Iron in the structure of W. Succinogenes Nrfa Y218F (pdb 3bng)

The binding sites of Iron atom in the structure of W. Succinogenes Nrfa Y218F (pdb code 3bng). This binding sites where shown with 5.0 Angstroms radius around Iron atom. The 3bng structure was solved by P.LUKAT, O.EINSLE, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 42.5-1.5 Space group I4122 a (A) 120.030 b (A) 120.030 c (A) 186.276 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 18.1 Rfree (%) 21.5 Iron Binding Sites: Iron binding site 1 out of 5 in 3bng Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Iron in the PDB 3bng. 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: Lys134, A: His277, A: Hem513, A: Hem515, A: Hoh519, A: Hoh569, A: Hoh581, A: Hoh1047, conact list: Atom Atom Distance (A) Fe CE A:Lys134 3.12 Fe CD A:Lys134 4.50 Fe NZ A:Lys134 2.15 Fe NE2 A:His277 4.08 Fe CD2 A:His277 4.81 Fe C2D A:Hem513 4.28 Fe NC A:Hem513 2.06 Fe CHB A:Hem513 3.38 Fe CHC A:Hem513 3.44 Fe C3D A:Hem513 4.29 Fe NA A:Hem513 1.98 Fe CHA A:Hem513 3.44 Fe C2A A:Hem513 4.23 Fe C1D A:Hem513 3.04 Fe C4A A:Hem513 3.01 Fe C4B A:Hem513 3.04 Fe C3A A:Hem513 4.23 Fe C4C A:Hem513 3.07 Fe C2B A:Hem513 4.25 Fe C1C A:Hem513 3.07 Fe C2C A:Hem513 4.29 Fe ND A:Hem513 2.03 Fe CHD A:Hem513 3.42 Fe C1B A:Hem513 3.03 Fe NB A:Hem513 2.00 Fe FE A:Hem513 0.00 Fe C3C A:Hem513 4.28 Fe C3B A:Hem513 4.25 Fe C4D A:Hem513 3.06 Fe C1A A:Hem513 3.01 Fe CMD A:Hem515 4.82 Fe O A:Hoh519 4.26 Fe O A:Hoh569 4.61 Fe O A:Hoh581 4.17 Fe O A:Hoh1047 2.15 interactive model: Iron binding site 2 out of 5 in 3bng Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Iron in the PDB 3bng. 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: His172, A: Met300, A: His313, A: Hem514, conact list: Atom Atom Distance (A) Fe NE2 A:His172 2.00 Fe ND1 A:His172 4.05 Fe CD2 A:His172 3.03 Fe CE1 A:His172 2.92 Fe CG A:His172 4.13 Fe CE A:Met300 4.45 Fe NE2 A:His313 2.05 Fe ND1 A:His313 4.16 Fe CD2 A:His313 3.01 Fe CE1 A:His313 3.07 Fe CG A:His313 4.17 Fe C2D A:Hem514 4.27 Fe NC A:Hem514 2.00 Fe CHB A:Hem514 3.39 Fe CHC A:Hem514 3.43 Fe C3D A:Hem514 4.28 Fe NA A:Hem514 2.05 Fe CHA A:Hem514 3.42 Fe C2A A:Hem514 4.29 Fe C1D A:Hem514 3.04 Fe C4A A:Hem514 3.04 Fe C4B A:Hem514 3.03 Fe C3A A:Hem514 4.27 Fe C4C A:Hem514 3.03 Fe C2B A:Hem514 4.27 Fe C1C A:Hem514 3.06 Fe C2C A:Hem514 4.28 Fe ND A:Hem514 2.02 Fe CHD A:Hem514 3.42 Fe C1B A:Hem514 3.02 Fe NB A:Hem514 2.01 Fe FE A:Hem514 0.00 Fe C3C A:Hem514 4.26 Fe C3B A:Hem514 4.26 Fe C4D A:Hem514 3.04 Fe C1A A:Hem514 3.07 interactive model: Iron binding site 3 out of 5 in 3bng Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Iron in the PDB 3bng. 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: His102, A: Ile166, A: His215, A: Val315, A: Hem515, conact list: Atom Atom Distance (A) Fe NE2 A:His102 2.06 Fe ND1 A:His102 4.13 Fe CD2 A:His102 3.12 Fe CE1 A:His102 2.99 Fe CG A:His102 4.23 Fe CD1 A:Ile166 4.81 Fe NE2 A:His215 2.04 Fe ND1 A:His215 4.12 Fe CD2 A:His215 3.08 Fe CE1 A:His215 2.97 Fe CG A:His215 4.19 Fe CG1 A:Val315 4.98 Fe C2D A:Hem515 4.27 Fe NC A:Hem515 2.01 Fe CHB A:Hem515 3.41 Fe CHC A:Hem515 3.44 Fe C3D A:Hem515 4.27 Fe NA A:Hem515 2.01 Fe CHA A:Hem515 3.45 Fe C2A A:Hem515 4.27 Fe C1D A:Hem515 3.00 Fe C4A A:Hem515 3.04 Fe C4B A:Hem515 3.04 Fe C3A A:Hem515 4.27 Fe C4C A:Hem515 3.01 Fe C2B A:Hem515 4.27 Fe C1C A:Hem515 3.04 Fe C2C A:Hem515 4.24 Fe ND A:Hem515 1.99 Fe CHD A:Hem515 3.37 Fe C1B A:Hem515 3.03 Fe NB A:Hem515 2.01 Fe FE A:Hem515 0.00 Fe C3C A:Hem515 4.25 Fe C3B A:Hem515 4.25 Fe C4D A:Hem515 3.04 Fe C1A A:Hem515 3.05 interactive model: Iron binding site 4 out of 5 in 3bng Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Iron in the PDB 3bng. 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: His299, A: His405, A: Hem516, conact list: Atom Atom Distance (A) Fe NE2 A:His299 2.08 Fe ND1 A:His299 4.18 Fe CD2 A:His299 3.05 Fe CE1 A:His299 3.08 Fe CG A:His299 4.20 Fe NE2 A:His405 2.13 Fe ND1 A:His405 4.16 Fe CD2 A:His405 3.18 Fe CE1 A:His405 3.02 Fe CG A:His405 4.27 Fe C2D A:Hem516 4.24 Fe NC A:Hem516 2.02 Fe CHB A:Hem516 3.37 Fe CHC A:Hem516 3.40 Fe C3D A:Hem516 4.24 Fe NA A:Hem516 1.99 Fe CHA A:Hem516 3.42 Fe C2A A:Hem516 4.26 Fe C1D A:Hem516 2.99 Fe C4A A:Hem516 3.00 Fe C4B A:Hem516 3.00 Fe C3A A:Hem516 4.25 Fe C4C A:Hem516 3.02 Fe C2B A:Hem516 4.21 Fe C1C A:Hem516 3.03 Fe C2C A:Hem516 4.27 Fe ND A:Hem516 1.98 Fe CHD A:Hem516 3.38 Fe C1B A:Hem516 2.99 Fe NB A:Hem516 1.97 Fe FE A:Hem516 0.00 Fe C3C A:Hem516 4.24 Fe C3B A:Hem516 4.20 Fe C4D A:Hem516 3.02 Fe C1A A:Hem516 3.04 interactive model: Iron binding site 5 out of 5 in 3bng Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Iron in the PDB 3bng. 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: His288, A: His330, A: Hem516, A: Hem517, conact list: Atom Atom Distance (A) Fe NE2 A:His288 2.02 Fe ND1 A:His288 4.10 Fe CD2 A:His288 3.04 Fe CE1 A:His288 2.97 Fe CG A:His288 4.17 Fe NE2 A:His330 2.05 Fe ND1 A:His330 4.07 Fe CD2 A:His330 3.15 Fe CE1 A:His330 2.90 Fe CG A:His330 4.21 Fe CBC A:Hem516 4.80 Fe C2D A:Hem517 4.28 Fe NC A:Hem517 2.03 Fe CHB A:Hem517 3.41 Fe CHC A:Hem517 3.40 Fe C3D A:Hem517 4.30 Fe NA A:Hem517 2.01 Fe CHA A:Hem517 3.42 Fe C2A A:Hem517 4.25 Fe C1D A:Hem517 3.04 Fe C4A A:Hem517 3.03 Fe C4B A:Hem517 3.04 Fe C3A A:Hem517 4.26 Fe C4C A:Hem517 3.02 Fe C2B A:Hem517 4.26 Fe C1C A:Hem517 3.06 Fe C2C A:Hem517 4.28 Fe ND A:Hem517 2.05 Fe CHD A:Hem517 3.37 Fe C1B A:Hem517 3.05 Fe NB A:Hem517 2.02 Fe FE A:Hem517 0.00 Fe C3C A:Hem517 4.26 Fe C3B A:Hem517 4.26 Fe C4D A:Hem517 3.08 Fe C1A A:Hem517 3.03 interactive model: