Iron in the structure of A Novel Iron Centre in the Split-Soret Cytochrome C From Desulfovibrio Desulfuricans Atcc 27774 (pdb 1h21)

The binding sites of Iron atom in the structure of A Novel Iron Centre in the Split-Soret Cytochrome C From Desulfovibrio Desulfuricans Atcc 27774 (pdb code 1h21). This binding sites where shown with 5.0 Angstroms radius around Iron atom. The 1h21 structure was solved by I.A.ABREU, A.I.LOURENCO, A.V.XAVIER, J.LEGALL, A.V.COELHO, P.M.MATIAS, D.M.PINTO, M.A.CARRONDO, M.TEIXEIRA, L.M.SARAIVA, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 20.0-2.5 Space group P212121 a (A) 96.060 b (A) 100.130 c (A) 109.300 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 19.9 Rfree (%) 26.4 Iron Binding Sites: Iron binding site 1 out of 8 in 1h21 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Iron in the PDB 1h21. 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: His213, B: His246, A: Hec1248, conact list: Atom Atom Distance (A) Fe NE2 A:His213 2.00 Fe ND1 A:His213 4.07 Fe CD2 A:His213 3.14 Fe CE1 A:His213 2.88 Fe CG A:His213 4.21 Fe NE2 B:His246 2.02 Fe ND1 B:His246 4.16 Fe CD2 B:His246 3.07 Fe CE1 B:His246 3.01 Fe CG B:His246 4.21 Fe C2D A:Hec1248 4.32 Fe NC A:Hec1248 1.99 Fe CHB A:Hec1248 3.39 Fe CHC A:Hec1248 3.42 Fe C3D A:Hec1248 4.30 Fe NA A:Hec1248 1.94 Fe CHA A:Hec1248 3.39 Fe C2A A:Hec1248 4.24 Fe C1D A:Hec1248 3.07 Fe C4A A:Hec1248 3.03 Fe C4B A:Hec1248 3.06 Fe C3A A:Hec1248 4.29 Fe C4C A:Hec1248 3.05 Fe C2B A:Hec1248 4.28 Fe C1C A:Hec1248 3.05 Fe C2C A:Hec1248 4.29 Fe ND A:Hec1248 2.01 Fe CHD A:Hec1248 3.43 Fe C1B A:Hec1248 3.01 Fe NB A:Hec1248 1.97 Fe FE A:Hec1248 0.00 Fe C3C A:Hec1248 4.28 Fe C3B A:Hec1248 4.34 Fe C4D A:Hec1248 3.05 Fe C1A A:Hec1248 3.00 interactive model: Iron binding site 2 out of 8 in 1h21 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Iron in the PDB 1h21. 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: His233, B: His148, A: Hec1249, conact list: Atom Atom Distance (A) Fe NE2 A:His233 2.04 Fe ND1 A:His233 4.16 Fe CD2 A:His233 3.13 Fe CE1 A:His233 2.99 Fe CG A:His233 4.26 Fe NE2 B:His148 1.97 Fe ND1 B:His148 4.03 Fe CD2 B:His148 3.11 Fe CE1 B:His148 2.85 Fe CG B:His148 4.17 Fe C2D A:Hec1249 4.31 Fe NC A:Hec1249 1.94 Fe CHB A:Hec1249 3.34 Fe CHC A:Hec1249 3.28 Fe C3D A:Hec1249 4.31 Fe NA A:Hec1249 1.94 Fe CHA A:Hec1249 3.41 Fe C2A A:Hec1249 4.25 Fe C1D A:Hec1249 3.05 Fe C4A A:Hec1249 2.97 Fe C4B A:Hec1249 2.93 Fe C3A A:Hec1249 4.21 Fe C4C A:Hec1249 3.01 Fe C2B A:Hec1249 4.17 Fe C1C A:Hec1249 2.96 Fe C2C A:Hec1249 4.19 Fe ND A:Hec1249 1.98 Fe CHD A:Hec1249 3.42 Fe C1B A:Hec1249 2.96 Fe NB A:Hec1249 1.91 Fe FE A:Hec1249 0.00 Fe C3C A:Hec1249 4.21 Fe C3B A:Hec1249 4.20 Fe C4D A:Hec1249 3.05 Fe C1A A:Hec1249 3.00 interactive model: Iron binding site 3 out of 8 in 1h21 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Iron in the PDB 1h21. 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: His246, A: Pro247, B: His213, B: Hec1248, conact list: Atom Atom Distance (A) Fe NE2 A:His246 1.95 Fe ND1 A:His246 4.09 Fe CD2 A:His246 2.91 Fe CE1 A:His246 2.99 Fe CG A:His246 4.08 Fe O A:Pro247 4.93 Fe NE2 B:His213 2.02 Fe ND1 B:His213 4.09 Fe CD2 B:His213 3.15 Fe CE1 B:His213 2.90 Fe CG B:His213 4.23 Fe C2D B:Hec1248 4.30 Fe NC B:Hec1248 1.99 Fe CHB B:Hec1248 3.44 Fe CHC B:Hec1248 3.46 Fe C3D B:Hec1248 4.32 Fe NA B:Hec1248 1.99 Fe CHA B:Hec1248 3.39 Fe C2A B:Hec1248 4.28 Fe C1D B:Hec1248 3.06 Fe C4A B:Hec1248 3.08 Fe C4B B:Hec1248 3.08 Fe C3A B:Hec1248 4.32 Fe C4C B:Hec1248 3.05 Fe C2B B:Hec1248 4.31 Fe C1C B:Hec1248 3.07 Fe C2C B:Hec1248 4.32 Fe ND B:Hec1248 1.99 Fe CHD B:Hec1248 3.41 Fe C1B B:Hec1248 3.05 Fe NB B:Hec1248 2.00 Fe FE B:Hec1248 0.00 Fe C3C B:Hec1248 4.33 Fe C3B B:Hec1248 4.35 Fe C4D B:Hec1248 3.04 Fe C1A B:Hec1248 3.05 interactive model: Iron binding site 4 out of 8 in 1h21 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Iron in the PDB 1h21. 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: His148, B: His233, B: Hec1249, conact list: Atom Atom Distance (A) Fe NE2 A:His148 1.98 Fe ND1 A:His148 4.05 Fe CD2 A:His148 2.99 Fe CE1 A:His148 2.93 Fe CG A:His148 4.10 Fe NE2 B:His233 1.99 Fe ND1 B:His233 4.10 Fe CD2 B:His233 3.09 Fe CE1 B:His233 2.93 Fe CG B:His233 4.20 Fe C2D B:Hec1249 4.16 Fe NC B:Hec1249 1.98 Fe CHB B:Hec1249 3.46 Fe CHC B:Hec1249 3.40 Fe C3D B:Hec1249 4.21 Fe NA B:Hec1249 1.97 Fe CHA B:Hec1249 3.35 Fe C2A B:Hec1249 4.26 Fe C1D B:Hec1249 2.94 Fe C4A B:Hec1249 3.04 Fe C4B B:Hec1249 3.05 Fe C3A B:Hec1249 4.28 Fe C4C B:Hec1249 3.05 Fe C2B B:Hec1249 4.35 Fe C1C B:Hec1249 3.02 Fe C2C B:Hec1249 4.26 Fe ND B:Hec1249 1.90 Fe CHD B:Hec1249 3.36 Fe C1B B:Hec1249 3.09 Fe NB B:Hec1249 2.02 Fe FE B:Hec1249 0.00 Fe C3C B:Hec1249 4.31 Fe C3B B:Hec1249 4.31 Fe C4D B:Hec1249 2.97 Fe C1A B:Hec1249 3.00 interactive model: Iron binding site 5 out of 8 in 1h21 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Iron in the PDB 1h21. 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: His233, D: His148, C: Hec1248, conact list: Atom Atom Distance (A) Fe NE2 C:His233 1.98 Fe ND1 C:His233 4.07 Fe CD2 C:His233 3.12 Fe CE1 C:His233 2.88 Fe CG C:His233 4.20 Fe NE2 D:His148 1.98 Fe ND1 D:His148 4.07 Fe CD2 D:His148 3.07 Fe CE1 D:His148 2.91 Fe CG D:His148 4.16 Fe C2D C:Hec1248 4.19 Fe NC C:Hec1248 2.03 Fe CHB C:Hec1248 3.40 Fe CHC C:Hec1248 3.48 Fe C3D C:Hec1248 4.18 Fe NA C:Hec1248 1.96 Fe CHA C:Hec1248 3.40 Fe C2A C:Hec1248 4.29 Fe C1D C:Hec1248 2.96 Fe C4A C:Hec1248 3.01 Fe C4B C:Hec1248 3.08 Fe C3A C:Hec1248 4.24 Fe C4C C:Hec1248 3.08 Fe C2B C:Hec1248 4.29 Fe C1C C:Hec1248 3.12 Fe C2C C:Hec1248 4.36 Fe ND C:Hec1248 1.91 Fe CHD C:Hec1248 3.39 Fe C1B C:Hec1248 3.03 Fe NB C:Hec1248 1.98 Fe FE C:Hec1248 0.00 Fe C3C C:Hec1248 4.34 Fe C3B C:Hec1248 4.34 Fe C4D C:Hec1248 2.98 Fe C1A C:Hec1248 3.03 interactive model: Iron binding site 6 out of 8 in 1h21 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 6 of Iron in the PDB 1h21. 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: His213, D: His246, D: Hec1248, conact list: Atom Atom Distance (A) Fe NE2 C:His213 1.91 Fe ND1 C:His213 4.00 Fe CD2 C:His213 3.02 Fe CE1 C:His213 2.83 Fe CG C:His213 4.11 Fe NE2 D:His246 1.95 Fe ND1 D:His246 4.10 Fe CD2 D:His246 2.92 Fe CE1 D:His246 2.98 Fe CG D:His246 4.09 Fe C2D D:Hec1248 4.29 Fe NC D:Hec1248 1.91 Fe CHB D:Hec1248 3.49 Fe CHC D:Hec1248 3.42 Fe C3D D:Hec1248 4.37 Fe NA D:Hec1248 2.05 Fe CHA D:Hec1248 3.48 Fe C2A D:Hec1248 4.35 Fe C1D D:Hec1248 3.01 Fe C4A D:Hec1248 3.12 Fe C4B D:Hec1248 3.08 Fe C3A D:Hec1248 4.37 Fe C4C D:Hec1248 2.96 Fe C2B D:Hec1248 4.37 Fe C1C D:Hec1248 2.99 Fe C2C D:Hec1248 4.23 Fe ND D:Hec1248 1.99 Fe CHD D:Hec1248 3.34 Fe C1B D:Hec1248 3.10 Fe NB D:Hec1248 2.01 Fe FE D:Hec1248 0.00 Fe C3C D:Hec1248 4.23 Fe C3B D:Hec1248 4.37 Fe C4D D:Hec1248 3.10 Fe C1A D:Hec1248 3.12 interactive model: Iron binding site 7 out of 8 in 1h21 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 7 of Iron in the PDB 1h21. 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: His246, D: His213, D: Hec1249, conact list: Atom Atom Distance (A) Fe NE2 C:His246 2.01 Fe ND1 C:His246 4.14 Fe CD2 C:His246 3.09 Fe CE1 C:His246 2.97 Fe CG C:His246 4.22 Fe NE2 D:His213 1.99 Fe ND1 D:His213 4.01 Fe CD2 D:His213 3.12 Fe CE1 D:His213 2.83 Fe CG D:His213 4.17 Fe C2D D:Hec1249 4.32 Fe NC D:Hec1249 2.01 Fe CHB D:Hec1249 3.44 Fe CHC D:Hec1249 3.49 Fe C3D D:Hec1249 4.26 Fe NA D:Hec1249 1.96 Fe CHA D:Hec1249 3.31 Fe C2A D:Hec1249 4.22 Fe C1D D:Hec1249 3.09 Fe C4A D:Hec1249 3.06 Fe C4B D:Hec1249 3.10 Fe C3A D:Hec1249 4.30 Fe C4C D:Hec1249 3.09 Fe C2B D:Hec1249 4.31 Fe C1C D:Hec1249 3.09 Fe C2C D:Hec1249 4.30 Fe ND D:Hec1249 1.97 Fe CHD D:Hec1249 3.51 Fe C1B D:Hec1249 3.06 Fe NB D:Hec1249 2.01 Fe FE D:Hec1249 0.00 Fe C3C D:Hec1249 4.31 Fe C3B D:Hec1249 4.35 Fe C4D D:Hec1249 2.97 Fe C1A D:Hec1249 2.97 interactive model: Iron binding site 8 out of 8 in 1h21 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 8 of Iron in the PDB 1h21. 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: His148, D: His233, D: Hec1250, conact list: Atom Atom Distance (A) Fe NE2 C:His148 2.04 Fe ND1 C:His148 4.11 Fe CD2 C:His148 3.12 Fe CE1 C:His148 2.96 Fe CG C:His148 4.21 Fe NE2 D:His233 1.98 Fe ND1 D:His233 4.11 Fe CD2 D:His233 3.07 Fe CE1 D:His233 2.94 Fe CG D:His233 4.20 Fe C2D D:Hec1250 4.21 Fe NC D:Hec1250 1.94 Fe CHB D:Hec1250 3.32 Fe CHC D:Hec1250 3.34 Fe C3D D:Hec1250 4.24 Fe NA D:Hec1250 1.96 Fe CHA D:Hec1250 3.41 Fe C2A D:Hec1250 4.29 Fe C1D D:Hec1250 2.96 Fe C4A D:Hec1250 3.00 Fe C4B D:Hec1250 2.99 Fe C3A D:Hec1250 4.25 Fe C4C D:Hec1250 2.95 Fe C2B D:Hec1250 4.18 Fe C1C D:Hec1250 2.99 Fe C2C D:Hec1250 4.24 Fe ND D:Hec1250 1.96 Fe CHD D:Hec1250 3.29 Fe C1B D:Hec1250 2.93 Fe NB D:Hec1250 1.91 Fe FE D:Hec1250 0.00 Fe C3C D:Hec1250 4.22 Fe C3B D:Hec1250 4.27 Fe C4D D:Hec1250 3.03 Fe C1A D:Hec1250 3.03 interactive model: