Iron in the structure of Photosynthetic Reaction Center From Rhodopseudomonas Viridis - His L168 Phe Mutant (Terbutryn Complex) (pdb 1dxr)

The binding sites of Iron atom in the structure of Photosynthetic Reaction Center From Rhodopseudomonas Viridis - His L168 Phe Mutant (Terbutryn Complex) (pdb code 1dxr). This binding sites where shown with 5.0 Angstroms radius around Iron atom. The 1dxr structure was solved by C.R.D.LANCASTER, M.BIBIKOVA, P.SABATINO, D.OESTERHELT, H.MICHEL, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 10.0-2.0 Space group P43212 a (A) 223.500 b (A) 223.500 c (A) 113.600 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 19.4 Rfree (%) 21.8 Iron Binding Sites: Iron binding site 1 out of 5 in 1dxr Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Iron in the PDB 1dxr. 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: Met74, C: His91, C: Hec401, conact list: Atom Atom Distance (A) Fe CB C:Met74 4.26 Fe CE C:Met74 3.48 Fe CG C:Met74 3.52 Fe SD C:Met74 2.21 Fe NE2 C:His91 1.94 Fe ND1 C:His91 4.05 Fe CD2 C:His91 3.01 Fe CE1 C:His91 2.89 Fe CG C:His91 4.13 Fe C2D C:Hec401 4.28 Fe NC C:Hec401 1.98 Fe CHB C:Hec401 3.43 Fe CHC C:Hec401 3.47 Fe C3D C:Hec401 4.28 Fe NA C:Hec401 2.02 Fe CHA C:Hec401 3.44 Fe C2A C:Hec401 4.29 Fe C1D C:Hec401 3.04 Fe C4A C:Hec401 3.06 Fe C4B C:Hec401 3.11 Fe C3A C:Hec401 4.29 Fe C4C C:Hec401 2.99 Fe C2B C:Hec401 4.31 Fe C1C C:Hec401 3.04 Fe C2C C:Hec401 4.25 Fe ND C:Hec401 2.02 Fe CHD C:Hec401 3.38 Fe C1B C:Hec401 3.07 Fe NB C:Hec401 2.06 Fe FE C:Hec401 0.00 Fe C3C C:Hec401 4.22 Fe C3B C:Hec401 4.33 Fe C4D C:Hec401 3.07 Fe C1A C:Hec401 3.06 interactive model: Iron binding site 2 out of 5 in 1dxr Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Iron in the PDB 1dxr. 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: Met110, C: His136, C: Hec402, conact list: Atom Atom Distance (A) Fe CB C:Met110 4.17 Fe CE C:Met110 3.48 Fe CG C:Met110 3.51 Fe SD C:Met110 2.22 Fe NE2 C:His136 1.98 Fe ND1 C:His136 4.10 Fe CD2 C:His136 3.06 Fe CE1 C:His136 2.92 Fe CG C:His136 4.18 Fe C2D C:Hec402 4.28 Fe NC C:Hec402 2.05 Fe CHB C:Hec402 3.42 Fe CHC C:Hec402 3.48 Fe C3D C:Hec402 4.29 Fe NA C:Hec402 2.05 Fe CHA C:Hec402 3.46 Fe C2A C:Hec402 4.32 Fe C1D C:Hec402 3.04 Fe C4A C:Hec402 3.06 Fe C4B C:Hec402 3.09 Fe C3A C:Hec402 4.30 Fe C4C C:Hec402 3.06 Fe C2B C:Hec402 4.29 Fe C1C C:Hec402 3.09 Fe C2C C:Hec402 4.31 Fe ND C:Hec402 2.02 Fe CHD C:Hec402 3.41 Fe C1B C:Hec402 3.05 Fe NB C:Hec402 2.03 Fe FE C:Hec402 0.00 Fe C3C C:Hec402 4.29 Fe C3B C:Hec402 4.31 Fe C4D C:Hec402 3.07 Fe C1A C:Hec402 3.09 interactive model: Iron binding site 3 out of 5 in 1dxr Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Iron in the PDB 1dxr. 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: Met233, C: His248, C: Arg264, C: Hec403, conact list: Atom Atom Distance (A) Fe CB C:Met233 4.27 Fe CE C:Met233 3.50 Fe CG C:Met233 3.49 Fe SD C:Met233 2.22 Fe NE2 C:His248 1.91 Fe ND1 C:His248 4.05 Fe CD2 C:His248 2.93 Fe CE1 C:His248 2.91 Fe CG C:His248 4.08 Fe NE C:Arg264 4.99 Fe C2D C:Hec403 4.28 Fe NC C:Hec403 2.00 Fe CHB C:Hec403 3.46 Fe CHC C:Hec403 3.41 Fe C3D C:Hec403 4.28 Fe NA C:Hec403 2.00 Fe CHA C:Hec403 3.43 Fe C2A C:Hec403 4.26 Fe C1D C:Hec403 3.05 Fe C4A C:Hec403 3.05 Fe C4B C:Hec403 3.06 Fe C3A C:Hec403 4.26 Fe C4C C:Hec403 3.03 Fe C2B C:Hec403 4.32 Fe C1C C:Hec403 3.03 Fe C2C C:Hec403 4.25 Fe ND C:Hec403 2.01 Fe CHD C:Hec403 3.42 Fe C1B C:Hec403 3.10 Fe NB C:Hec403 2.04 Fe FE C:Hec403 0.00 Fe C3C C:Hec403 4.25 Fe C3B C:Hec403 4.31 Fe C4D C:Hec403 3.05 Fe C1A C:Hec403 3.04 interactive model: Iron binding site 4 out of 5 in 1dxr Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Iron in the PDB 1dxr. 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: His124, C: His309, C: Pro315, C: Hec404, conact list: Atom Atom Distance (A) Fe NE2 C:His124 2.05 Fe ND1 C:His124 4.16 Fe CD2 C:His124 3.14 Fe CE1 C:His124 2.98 Fe CG C:His124 4.26 Fe NE2 C:His309 2.02 Fe ND1 C:His309 4.14 Fe CD2 C:His309 3.08 Fe CE1 C:His309 2.97 Fe CG C:His309 4.21 Fe CD C:Pro315 4.95 Fe CG C:Pro315 4.97 Fe C2D C:Hec404 4.24 Fe NC C:Hec404 2.02 Fe CHB C:Hec404 3.42 Fe CHC C:Hec404 3.47 Fe C3D C:Hec404 4.25 Fe NA C:Hec404 2.05 Fe CHA C:Hec404 3.46 Fe C2A C:Hec404 4.33 Fe C1D C:Hec404 3.01 Fe C4A C:Hec404 3.08 Fe C4B C:Hec404 3.09 Fe C3A C:Hec404 4.32 Fe C4C C:Hec404 3.02 Fe C2B C:Hec404 4.27 Fe C1C C:Hec404 3.09 Fe C2C C:Hec404 4.30 Fe ND C:Hec404 1.99 Fe CHD C:Hec404 3.37 Fe C1B C:Hec404 3.03 Fe NB C:Hec404 2.02 Fe FE C:Hec404 0.00 Fe C3C C:Hec404 4.28 Fe C3B C:Hec404 4.30 Fe C4D C:Hec404 3.04 Fe C1A C:Hec404 3.10 interactive model: Iron binding site 5 out of 5 in 1dxr Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Iron in the PDB 1dxr. 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: L: His190, L: Ile194, L: His230, M: His217, M: Ile221, M: Glu232, M: His264, M: Hoh2083, conact list: Atom Atom Distance (A) Fe NE2 L:His190 1.98 Fe ND1 L:His190 4.07 Fe CD2 L:His190 3.15 Fe CE1 L:His190 2.86 Fe CG L:His190 4.23 Fe CG1 L:Ile194 4.58 Fe NE2 L:His230 2.27 Fe ND1 L:His230 4.36 Fe CD2 L:His230 3.37 Fe CE1 L:His230 3.16 Fe CG L:His230 4.48 Fe NE2 M:His217 2.10 Fe ND1 M:His217 4.20 Fe CD2 M:His217 3.19 Fe CE1 M:His217 3.02 Fe CG M:His217 4.31 Fe CG1 M:Ile221 4.56 Fe OE1 M:Glu232 2.41 Fe CB M:Glu232 4.94 Fe OE2 M:Glu232 1.98 Fe CD M:Glu232 2.51 Fe CG M:Glu232 4.03 Fe NE2 M:His264 2.18 Fe ND1 M:His264 4.28 Fe CD2 M:His264 3.28 Fe CE1 M:His264 3.09 Fe CG M:His264 4.40 Fe O M:Hoh2083 4.75 interactive model: