Iron in the structure of Crystal Structure Of The Succinate Complexed Form Of the Flavocytochrome C Fumarate Reductase of Shewanella Putrefaciens Strain Mr-1 (pdb 1d4d)

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 Iron Binding Sites: 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: