The binding sites of Iron atom in the structure of Crystal Structure Of The Succinate Complexed Form Of the Flavocytochrome C Fumarate Reductase of Shewanella Putrefaciens Strain Mr-1 (pdb code 1d4d). This binding sites where shown with 5.0 Angstroms radius around Iron atom. The 1d4d structure was solved by D.LEYS, A.S.TSAPIN, T.E.MEYER, M.A.CUSANOVICH, J.J.VAN BEEUMEN, with X-Ray Crystallography technique, brief refinement statistics is given in the table below:
Resolution (A) | 8.5-2.5 | Space group | P43212 | a (A) | 72.863 | b (A) | 72.863 | c (A) | 216.469 | alpha (°) | 90.00 | beta (°) | 90.00 | gamma (°) | 90.00 | Rfactor (%) | 23.9 | Rfree (%) | 30.5 |
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Iron binding site 1 out of 4 in 1d4d
|  Click to enlarge |  Click to enlarge | Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Iron in the PDB 1d4d. 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: His63, A: His88, A: Hem601, | conact list:
Atom | Atom | Distance (A) | Fe | NE2 A:His63 | 1.94 | Fe | ND1 A:His63 | 3.91 | Fe | CD2 A:His63 | 3.12 | Fe | CE1 A:His63 | 2.69 | Fe | CG A:His63 | 4.12 | Fe | NE2 A:His88 | 1.94 | Fe | ND1 A:His88 | 3.86 | Fe | CD2 A:His88 | 3.14 | Fe | CE1 A:His88 | 2.67 | Fe | CG A:His88 | 4.11 | Fe | C2D A:Hem601 | 4.22 | Fe | NC A:Hem601 | 2.00 | Fe | CHB A:Hem601 | 3.40 | Fe | CHC A:Hem601 | 3.40 | Fe | C3D A:Hem601 | 4.22 | Fe | NA A:Hem601 | 2.02 | Fe | CHA A:Hem601 | 3.39 | Fe | C2A A:Hem601 | 4.28 | Fe | C1D A:Hem601 | 3.02 | Fe | C4A A:Hem601 | 3.03 | Fe | C4B A:Hem601 | 3.06 | Fe | C3A A:Hem601 | 4.27 | Fe | C4C A:Hem601 | 3.04 | Fe | C2B A:Hem601 | 4.27 | Fe | C1C A:Hem601 | 3.02 | Fe | C2C A:Hem601 | 4.24 | Fe | ND A:Hem601 | 1.99 | Fe | CHD A:Hem601 | 3.38 | Fe | C1B A:Hem601 | 3.04 | Fe | NB A:Hem601 | 2.01 | Fe | FE A:Hem601 | 0.00 | Fe | C3C A:Hem601 | 4.22 | Fe | C3B A:Hem601 | 4.26 | Fe | C4D A:Hem601 | 3.01 | Fe | C1A A:Hem601 | 3.07 |
| interactive model:
| Iron binding site 2 out of 4 in 1d4d
|  Click to enlarge |  Click to enlarge | Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Iron in the PDB 1d4d. 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: His60, A: His74, A: Hem602, | conact list:
Atom | Atom | Distance (A) | Fe | NE2 A:His60 | 2.04 | Fe | ND1 A:His60 | 4.15 | Fe | CD2 A:His60 | 2.92 | Fe | CE1 A:His60 | 3.08 | Fe | CG A:His60 | 4.11 | Fe | NE2 A:His74 | 2.04 | Fe | ND1 A:His74 | 4.18 | Fe | CD2 A:His74 | 2.84 | Fe | CE1 A:His74 | 3.16 | Fe | CG A:His74 | 4.07 | Fe | C2D A:Hem602 | 4.23 | Fe | NC A:Hem602 | 2.00 | Fe | CHB A:Hem602 | 3.42 | Fe | CHC A:Hem602 | 3.42 | Fe | C3D A:Hem602 | 4.22 | Fe | NA A:Hem602 | 2.01 | Fe | CHA A:Hem602 | 3.36 | Fe | C2A A:Hem602 | 4.26 | Fe | C1D A:Hem602 | 3.02 | Fe | C4A A:Hem602 | 3.06 | Fe | C4B A:Hem602 | 3.04 | Fe | C3A A:Hem602 | 4.28 | Fe | C4C A:Hem602 | 3.04 | Fe | C2B A:Hem602 | 4.26 | Fe | C1C A:Hem602 | 3.03 | Fe | C2C A:Hem602 | 4.25 | Fe | ND A:Hem602 | 1.97 | Fe | CHD A:Hem602 | 3.39 | Fe | C1B A:Hem602 | 3.04 | Fe | NB A:Hem602 | 2.02 | Fe | FE A:Hem602 | 0.00 | Fe | C3C A:Hem602 | 4.24 | Fe | C3B A:Hem602 | 4.24 | Fe | C4D A:Hem602 | 2.99 | Fe | C1A A:Hem602 | 3.05 |
| interactive model:
| Iron binding site 3 out of 4 in 1d4d
|  Click to enlarge |  Click to enlarge | Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Iron in the PDB 1d4d. 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: His19, A: His77, A: Hem603, | conact list:
Atom | Atom | Distance (A) | Fe | NE2 A:His19 | 1.89 | Fe | ND1 A:His19 | 3.98 | Fe | CD2 A:His19 | 2.86 | Fe | CE1 A:His19 | 2.88 | Fe | CG A:His19 | 3.97 | Fe | NE2 A:His77 | 2.00 | Fe | ND1 A:His77 | 4.05 | Fe | CD2 A:His77 | 3.01 | Fe | CE1 A:His77 | 2.93 | Fe | CG A:His77 | 4.10 | Fe | C2D A:Hem603 | 4.25 | Fe | NC A:Hem603 | 2.01 | Fe | CHB A:Hem603 | 3.41 | Fe | CHC A:Hem603 | 3.46 | Fe | C3D A:Hem603 | 4.24 | Fe | NA A:Hem603 | 2.01 | Fe | CHA A:Hem603 | 3.38 | Fe | C2A A:Hem603 | 4.19 | Fe | C1D A:Hem603 | 3.04 | Fe | C4A A:Hem603 | 2.99 | Fe | C4B A:Hem603 | 3.07 | Fe | C3A A:Hem603 | 4.17 | Fe | C4C A:Hem603 | 3.04 | Fe | C2B A:Hem603 | 4.28 | Fe | C1C A:Hem603 | 3.05 | Fe | C2C A:Hem603 | 4.27 | Fe | ND A:Hem603 | 2.00 | Fe | CHD A:Hem603 | 3.39 | Fe | C1B A:Hem603 | 3.04 | Fe | NB A:Hem603 | 2.01 | Fe | FE A:Hem603 | 0.00 | Fe | C3C A:Hem603 | 4.26 | Fe | C3B A:Hem603 | 4.28 | Fe | C4D A:Hem603 | 3.03 | Fe | C1A A:Hem603 | 3.03 |
| interactive model:
| Iron binding site 4 out of 4 in 1d4d
|  Click to enlarge |  Click to enlarge | Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Iron in the PDB 1d4d. 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: Leu5, A: His9, A: His42, A: Hem604, | conact list:
Atom | Atom | Distance (A) | Fe | CD2 A:Leu5 | 4.97 | Fe | NE2 A:His9 | 2.05 | Fe | ND1 A:His9 | 3.97 | Fe | CD2 A:His9 | 3.23 | Fe | CE1 A:His9 | 2.75 | Fe | CG A:His9 | 4.21 | Fe | NE2 A:His42 | 2.09 | Fe | ND1 A:His42 | 4.13 | Fe | CD2 A:His42 | 3.16 | Fe | CE1 A:His42 | 2.98 | Fe | CG A:His42 | 4.25 | Fe | C2D A:Hem604 | 4.29 | Fe | NC A:Hem604 | 1.99 | Fe | CHB A:Hem604 | 3.39 | Fe | CHC A:Hem604 | 3.39 | Fe | C3D A:Hem604 | 4.32 | Fe | NA A:Hem604 | 1.98 | Fe | CHA A:Hem604 | 3.38 | Fe | C2A A:Hem604 | 4.22 | Fe | C1D A:Hem604 | 3.06 | Fe | C4A A:Hem604 | 3.01 | Fe | C4B A:Hem604 | 3.08 | Fe | C3A A:Hem604 | 4.22 | Fe | C4C A:Hem604 | 3.02 | Fe | C2B A:Hem604 | 4.27 | Fe | C1C A:Hem604 | 3.00 | Fe | C2C A:Hem604 | 4.21 | Fe | ND A:Hem604 | 2.03 | Fe | CHD A:Hem604 | 3.39 | Fe | C1B A:Hem604 | 3.05 | Fe | NB A:Hem604 | 2.03 | Fe | FE A:Hem604 | 0.00 | Fe | C3C A:Hem604 | 4.22 | Fe | C3B A:Hem604 | 4.27 | Fe | C4D A:Hem604 | 3.07 | Fe | C1A A:Hem604 | 2.99 |
| interactive model:
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