Iron in the structure of Crystal Structure of the Cu,Mo-Co Dehydrogenase (Codh); Carbon Monoxide Reduced State (pdb 1n63)

The binding sites of Iron atom in the structure of Crystal Structure of the Cu,Mo-Co Dehydrogenase (Codh); Carbon Monoxide Reduced State (pdb code 1n63). This binding sites where shown with 5.0 Angstroms radius around Iron atom. The 1n63 structure was solved by H.DOBBEK, L.GREMER, R.KIEFERSAUER, R.HUBER, O.MEYER, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 17.0-1.2 Space group P212121 a (A) 118.962 b (A) 131.270 c (A) 159.648 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 14.9 Rfree (%) 18.5 Iron Binding Sites: Iron binding site 1 out of 8 in 1n63 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Iron in the PDB 1n63. 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: Gln101, A: Cys102, A: Gly103, A: Tyr104, A: Cys105, A: Cys137, A: Arg138, A: Cys139, A: Fes3907, B: Hoh3935, conact list: Atom Atom Distance (A) Fe N A:Gln101 4.78 Fe CB A:Gln101 4.94 Fe C A:Gln101 4.68 Fe N A:Cys102 3.55 Fe CB A:Cys102 3.42 Fe SG A:Cys102 2.32 Fe C A:Cys102 4.28 Fe CA A:Cys102 3.89 Fe N A:Gly103 3.93 Fe C A:Gly103 4.99 Fe CA A:Gly103 4.92 Fe N A:Tyr104 4.16 Fe CB A:Tyr104 4.85 Fe CA A:Tyr104 4.98 Fe N A:Cys105 4.75 Fe SG A:Cys105 4.73 Fe SG A:Cys137 4.38 Fe N A:Arg138 4.77 Fe C A:Arg138 4.94 Fe N A:Cys139 3.99 Fe CB A:Cys139 3.33 Fe SG A:Cys139 2.35 Fe CA A:Cys139 4.27 Fe S1 A:Fes3907 2.25 Fe S2 A:Fes3907 2.28 Fe FE1 A:Fes3907 0.00 Fe FE2 A:Fes3907 2.72 Fe O B:Hoh3935 4.00 interactive model: Iron binding site 2 out of 8 in 1n63 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Iron in the PDB 1n63. 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: Cys102, A: Tyr104, A: Cys105, A: Leu136, A: Cys137, A: Arg138, A: Cys139, A: Thr140, A: Fes3907, A: Hoh3912, conact list: Atom Atom Distance (A) Fe SG A:Cys102 4.71 Fe N A:Tyr104 4.93 Fe N A:Cys105 4.01 Fe CB A:Cys105 3.38 Fe SG A:Cys105 2.28 Fe C A:Cys105 4.95 Fe CA A:Cys105 4.27 Fe O A:Leu136 4.99 Fe CB A:Cys137 3.36 Fe SG A:Cys137 2.37 Fe C A:Cys137 4.37 Fe CA A:Cys137 3.72 Fe N A:Arg138 4.09 Fe N A:Cys139 4.24 Fe CB A:Cys139 4.44 Fe SG A:Cys139 4.48 Fe CA A:Cys139 4.92 Fe CG2 A:Thr140 4.77 Fe S1 A:Fes3907 2.22 Fe S2 A:Fes3907 2.24 Fe FE1 A:Fes3907 2.72 Fe FE2 A:Fes3907 0.00 Fe O A:Hoh3912 4.38 interactive model: Iron binding site 3 out of 8 in 1n63 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Iron in the PDB 1n63. 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: Gly41, A: Cys42, A: Ser45, A: His46, A: Cys47, A: Gly48, A: Ala49, A: Cys50, A: Cys62, A: Fes3908, A: Hoh3952, conact list: Atom Atom Distance (A) Fe O A:Gly41 4.97 Fe N A:Gly41 4.19 Fe C A:Gly41 4.23 Fe CA A:Gly41 4.52 Fe O A:Cys42 4.06 Fe N A:Cys42 3.50 Fe CB A:Cys42 3.50 Fe SG A:Cys42 2.35 Fe C A:Cys42 4.18 Fe CA A:Cys42 3.88 Fe N A:Ser45 4.76 Fe C A:Ser45 4.70 Fe CA A:Ser45 4.66 Fe N A:His46 4.37 Fe C A:His46 4.58 Fe N A:Cys47 3.45 Fe CB A:Cys47 3.45 Fe SG A:Cys47 2.32 Fe C A:Cys47 4.23 Fe CA A:Cys47 3.83 Fe N A:Gly48 3.84 Fe CA A:Gly48 4.84 Fe N A:Ala49 4.50 Fe SG A:Cys50 4.68 Fe SG A:Cys62 4.40 Fe S1 A:Fes3908 2.28 Fe S2 A:Fes3908 2.24 Fe FE1 A:Fes3908 0.00 Fe FE2 A:Fes3908 2.73 Fe O A:Hoh3952 3.99 interactive model: Iron binding site 4 out of 8 in 1n63 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Iron in the PDB 1n63. 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: Cys42, A: Ser45, A: Cys47, A: Gly48, A: Ala49, A: Cys50, A: Lys60, A: Cys62, A: Fes3908, A: Hoh3952, conact list: Atom Atom Distance (A) Fe SG A:Cys42 4.55 Fe CA A:Ser45 4.81 Fe SG A:Cys47 4.48 Fe N A:Gly48 4.59 Fe CA A:Gly48 4.90 Fe N A:Ala49 4.82 Fe N A:Cys50 4.32 Fe CB A:Cys50 3.43 Fe SG A:Cys50 2.31 Fe CA A:Cys50 4.50 Fe CB A:Lys60 4.45 Fe CG A:Lys60 4.78 Fe CA A:Lys60 5.00 Fe N A:Cys62 4.26 Fe CB A:Cys62 3.28 Fe SG A:Cys62 2.33 Fe CA A:Cys62 4.34 Fe S1 A:Fes3908 2.18 Fe S2 A:Fes3908 2.22 Fe FE1 A:Fes3908 2.73 Fe FE2 A:Fes3908 0.00 Fe O A:Hoh3952 3.98 interactive model: Iron binding site 5 out of 8 in 1n63 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Iron in the PDB 1n63. 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: Gln101, D: Cys102, D: Gly103, D: Tyr104, D: Cys105, D: Cys137, D: Arg138, D: Cys139, D: Fes4907, E: Hoh4929, conact list: Atom Atom Distance (A) Fe N D:Gln101 4.75 Fe CB D:Gln101 4.99 Fe C D:Gln101 4.64 Fe N D:Cys102 3.54 Fe CB D:Cys102 3.43 Fe SG D:Cys102 2.30 Fe C D:Cys102 4.29 Fe CA D:Cys102 3.93 Fe N D:Gly103 3.97 Fe C D:Gly103 4.98 Fe CA D:Gly103 4.92 Fe N D:Tyr104 4.19 Fe CB D:Tyr104 4.84 Fe N D:Cys105 4.75 Fe SG D:Cys105 4.77 Fe SG D:Cys137 4.39 Fe N D:Arg138 4.76 Fe C D:Arg138 4.94 Fe N D:Cys139 4.00 Fe CB D:Cys139 3.34 Fe SG D:Cys139 2.34 Fe CA D:Cys139 4.29 Fe S1 D:Fes4907 2.27 Fe S2 D:Fes4907 2.28 Fe FE1 D:Fes4907 0.00 Fe FE2 D:Fes4907 2.74 Fe O E:Hoh4929 3.96 interactive model: Iron binding site 6 out of 8 in 1n63 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 6 of Iron in the PDB 1n63. 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: Cys102, D: Tyr104, D: Cys105, D: Leu136, D: Cys137, D: Arg138, D: Cys139, D: Thr140, D: Fes4907, D: Hoh4918, conact list: Atom Atom Distance (A) Fe SG D:Cys102 4.71 Fe N D:Tyr104 4.95 Fe N D:Cys105 4.02 Fe CB D:Cys105 3.39 Fe SG D:Cys105 2.30 Fe C D:Cys105 4.94 Fe CA D:Cys105 4.27 Fe O D:Leu136 4.98 Fe CB D:Cys137 3.41 Fe SG D:Cys137 2.36 Fe C D:Cys137 4.35 Fe CA D:Cys137 3.74 Fe N D:Arg138 4.07 Fe N D:Cys139 4.23 Fe CB D:Cys139 4.42 Fe SG D:Cys139 4.47 Fe CA D:Cys139 4.92 Fe CG2 D:Thr140 4.75 Fe S1 D:Fes4907 2.22 Fe S2 D:Fes4907 2.23 Fe FE1 D:Fes4907 2.74 Fe FE2 D:Fes4907 0.00 Fe O D:Hoh4918 4.38 interactive model: Iron binding site 7 out of 8 in 1n63 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 7 of Iron in the PDB 1n63. 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: Gly41, D: Cys42, D: Ser45, D: His46, D: Cys47, D: Gly48, D: Ala49, D: Cys50, D: Cys62, D: Fes4908, F: Hoh4960, conact list: Atom Atom Distance (A) Fe O D:Gly41 4.97 Fe N D:Gly41 4.18 Fe C D:Gly41 4.22 Fe CA D:Gly41 4.51 Fe O D:Cys42 4.07 Fe N D:Cys42 3.52 Fe CB D:Cys42 3.48 Fe SG D:Cys42 2.35 Fe C D:Cys42 4.17 Fe CA D:Cys42 3.91 Fe N D:Ser45 4.74 Fe C D:Ser45 4.69 Fe CA D:Ser45 4.68 Fe N D:His46 4.35 Fe C D:His46 4.59 Fe N D:Cys47 3.49 Fe CB D:Cys47 3.44 Fe SG D:Cys47 2.30 Fe C D:Cys47 4.25 Fe CA D:Cys47 3.86 Fe N D:Gly48 3.86 Fe CA D:Gly48 4.83 Fe N D:Ala49 4.50 Fe SG D:Cys50 4.68 Fe SG D:Cys62 4.39 Fe S1 D:Fes4908 2.26 Fe S2 D:Fes4908 2.25 Fe FE1 D:Fes4908 0.00 Fe FE2 D:Fes4908 2.74 Fe O F:Hoh4960 4.12 interactive model: Iron binding site 8 out of 8 in 1n63 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 8 of Iron in the PDB 1n63. 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: Cys42, D: Ser45, D: Cys47, D: Gly48, D: Ala49, D: Cys50, D: Lys60, D: Cys62, D: Fes4908, F: Hoh4960, conact list: Atom Atom Distance (A) Fe SG D:Cys42 4.57 Fe CA D:Ser45 4.82 Fe SG D:Cys47 4.47 Fe N D:Gly48 4.63 Fe CA D:Gly48 4.91 Fe N D:Ala49 4.81 Fe N D:Cys50 4.29 Fe CB D:Cys50 3.37 Fe SG D:Cys50 2.30 Fe CA D:Cys50 4.49 Fe CB D:Lys60 4.46 Fe CG D:Lys60 4.77 Fe N D:Cys62 4.23 Fe CB D:Cys62 3.23 Fe SG D:Cys62 2.32 Fe CA D:Cys62 4.35 Fe S1 D:Fes4908 2.19 Fe S2 D:Fes4908 2.21 Fe FE1 D:Fes4908 2.74 Fe FE2 D:Fes4908 0.00 Fe O F:Hoh4960 4.04 interactive model: