Iron in the structure of Structure of Protoglobin From Methanosarcina Acetivorans C2A (pdb 2vee)

The binding sites of Iron atom in the structure of Structure of Protoglobin From Methanosarcina Acetivorans C2A (pdb code 2vee). This binding sites where shown with 5.0 Angstroms radius around Iron atom. The 2vee structure was solved by M.NARDINI, A.PESCE, L.THIJS, J.A.SAITO, S.DEWILDE, M.ALAM, P.ASCENZI, M.COLETTA, C.CIACCIO, L.MOENS, M.BOLOGNESI, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 160.1-2.6 Space group P1211 a (A) 101.930 b (A) 48.531 c (A) 161.072 alpha (°) 90.00 beta (°) 98.44 gamma (°) 90.00 Rfactor (%) 20.5 Rfree (%) 26.3 Iron Binding Sites: Iron binding site 1 out of 8 in 2vee Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Iron in the PDB 2vee. 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: Phe93, A: His120, A: Hem1196, conact list: Atom Atom Distance (A) Fe CE2 A:Phe93 4.12 Fe CD2 A:Phe93 4.94 Fe CZ A:Phe93 4.65 Fe NE2 A:His120 2.23 Fe ND1 A:His120 4.26 Fe CD2 A:His120 3.21 Fe CE1 A:His120 3.15 Fe CG A:His120 4.32 Fe C2D A:Hem1196 4.22 Fe NC A:Hem1196 1.97 Fe CHB A:Hem1196 3.45 Fe CHC A:Hem1196 3.38 Fe C3D A:Hem1196 4.23 Fe NA A:Hem1196 2.07 Fe CHA A:Hem1196 3.39 Fe C2A A:Hem1196 4.30 Fe C1D A:Hem1196 3.00 Fe C4A A:Hem1196 3.09 Fe C4B A:Hem1196 3.10 Fe C3A A:Hem1196 4.30 Fe C4C A:Hem1196 2.97 Fe C2B A:Hem1196 4.34 Fe C1C A:Hem1196 3.00 Fe C2C A:Hem1196 4.20 Fe ND A:Hem1196 2.04 Fe CHD A:Hem1196 3.31 Fe C1B A:Hem1196 3.12 Fe NB A:Hem1196 2.09 Fe FE A:Hem1196 0.00 Fe C3C A:Hem1196 4.19 Fe C3B A:Hem1196 4.33 Fe C4D A:Hem1196 3.03 Fe C1A A:Hem1196 3.07 interactive model: Iron binding site 2 out of 8 in 2vee Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Iron in the PDB 2vee. 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: Phe93, B: His120, B: Hem1196, conact list: Atom Atom Distance (A) Fe CE2 B:Phe93 4.05 Fe CD2 B:Phe93 4.82 Fe CZ B:Phe93 4.72 Fe NE2 B:His120 2.24 Fe ND1 B:His120 4.22 Fe CD2 B:His120 3.35 Fe CE1 B:His120 3.04 Fe CG B:His120 4.40 Fe C2D B:Hem1196 4.24 Fe NC B:Hem1196 2.00 Fe CHB B:Hem1196 3.41 Fe CHC B:Hem1196 3.35 Fe C3D B:Hem1196 4.25 Fe NA B:Hem1196 2.07 Fe CHA B:Hem1196 3.43 Fe C2A B:Hem1196 4.32 Fe C1D B:Hem1196 3.03 Fe C4A B:Hem1196 3.07 Fe C4B B:Hem1196 3.04 Fe C3A B:Hem1196 4.29 Fe C4C B:Hem1196 3.02 Fe C2B B:Hem1196 4.28 Fe C1C B:Hem1196 3.01 Fe C2C B:Hem1196 4.23 Fe ND B:Hem1196 2.07 Fe CHD B:Hem1196 3.36 Fe C1B B:Hem1196 3.06 Fe NB B:Hem1196 2.03 Fe FE B:Hem1196 0.00 Fe C3C B:Hem1196 4.24 Fe C3B B:Hem1196 4.27 Fe C4D B:Hem1196 3.05 Fe C1A B:Hem1196 3.10 interactive model: Iron binding site 3 out of 8 in 2vee Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Iron in the PDB 2vee. 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: Phe93, C: His120, C: Hem1196, conact list: Atom Atom Distance (A) Fe CE2 C:Phe93 4.05 Fe CD2 C:Phe93 4.84 Fe CZ C:Phe93 4.58 Fe NE2 C:His120 2.21 Fe ND1 C:His120 4.20 Fe CD2 C:His120 3.29 Fe CE1 C:His120 3.04 Fe CG C:His120 4.35 Fe C2D C:Hem1196 4.30 Fe NC C:Hem1196 2.04 Fe CHB C:Hem1196 3.39 Fe CHC C:Hem1196 3.37 Fe C3D C:Hem1196 4.28 Fe NA C:Hem1196 2.03 Fe CHA C:Hem1196 3.39 Fe C2A C:Hem1196 4.27 Fe C1D C:Hem1196 3.09 Fe C4A C:Hem1196 3.04 Fe C4B C:Hem1196 3.04 Fe C3A C:Hem1196 4.25 Fe C4C C:Hem1196 3.07 Fe C2B C:Hem1196 4.27 Fe C1C C:Hem1196 3.04 Fe C2C C:Hem1196 4.26 Fe ND C:Hem1196 2.11 Fe CHD C:Hem1196 3.43 Fe C1B C:Hem1196 3.05 Fe NB C:Hem1196 2.03 Fe FE C:Hem1196 0.00 Fe C3C C:Hem1196 4.28 Fe C3B C:Hem1196 4.27 Fe C4D C:Hem1196 3.06 Fe C1A C:Hem1196 3.05 interactive model: Iron binding site 4 out of 8 in 2vee Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Iron in the PDB 2vee. 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: Phe93, D: His120, D: Hem1196, conact list: Atom Atom Distance (A) Fe CE2 D:Phe93 3.91 Fe CD2 D:Phe93 4.76 Fe CZ D:Phe93 4.49 Fe NE2 D:His120 2.29 Fe ND1 D:His120 4.29 Fe CD2 D:His120 3.36 Fe CE1 D:His120 3.12 Fe CG D:His120 4.43 Fe C2D D:Hem1196 4.22 Fe NC D:Hem1196 1.97 Fe CHB D:Hem1196 3.41 Fe CHC D:Hem1196 3.39 Fe C3D D:Hem1196 4.26 Fe NA D:Hem1196 2.05 Fe CHA D:Hem1196 3.42 Fe C2A D:Hem1196 4.30 Fe C1D D:Hem1196 2.99 Fe C4A D:Hem1196 3.06 Fe C4B D:Hem1196 3.09 Fe C3A D:Hem1196 4.28 Fe C4C D:Hem1196 2.97 Fe C2B D:Hem1196 4.31 Fe C1C D:Hem1196 3.01 Fe C2C D:Hem1196 4.21 Fe ND D:Hem1196 2.05 Fe CHD D:Hem1196 3.29 Fe C1B D:Hem1196 3.08 Fe NB D:Hem1196 2.07 Fe FE D:Hem1196 0.00 Fe C3C D:Hem1196 4.19 Fe C3B D:Hem1196 4.31 Fe C4D D:Hem1196 3.06 Fe C1A D:Hem1196 3.08 interactive model: Iron binding site 5 out of 8 in 2vee Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Iron in the PDB 2vee. 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: E: Phe93, E: His120, E: Hem1196, conact list: Atom Atom Distance (A) Fe CE2 E:Phe93 4.10 Fe CD2 E:Phe93 4.78 Fe CZ E:Phe93 4.77 Fe NE2 E:His120 2.18 Fe ND1 E:His120 4.21 Fe CD2 E:His120 3.22 Fe CE1 E:His120 3.07 Fe CG E:His120 4.31 Fe C2D E:Hem1196 4.30 Fe NC E:Hem1196 1.97 Fe CHB E:Hem1196 3.41 Fe CHC E:Hem1196 3.36 Fe C3D E:Hem1196 4.29 Fe NA E:Hem1196 2.02 Fe CHA E:Hem1196 3.40 Fe C2A E:Hem1196 4.25 Fe C1D E:Hem1196 3.09 Fe C4A E:Hem1196 3.03 Fe C4B E:Hem1196 3.04 Fe C3A E:Hem1196 4.24 Fe C4C E:Hem1196 3.00 Fe C2B E:Hem1196 4.28 Fe C1C E:Hem1196 3.00 Fe C2C E:Hem1196 4.20 Fe ND E:Hem1196 2.12 Fe CHD E:Hem1196 3.39 Fe C1B E:Hem1196 3.06 Fe NB E:Hem1196 2.03 Fe FE E:Hem1196 0.00 Fe C3C E:Hem1196 4.20 Fe C3B E:Hem1196 4.27 Fe C4D E:Hem1196 3.08 Fe C1A E:Hem1196 3.03 interactive model: Iron binding site 6 out of 8 in 2vee Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 6 of Iron in the PDB 2vee. 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: F: Phe93, F: His120, F: Hem1196, conact list: Atom Atom Distance (A) Fe CE2 F:Phe93 4.23 Fe CD2 F:Phe93 4.89 Fe CZ F:Phe93 4.99 Fe NE2 F:His120 2.22 Fe ND1 F:His120 4.23 Fe CD2 F:His120 3.27 Fe CE1 F:His120 3.08 Fe CG F:His120 4.35 Fe C2D F:Hem1196 4.29 Fe NC F:Hem1196 1.95 Fe CHB F:Hem1196 3.43 Fe CHC F:Hem1196 3.26 Fe C3D F:Hem1196 4.30 Fe NA F:Hem1196 2.09 Fe CHA F:Hem1196 3.46 Fe C2A F:Hem1196 4.32 Fe C1D F:Hem1196 3.09 Fe C4A F:Hem1196 3.09 Fe C4B F:Hem1196 2.96 Fe C3A F:Hem1196 4.30 Fe C4C F:Hem1196 3.00 Fe C2B F:Hem1196 4.25 Fe C1C F:Hem1196 2.94 Fe C2C F:Hem1196 4.16 Fe ND F:Hem1196 2.15 Fe CHD F:Hem1196 3.39 Fe C1B F:Hem1196 3.06 Fe NB F:Hem1196 2.00 Fe FE F:Hem1196 0.00 Fe C3C F:Hem1196 4.19 Fe C3B F:Hem1196 4.21 Fe C4D F:Hem1196 3.11 Fe C1A F:Hem1196 3.11 interactive model: Iron binding site 7 out of 8 in 2vee Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 7 of Iron in the PDB 2vee. 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: G: Phe93, G: His120, G: Hem1196, conact list: Atom Atom Distance (A) Fe CE2 G:Phe93 4.15 Fe CD2 G:Phe93 4.90 Fe CZ G:Phe93 4.77 Fe NE2 G:His120 2.15 Fe ND1 G:His120 4.21 Fe CD2 G:His120 3.20 Fe CE1 G:His120 3.06 Fe CG G:His120 4.31 Fe C2D G:Hem1196 4.27 Fe NC G:Hem1196 2.00 Fe CHB G:Hem1196 3.41 Fe CHC G:Hem1196 3.40 Fe C3D G:Hem1196 4.26 Fe NA G:Hem1196 2.04 Fe CHA G:Hem1196 3.40 Fe C2A G:Hem1196 4.27 Fe C1D G:Hem1196 3.06 Fe C4A G:Hem1196 3.04 Fe C4B G:Hem1196 3.09 Fe C3A G:Hem1196 4.26 Fe C4C G:Hem1196 3.01 Fe C2B G:Hem1196 4.31 Fe C1C G:Hem1196 3.03 Fe C2C G:Hem1196 4.23 Fe ND G:Hem1196 2.10 Fe CHD G:Hem1196 3.38 Fe C1B G:Hem1196 3.08 Fe NB G:Hem1196 2.07 Fe FE G:Hem1196 0.00 Fe C3C G:Hem1196 4.22 Fe C3B G:Hem1196 4.31 Fe C4D G:Hem1196 3.06 Fe C1A G:Hem1196 3.06 interactive model: Iron binding site 8 out of 8 in 2vee Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 8 of Iron in the PDB 2vee. 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: H: Phe93, H: His120, H: Hem1196, conact list: Atom Atom Distance (A) Fe CE2 H:Phe93 4.03 Fe CD2 H:Phe93 4.79 Fe CZ H:Phe93 4.63 Fe NE2 H:His120 2.17 Fe ND1 H:His120 4.16 Fe CD2 H:His120 3.24 Fe CE1 H:His120 3.00 Fe CG H:His120 4.30 Fe C2D H:Hem1196 4.24 Fe NC H:Hem1196 2.01 Fe CHB H:Hem1196 3.41 Fe CHC H:Hem1196 3.39 Fe C3D H:Hem1196 4.24 Fe NA H:Hem1196 2.05 Fe CHA H:Hem1196 3.39 Fe C2A H:Hem1196 4.27 Fe C1D H:Hem1196 3.03 Fe C4A H:Hem1196 3.05 Fe C4B H:Hem1196 3.07 Fe C3A H:Hem1196 4.26 Fe C4C H:Hem1196 3.02 Fe C2B H:Hem1196 4.30 Fe C1C H:Hem1196 3.04 Fe C2C H:Hem1196 4.25 Fe ND H:Hem1196 2.06 Fe CHD H:Hem1196 3.36 Fe C1B H:Hem1196 3.07 Fe NB H:Hem1196 2.05 Fe FE H:Hem1196 0.00 Fe C3C H:Hem1196 4.24 Fe C3B H:Hem1196 4.30 Fe C4D H:Hem1196 3.04 Fe C1A H:Hem1196 3.06 interactive model: