Iron in the structure of Structure Of Septuple Mutant of Rat Outer Mitochondrial Membrane Cytochrome B5 (pdb 2i89)

The binding sites of Iron atom in the structure of Structure Of Septuple Mutant of Rat Outer Mitochondrial Membrane Cytochrome B5 (pdb code 2i89). This binding sites where shown with 5.0 Angstroms radius around Iron atom. The 2i89 structure was solved by S.TERZYAN, X.C ZHANG, D.R.BENSON, L.WANG, N.SUN, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 50.0-2.1 Space group P212121 a (A) 39.965 b (A) 51.409 c (A) 167.435 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 20.8 Rfree (%) 27.8 Iron Binding Sites: Iron binding site 1 out of 8 in 2i89 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Iron in the PDB 2i89. 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: His39, A: Gly41, A: His63, A: Hem201, conact list: Atom Atom Distance (A) Fe NE2 A:His39 2.17 Fe ND1 A:His39 4.28 Fe CD2 A:His39 2.89 Fe CE1 A:His39 3.30 Fe CG A:His39 4.13 Fe N A:Gly41 5.00 Fe NE2 A:His63 2.11 Fe ND1 A:His63 4.20 Fe CD2 A:His63 3.04 Fe CE1 A:His63 3.12 Fe CG A:His63 4.19 Fe C2D A:Hem201 4.29 Fe C2D A:Hem201 4.26 Fe NC A:Hem201 2.01 Fe NC A:Hem201 1.97 Fe CHB A:Hem201 3.33 Fe CHB A:Hem201 3.39 Fe CHC A:Hem201 3.49 Fe CHC A:Hem201 3.46 Fe C3D A:Hem201 4.32 Fe C3D A:Hem201 4.31 Fe NA A:Hem201 1.96 Fe NA A:Hem201 2.02 Fe CHA A:Hem201 3.46 Fe CHA A:Hem201 3.47 Fe C2A A:Hem201 4.24 Fe C2A A:Hem201 4.28 Fe C1D A:Hem201 3.03 Fe C1D A:Hem201 2.99 Fe C4A A:Hem201 2.99 Fe C4A A:Hem201 3.05 Fe C4B A:Hem201 3.06 Fe C4B A:Hem201 3.07 Fe C3A A:Hem201 4.21 Fe C3A A:Hem201 4.27 Fe C4C A:Hem201 3.08 Fe C4C A:Hem201 3.02 Fe C2B A:Hem201 4.20 Fe C2B A:Hem201 4.23 Fe C1C A:Hem201 3.11 Fe C1C A:Hem201 3.07 Fe C2C A:Hem201 4.36 Fe C2C A:Hem201 4.32 Fe ND A:Hem201 1.97 Fe ND A:Hem201 1.95 Fe CHD A:Hem201 3.42 Fe CHD A:Hem201 3.36 Fe C1B A:Hem201 2.96 Fe C1B A:Hem201 3.00 Fe NB A:Hem201 1.95 Fe NB A:Hem201 1.96 Fe FE A:Hem201 0.00 Fe FE A:Hem201 0.06 Fe C3C A:Hem201 4.36 Fe C3C A:Hem201 4.31 Fe C3B A:Hem201 4.30 Fe C3B A:Hem201 4.34 Fe C4D A:Hem201 3.06 Fe C4D A:Hem201 3.06 Fe C1A A:Hem201 3.06 Fe C1A A:Hem201 3.09 interactive model: Iron binding site 2 out of 8 in 2i89 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Iron in the PDB 2i89. 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: His39, A: Gly41, A: His63, A: Hem201, conact list: Atom Atom Distance (A) Fe NE2 A:His39 2.17 Fe ND1 A:His39 4.29 Fe CD2 A:His39 2.88 Fe CE1 A:His39 3.32 Fe CG A:His39 4.12 Fe N A:Gly41 4.98 Fe NE2 A:His63 2.12 Fe ND1 A:His63 4.21 Fe CD2 A:His63 3.03 Fe CE1 A:His63 3.14 Fe CG A:His63 4.18 Fe C2D A:Hem201 4.23 Fe C2D A:Hem201 4.29 Fe NC A:Hem201 1.99 Fe NC A:Hem201 2.02 Fe CHB A:Hem201 3.38 Fe CHB A:Hem201 3.34 Fe CHC A:Hem201 3.51 Fe CHC A:Hem201 3.48 Fe C3D A:Hem201 4.27 Fe C3D A:Hem201 4.32 Fe NA A:Hem201 1.98 Fe NA A:Hem201 1.96 Fe CHA A:Hem201 3.44 Fe CHA A:Hem201 3.45 Fe C2A A:Hem201 4.26 Fe C2A A:Hem201 4.23 Fe C1D A:Hem201 2.98 Fe C1D A:Hem201 3.03 Fe C4A A:Hem201 3.03 Fe C4A A:Hem201 2.99 Fe C4B A:Hem201 3.10 Fe C4B A:Hem201 3.07 Fe C3A A:Hem201 4.24 Fe C3A A:Hem201 4.22 Fe C4C A:Hem201 3.05 Fe C4C A:Hem201 3.08 Fe C2B A:Hem201 4.26 Fe C2B A:Hem201 4.20 Fe C1C A:Hem201 3.11 Fe C1C A:Hem201 3.12 Fe C2C A:Hem201 4.35 Fe C2C A:Hem201 4.37 Fe ND A:Hem201 1.92 Fe ND A:Hem201 1.97 Fe CHD A:Hem201 3.37 Fe CHD A:Hem201 3.41 Fe C1B A:Hem201 3.01 Fe C1B A:Hem201 2.96 Fe NB A:Hem201 2.00 Fe NB A:Hem201 1.94 Fe FE A:Hem201 0.06 Fe FE A:Hem201 0.00 Fe C3C A:Hem201 4.33 Fe C3C A:Hem201 4.36 Fe C3B A:Hem201 4.35 Fe C3B A:Hem201 4.32 Fe C4D A:Hem201 3.02 Fe C4D A:Hem201 3.06 Fe C1A A:Hem201 3.06 Fe C1A A:Hem201 3.05 interactive model: Iron binding site 3 out of 8 in 2i89 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Iron in the PDB 2i89. 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: His39, B: Gly41, B: His63, B: Hem701, conact list: Atom Atom Distance (A) Fe NE2 B:His39 2.02 Fe ND1 B:His39 4.11 Fe CD2 B:His39 3.01 Fe CE1 B:His39 3.01 Fe CG B:His39 4.15 Fe N B:Gly41 4.89 Fe NE2 B:His63 2.15 Fe ND1 B:His63 4.23 Fe CD2 B:His63 3.17 Fe CE1 B:His63 3.09 Fe CG B:His63 4.29 Fe C2D B:Hem701 4.29 Fe C2D B:Hem701 4.24 Fe NC B:Hem701 2.01 Fe NC B:Hem701 2.00 Fe CHB B:Hem701 3.33 Fe CHB B:Hem701 3.38 Fe CHC B:Hem701 3.46 Fe CHC B:Hem701 3.51 Fe C3D B:Hem701 4.34 Fe C3D B:Hem701 4.29 Fe NA B:Hem701 1.96 Fe NA B:Hem701 2.00 Fe CHA B:Hem701 3.49 Fe CHA B:Hem701 3.46 Fe C2A B:Hem701 4.25 Fe C2A B:Hem701 4.28 Fe C1D B:Hem701 3.02 Fe C1D B:Hem701 2.96 Fe C4A B:Hem701 2.98 Fe C4A B:Hem701 3.03 Fe C4B B:Hem701 3.06 Fe C4B B:Hem701 3.10 Fe C3A B:Hem701 4.21 Fe C3A B:Hem701 4.26 Fe C4C B:Hem701 3.08 Fe C4C B:Hem701 3.04 Fe C2B B:Hem701 4.21 Fe C2B B:Hem701 4.25 Fe C1C B:Hem701 3.10 Fe C1C B:Hem701 3.11 Fe C2C B:Hem701 4.34 Fe C2C B:Hem701 4.34 Fe ND B:Hem701 1.98 Fe ND B:Hem701 1.92 Fe CHD B:Hem701 3.41 Fe CHD B:Hem701 3.35 Fe C1B B:Hem701 2.96 Fe C1B B:Hem701 3.01 Fe NB B:Hem701 1.94 Fe NB B:Hem701 1.99 Fe FE B:Hem701 0.00 Fe FE B:Hem701 0.06 Fe C3C B:Hem701 4.35 Fe C3C B:Hem701 4.33 Fe C3B B:Hem701 4.32 Fe C3B B:Hem701 4.34 Fe C4D B:Hem701 3.08 Fe C4D B:Hem701 3.04 Fe C1A B:Hem701 3.08 Fe C1A B:Hem701 3.08 interactive model: Iron binding site 4 out of 8 in 2i89 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Iron in the PDB 2i89. 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: His39, B: Gly41, B: His63, B: Hem701, conact list: Atom Atom Distance (A) Fe NE2 B:His39 2.03 Fe ND1 B:His39 4.14 Fe CD2 B:His39 3.00 Fe CE1 B:His39 3.04 Fe CG B:His39 4.15 Fe N B:Gly41 4.91 Fe NE2 B:His63 2.14 Fe ND1 B:His63 4.22 Fe CD2 B:His63 3.14 Fe CE1 B:His63 3.10 Fe CG B:His63 4.27 Fe C2D B:Hem701 4.25 Fe C2D B:Hem701 4.29 Fe NC B:Hem701 1.96 Fe NC B:Hem701 2.02 Fe CHB B:Hem701 3.38 Fe CHB B:Hem701 3.33 Fe CHC B:Hem701 3.44 Fe CHC B:Hem701 3.48 Fe C3D B:Hem701 4.32 Fe C3D B:Hem701 4.34 Fe NA B:Hem701 2.02 Fe NA B:Hem701 1.98 Fe CHA B:Hem701 3.51 Fe CHA B:Hem701 3.48 Fe C2A B:Hem701 4.30 Fe C2A B:Hem701 4.26 Fe C1D B:Hem701 2.98 Fe C1D B:Hem701 3.02 Fe C4A B:Hem701 3.04 Fe C4A B:Hem701 2.99 Fe C4B B:Hem701 3.06 Fe C4B B:Hem701 3.06 Fe C3A B:Hem701 4.27 Fe C3A B:Hem701 4.22 Fe C4C B:Hem701 3.02 Fe C4C B:Hem701 3.08 Fe C2B B:Hem701 4.24 Fe C2B B:Hem701 4.19 Fe C1C B:Hem701 3.06 Fe C1C B:Hem701 3.11 Fe C2C B:Hem701 4.29 Fe C2C B:Hem701 4.35 Fe ND B:Hem701 1.95 Fe ND B:Hem701 1.97 Fe CHD B:Hem701 3.36 Fe CHD B:Hem701 3.41 Fe C1B B:Hem701 3.00 Fe C1B B:Hem701 2.96 Fe NB B:Hem701 1.97 Fe NB B:Hem701 1.94 Fe FE B:Hem701 0.06 Fe FE B:Hem701 0.00 Fe C3C B:Hem701 4.29 Fe C3C B:Hem701 4.36 Fe C3B B:Hem701 4.33 Fe C3B B:Hem701 4.29 Fe C4D B:Hem701 3.07 Fe C4D B:Hem701 3.08 Fe C1A B:Hem701 3.12 Fe C1A B:Hem701 3.08 interactive model: Iron binding site 5 out of 8 in 2i89 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Iron in the PDB 2i89. 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: His39, C: Gly41, C: Phe58, C: His63, C: Hem801, conact list: Atom Atom Distance (A) Fe NE2 C:His39 2.12 Fe ND1 C:His39 4.23 Fe CD2 C:His39 2.99 Fe CE1 C:His39 3.17 Fe CG C:His39 4.18 Fe N C:Gly41 4.84 Fe CE1 C:Phe58 4.93 Fe NE2 C:His63 2.19 Fe ND1 C:His63 4.26 Fe CD2 C:His63 3.22 Fe CE1 C:His63 3.11 Fe CG C:His63 4.34 Fe C2D C:Hem801 4.30 Fe C2D C:Hem801 4.21 Fe NC C:Hem801 2.00 Fe NC C:Hem801 1.95 Fe CHB C:Hem801 3.32 Fe CHB C:Hem801 3.41 Fe CHC C:Hem801 3.46 Fe CHC C:Hem801 3.45 Fe C3D C:Hem801 4.33 Fe C3D C:Hem801 4.27 Fe NA C:Hem801 1.95 Fe NA C:Hem801 2.04 Fe CHA C:Hem801 3.46 Fe CHA C:Hem801 3.46 Fe C2A C:Hem801 4.23 Fe C2A C:Hem801 4.30 Fe C1D C:Hem801 3.03 Fe C1D C:Hem801 2.94 Fe C4A C:Hem801 2.98 Fe C4A C:Hem801 3.08 Fe C4B C:Hem801 3.05 Fe C4B C:Hem801 3.06 Fe C3A C:Hem801 4.20 Fe C3A C:Hem801 4.29 Fe C4C C:Hem801 3.06 Fe C4C C:Hem801 3.00 Fe C2B C:Hem801 4.20 Fe C2B C:Hem801 4.24 Fe C1C C:Hem801 3.09 Fe C1C C:Hem801 3.05 Fe C2C C:Hem801 4.34 Fe C2C C:Hem801 4.28 Fe ND C:Hem801 1.98 Fe ND C:Hem801 1.91 Fe CHD C:Hem801 3.40 Fe CHD C:Hem801 3.32 Fe C1B C:Hem801 2.96 Fe C1B C:Hem801 3.02 Fe NB C:Hem801 1.95 Fe NB C:Hem801 1.99 Fe FE C:Hem801 0.00 Fe FE C:Hem801 0.09 Fe C3C C:Hem801 4.33 Fe C3C C:Hem801 4.27 Fe C3B C:Hem801 4.30 Fe C3B C:Hem801 4.32 Fe C4D C:Hem801 3.07 Fe C4D C:Hem801 3.03 Fe C1A C:Hem801 3.05 Fe C1A C:Hem801 3.10 interactive model: Iron binding site 6 out of 8 in 2i89 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 6 of Iron in the PDB 2i89. 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: His39, C: Gly41, C: Phe58, C: His63, C: Hem801, conact list: Atom Atom Distance (A) Fe NE2 C:His39 2.15 Fe ND1 C:His39 4.27 Fe CD2 C:His39 2.98 Fe CE1 C:His39 3.23 Fe CG C:His39 4.18 Fe N C:Gly41 4.86 Fe CE1 C:Phe58 4.89 Fe NE2 C:His63 2.17 Fe ND1 C:His63 4.26 Fe CD2 C:His63 3.18 Fe CE1 C:His63 3.13 Fe CG C:His63 4.31 Fe C2D C:Hem801 4.22 Fe C2D C:Hem801 4.28 Fe NC C:Hem801 1.94 Fe NC C:Hem801 2.02 Fe CHB C:Hem801 3.41 Fe CHB C:Hem801 3.32 Fe CHC C:Hem801 3.47 Fe CHC C:Hem801 3.45 Fe C3D C:Hem801 4.27 Fe C3D C:Hem801 4.32 Fe NA C:Hem801 2.01 Fe NA C:Hem801 1.97 Fe CHA C:Hem801 3.46 Fe CHA C:Hem801 3.45 Fe C2A C:Hem801 4.28 Fe C2A C:Hem801 4.24 Fe C1D C:Hem801 2.95 Fe C1D C:Hem801 3.02 Fe C4A C:Hem801 3.06 Fe C4A C:Hem801 2.99 Fe C4B C:Hem801 3.09 Fe C4B C:Hem801 3.03 Fe C3A C:Hem801 4.27 Fe C3A C:Hem801 4.21 Fe C4C C:Hem801 2.98 Fe C4C C:Hem801 3.08 Fe C2B C:Hem801 4.27 Fe C2B C:Hem801 4.17 Fe C1C C:Hem801 3.06 Fe C1C C:Hem801 3.09 Fe C2C C:Hem801 4.29 Fe C2C C:Hem801 4.33 Fe ND C:Hem801 1.91 Fe ND C:Hem801 1.96 Fe CHD C:Hem801 3.31 Fe CHD C:Hem801 3.42 Fe C1B C:Hem801 3.04 Fe C1B C:Hem801 2.93 Fe NB C:Hem801 2.01 Fe NB C:Hem801 1.93 Fe FE C:Hem801 0.09 Fe FE C:Hem801 0.00 Fe C3C C:Hem801 4.26 Fe C3C C:Hem801 4.35 Fe C3B C:Hem801 4.36 Fe C3B C:Hem801 4.27 Fe C4D C:Hem801 3.03 Fe C4D C:Hem801 3.06 Fe C1A C:Hem801 3.08 Fe C1A C:Hem801 3.06 interactive model: Iron binding site 7 out of 8 in 2i89 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 7 of Iron in the PDB 2i89. 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: His39, D: Gly41, D: Phe58, D: His63, D: Hem901, conact list: Atom Atom Distance (A) Fe NE2 D:His39 2.14 Fe ND1 D:His39 4.26 Fe CD2 D:His39 2.96 Fe CE1 D:His39 3.23 Fe CG D:His39 4.17 Fe N D:Gly41 4.83 Fe CA D:Gly41 4.97 Fe CE1 D:Phe58 4.98 Fe NE2 D:His63 2.16 Fe ND1 D:His63 4.29 Fe CD2 D:His63 2.89 Fe CE1 D:His63 3.31 Fe CG D:His63 4.13 Fe C2D D:Hem901 4.26 Fe C2D D:Hem901 4.24 Fe NC D:Hem901 2.01 Fe NC D:Hem901 1.97 Fe CHB D:Hem901 3.32 Fe CHB D:Hem901 3.37 Fe CHC D:Hem901 3.50 Fe CHC D:Hem901 3.47 Fe C3D D:Hem901 4.30 Fe C3D D:Hem901 4.31 Fe NA D:Hem901 1.95 Fe NA D:Hem901 2.01 Fe CHA D:Hem901 3.45 Fe CHA D:Hem901 3.46 Fe C2A D:Hem901 4.24 Fe C2A D:Hem901 4.27 Fe C1D D:Hem901 3.00 Fe C1D D:Hem901 2.97 Fe C4A D:Hem901 2.97 Fe C4A D:Hem901 3.03 Fe C4B D:Hem901 3.08 Fe C4B D:Hem901 3.05 Fe C3A D:Hem901 4.19 Fe C3A D:Hem901 4.25 Fe C4C D:Hem901 3.07 Fe C4C D:Hem901 3.03 Fe C2B D:Hem901 4.21 Fe C2B D:Hem901 4.20 Fe C1C D:Hem901 3.11 Fe C1C D:Hem901 3.08 Fe C2C D:Hem901 4.35 Fe C2C D:Hem901 4.31 Fe ND D:Hem901 1.95 Fe ND D:Hem901 1.94 Fe CHD D:Hem901 3.39 Fe CHD D:Hem901 3.35 Fe C1B D:Hem901 2.97 Fe C1B D:Hem901 2.98 Fe NB D:Hem901 1.96 Fe NB D:Hem901 1.95 Fe FE D:Hem901 0.00 Fe FE D:Hem901 0.07 Fe C3C D:Hem901 4.33 Fe C3C D:Hem901 4.30 Fe C3B D:Hem901 4.32 Fe C3B D:Hem901 4.28 Fe C4D D:Hem901 3.05 Fe C4D D:Hem901 3.06 Fe C1A D:Hem901 3.05 Fe C1A D:Hem901 3.08 interactive model: Iron binding site 8 out of 8 in 2i89 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 8 of Iron in the PDB 2i89. 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: His39, D: Gly41, D: Phe58, D: His63, D: Hem901, conact list: Atom Atom Distance (A) Fe NE2 D:His39 2.17 Fe ND1 D:His39 4.29 Fe CD2 D:His39 2.96 Fe CE1 D:His39 3.27 Fe CG D:His39 4.18 Fe N D:Gly41 4.83 Fe CA D:Gly41 4.99 Fe CE1 D:Phe58 4.97 Fe NE2 D:His63 2.16 Fe ND1 D:His63 4.29 Fe CD2 D:His63 2.86 Fe CE1 D:His63 3.32 Fe CG D:His63 4.10 Fe C2D D:Hem901 4.19 Fe C2D D:Hem901 4.27 Fe NC D:Hem901 1.99 Fe NC D:Hem901 2.03 Fe CHB D:Hem901 3.39 Fe CHB D:Hem901 3.31 Fe CHC D:Hem901 3.53 Fe CHC D:Hem901 3.50 Fe C3D D:Hem901 4.23 Fe C3D D:Hem901 4.32 Fe NA D:Hem901 1.97 Fe NA D:Hem901 1.94 Fe CHA D:Hem901 3.41 Fe CHA D:Hem901 3.43 Fe C2A D:Hem901 4.25 Fe C2A D:Hem901 4.21 Fe C1D D:Hem901 2.93 Fe C1D D:Hem901 3.01 Fe C4A D:Hem901 3.01 Fe C4A D:Hem901 2.96 Fe C4B D:Hem901 3.14 Fe C4B D:Hem901 3.05 Fe C3A D:Hem901 4.22 Fe C3A D:Hem901 4.18 Fe C4C D:Hem901 3.02 Fe C4C D:Hem901 3.10 Fe C2B D:Hem901 4.28 Fe C2B D:Hem901 4.17 Fe C1C D:Hem901 3.12 Fe C1C D:Hem901 3.13 Fe C2C D:Hem901 4.34 Fe C2C D:Hem901 4.37 Fe ND D:Hem901 1.89 Fe ND D:Hem901 1.96 Fe CHD D:Hem901 3.33 Fe CHD D:Hem901 3.42 Fe C1B D:Hem901 3.04 Fe C1B D:Hem901 2.94 Fe NB D:Hem901 2.03 Fe NB D:Hem901 1.93 Fe FE D:Hem901 0.07 Fe FE D:Hem901 0.00 Fe C3C D:Hem901 4.30 Fe C3C D:Hem901 4.37 Fe C3B D:Hem901 4.38 Fe C3B D:Hem901 4.27 Fe C4D D:Hem901 2.99 Fe C4D D:Hem901 3.05 Fe C1A D:Hem901 3.05 Fe C1A D:Hem901 3.03 interactive model: