | C2A B:Hem150 | 4.29 | Fe | C1D B:Hem150 | 3.08 | Fe | C4A B:Hem150 | 3.06 | Fe | C4B B:Hem150 | 3.10 | Fe | C3A B:Hem150 | 4.29 | Fe | C4C B:Hem150 | 3.05 | Fe | C2B B:Hem150 | 4.31 | Fe | C1C B:Hem150 | 3.06 | Fe | C2C B:Hem150 | 4.27 | Fe | ND B:Hem150 | 2.08 | Fe | CHD B:Hem150 | 3.42 | Fe | C1B B:Hem150 | 3.08 | Fe | NB B:Hem150 | 2.08 | Fe | FE B:Hem150 | 0.00 | Fe | C3C B:Hem150 | 4.27 | Fe | C3B B:Hem150 | 4.32 | Fe | C4D B:Hem150 | 3.09 | Fe | C1A B:Hem150 | 3.07 |
| interactive model:
| Iron binding site 3 out of 4 in 3nmk
|  Click to enlarge |  Click to enlarge | Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Iron in the PDB 3nmk. 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: Met7, C: His102, C: Hem150, | conact list:
Atom | Atom | Distance (A) | Fe | CB C:Met7 | 4.23 | Fe | CE C:Met7 | 3.29 | Fe | CG C:Met7 | 3.50 | Fe | SD C:Met7 | 2.28 | Fe | NE2 C:His102 | 1.95 | Fe | ND1 C:His102 | 3.95 | Fe | CD2 C:His102 | 3.03 | Fe | CE1 C:His102 | 2.81 | Fe | CG C:His102 | 4.09 | Fe | C2D C:Hem150 | 4.33 | Fe | NC C:Hem150 | 2.02 | Fe | CHB C:Hem150 | 3.47 | Fe | CHC C:Hem150 | 3.41 | Fe | C3D C:Hem150 | 4.33 | Fe | NA C:Hem150 | 2.06 | Fe | CHA C:Hem150 | 3.43 | Fe | C2A C:Hem150 | 4.31 | Fe | C1D C:Hem150 | 3.09 | Fe | C4A C:Hem150 | 3.10 | Fe | C4B C:Hem150 | 3.07 | Fe | C3A C:Hem150 | 4.31 | Fe | C4C C:Hem150 | 3.05 | Fe | C2B C:Hem150 | 4.31 | Fe | C1C C:Hem150 | 3.04 | Fe | C2C C:Hem150 | 4.26 | Fe | ND C:Hem150 | 2.08 | Fe | CHD C:Hem150 | 3.43 | Fe | C1B C:Hem150 | 3.09 | Fe | NB C:Hem150 | 2.07 | Fe | FE C:Hem150 | 0.00 | Fe | C3C C:Hem150 | 4.26 | Fe | C3B C:Hem150 | 4.29 | Fe | C4D C:Hem150 | 3.09 | Fe | C1A C:Hem150 | 3.08 |
| interactive model:
| Iron binding site 4 out of 4 in 3nmk
|  Click to enlarge |  Click to enlarge | Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Iron in the PDB 3nmk. 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: Met7, D: His102, D: Hem150, | conact list:
Atom | Atom | Distance (A) | Fe | CB D:Met7 | 4.22 | Fe | CE D:Met7 | 3.36 | Fe | CG D:Met7 | 3.49 | Fe | SD D:Met7 | 2.29 | Fe | NE2 D:His102 | 1.93 | Fe | ND1 D:His102 | 3.98 | Fe | CD2 D:His102 | 3.01 | Fe | CE1 D:His102 | 2.84 | Fe | CG D:His102 | 4.09 | Fe | C2D D:Hem150 | 4.36 | Fe | NC D:Hem150 | 2.00 | Fe | CHB D:Hem150 | 3.46 | Fe | CHC D:Hem150 | 3.39 | Fe | C3D D:Hem150 | 4.36 | Fe | NA D:Hem150 | 2.06 | Fe | CHA D:Hem150 | 3.45 | Fe | C2A D:Hem150 | 4.31 | Fe | C1D D:Hem150 | 3.12 | Fe | C4A D:Hem150 | 3.09 | Fe | C4B D:Hem150 | 3.04 | Fe | C3A D:Hem150 | 4.31 | Fe | C4C D:Hem150 | 3.05 | Fe | C2B D:Hem150 | 4.27 | Fe | C1C D:Hem150 | 3.01 | Fe | C2C D:Hem150 | 4.24 | Fe | ND D:Hem150 | 2.10 | Fe | CHD D:Hem150 | 3.45 | Fe | C1B D:Hem150 | 3.07 | Fe | NB D:Hem150 | 2.04 | Fe | FE D:Hem150 | 0.00 | Fe | C3C D:Hem150 | 4.26 | Fe | C3B D:Hem150 | 4.26 | Fe | C4D D:Hem150 | 3.10 | Fe | C1A D:Hem150 | 3.08 |
| interactive model:
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