Iron in the structure of Crystal Structure of Oxidized Cytochrome C6A From Arabidopsis Thaliana (pdb 2dge)

The binding sites of Iron atom in the structure of Crystal Structure of Oxidized Cytochrome C6A From Arabidopsis Thaliana (pdb code 2dge). This binding sites where shown with 5.0 Angstroms radius around Iron atom. The 2dge structure was solved by H.CHIDA, T.YOKOYAMA, F.KAWAI, A.NAKAZAWA, H.AKAZAKI, Y.TAKAYAMA, T.HIRANO, K.SURUGA, T.SATOH, S.YAMADA, R.KAWACHI, S.UNZAI, T.NISHIO, S.-Y.PARK, T.OKU, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 31.5-1.5 Space group P1 a (A) 50.443 b (A) 51.843 c (A) 53.685 alpha (°) 82.51 beta (°) 62.08 gamma (°) 63.26 Rfactor (%) 18.6 Rfree (%) 21.5 Iron Binding Sites: Iron binding site 1 out of 4 in 2dge Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Iron in the PDB 2dge. 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: His90, A: Met130, A: Hem200, conact list: Atom Atom Distance (A) Fe NE2 A:His90 1.97 Fe ND1 A:His90 4.08 Fe CD2 A:His90 2.93 Fe CE1 A:His90 2.99 Fe CG A:His90 4.09 Fe CB A:Met130 4.10 Fe CE A:Met130 3.46 Fe CG A:Met130 3.37 Fe SD A:Met130 2.31 Fe C2D A:Hem200 4.27 Fe NC A:Hem200 1.99 Fe CHB A:Hem200 3.41 Fe CHC A:Hem200 3.44 Fe C3D A:Hem200 4.31 Fe NA A:Hem200 1.99 Fe CHA A:Hem200 3.41 Fe C2A A:Hem200 4.24 Fe C1D A:Hem200 3.05 Fe C4A A:Hem200 3.03 Fe C4B A:Hem200 3.07 Fe C3A A:Hem200 4.24 Fe C4C A:Hem200 3.03 Fe C2B A:Hem200 4.27 Fe C1C A:Hem200 3.03 Fe C2C A:Hem200 4.23 Fe ND A:Hem200 2.05 Fe CHD A:Hem200 3.41 Fe C1B A:Hem200 3.04 Fe NB A:Hem200 2.03 Fe FE A:Hem200 0.00 Fe C3C A:Hem200 4.25 Fe C3B A:Hem200 4.29 Fe C4D A:Hem200 3.06 Fe C1A A:Hem200 3.02 interactive model: Iron binding site 2 out of 4 in 2dge Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Iron in the PDB 2dge. 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: His90, B: Met130, B: Hem200, conact list: Atom Atom Distance (A) Fe NE2 B:His90 1.93 Fe ND1 B:His90 4.04 Fe CD2 B:His90 2.94 Fe CE1 B:His90 2.93 Fe CG B:His90 4.08 Fe CB B:Met130 4.20 Fe CE B:Met130 3.45 Fe CG B:Met130 3.41 Fe SD B:Met130 2.32 Fe C2D B:Hem200 4.26 Fe NC B:Hem200 2.07 Fe CHB B:Hem200 3.44 Fe CHC B:Hem200 3.44 Fe C3D B:Hem200 4.25 Fe NA B:Hem200 2.04 Fe CHA B:Hem200 3.38 Fe C2A B:Hem200 4.28 Fe C1D B:Hem200 3.08 Fe C4A B:Hem200 3.08 Fe C4B B:Hem200 3.05 Fe C3A B:Hem200 4.30 Fe C4C B:Hem200 3.11 Fe C2B B:Hem200 4.26 Fe C1C B:Hem200 3.08 Fe C2C B:Hem200 4.30 Fe ND B:Hem200 2.05 Fe CHD B:Hem200 3.47 Fe C1B B:Hem200 3.05 Fe NB B:Hem200 2.03 Fe FE B:Hem200 0.00 Fe C3C B:Hem200 4.32 Fe C3B B:Hem200 4.27 Fe C4D B:Hem200 3.01 Fe C1A B:Hem200 3.05 interactive model: Iron binding site 3 out of 4 in 2dge Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Iron in the PDB 2dge. 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: His90, C: Met130, C: Hem200, conact list: Atom Atom Distance (A) Fe NE2 C:His90 1.95 Fe ND1 C:His90 4.07 Fe CD2 C:His90 2.93 Fe CE1 C:His90 2.96 Fe CG C:His90 4.09 Fe CB C:Met130 4.05 Fe CE C:Met130 3.40 Fe CG C:Met130 3.37 Fe SD C:Met130 2.30 Fe C2D C:Hem200 4.26 Fe NC C:Hem200 2.05 Fe CHB C:Hem200 3.44 Fe CHC C:Hem200 3.45 Fe C3D C:Hem200 4.25 Fe NA C:Hem200 2.04 Fe CHA C:Hem200 3.39 Fe C2A C:Hem200 4.28 Fe C1D C:Hem200 3.05 Fe C4A C:Hem200 3.09 Fe C4B C:Hem200 3.08 Fe C3A C:Hem200 4.30 Fe C4C C:Hem200 3.08 Fe C2B C:Hem200 4.28 Fe C1C C:Hem200 3.07 Fe C2C C:Hem200 4.28 Fe ND C:Hem200 2.02 Fe CHD C:Hem200 3.44 Fe C1B C:Hem200 3.06 Fe NB C:Hem200 2.03 Fe FE C:Hem200 0.00 Fe C3C C:Hem200 4.30 Fe C3B C:Hem200 4.30 Fe C4D C:Hem200 3.02 Fe C1A C:Hem200 3.04 interactive model: Iron binding site 4 out of 4 in 2dge Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Iron in the PDB 2dge. 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: His90, D: Met130, D: Hem200, conact list: Atom Atom Distance (A) Fe NE2 D:His90 1.93 Fe ND1 D:His90 4.03 Fe CD2 D:His90 2.94 Fe CE1 D:His90 2.92 Fe CG D:His90 4.08 Fe CB D:Met130 4.13 Fe CE D:Met130 3.42 Fe CG D:Met130 3.53 Fe SD D:Met130 2.31 Fe CA D:Met130 4.69 Fe C2D D:Hem200 4.27 Fe NC D:Hem200 2.04 Fe CHB D:Hem200 3.45 Fe CHC D:Hem200 3.44 Fe C3D D:Hem200 4.28 Fe NA D:Hem200 2.03 Fe CHA D:Hem200 3.43 Fe C2A D:Hem200 4.27 Fe C1D D:Hem200 3.05 Fe C4A D:Hem200 3.08 Fe C4B D:Hem200 3.07 Fe C3A D:Hem200 4.28 Fe C4C D:Hem200 3.08 Fe C2B D:Hem200 4.28 Fe C1C D:Hem200 3.07 Fe C2C D:Hem200 4.28 Fe ND D:Hem200 2.04 Fe CHD D:Hem200 3.42 Fe C1B D:Hem200 3.07 Fe NB D:Hem200 2.04 Fe FE D:Hem200 0.00 Fe C3C D:Hem200 4.30 Fe C3B D:Hem200 4.28 Fe C4D D:Hem200 3.06 Fe C1A D:Hem200 3.05 interactive model: