Iron in the structure of Crystal Structure of the Mo,Cu-Co Dehydrogenase (Codh), N- Butylisocyanide-Bound State (pdb 1n62)

The binding sites of Iron atom in the structure of Crystal Structure of the Mo,Cu-Co Dehydrogenase (Codh), N- Butylisocyanide-Bound State (pdb code 1n62). This binding sites where shown with 5.0 Angstroms radius around Iron atom. The 1n62 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) 17.8-1.1 Space group P212121 a (A) 117.860 b (A) 130.019 c (A) 156.231 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 14.4 Rfree (%) 17.2 Iron Binding Sites: Iron binding site 1 out of 8 in 1n62 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Iron in the PDB 1n62. 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: Hoh3926, conact list: Atom Atom Distance (A) Fe N A:Gln101 4.75 Fe CB A:Gln101 4.91 Fe C A:Gln101 4.61 Fe N A:Cys102 3.51 Fe CB A:Cys102 3.37 Fe SG A:Cys102 2.28 Fe C A:Cys102 4.21 Fe CA A:Cys102 3.84 Fe N A:Gly103 3.93 Fe C A:Gly103 4.95 Fe CA A:Gly103 4.90 Fe N A:Tyr104 4.14 Fe CB A:Tyr104 4.77 Fe CA A:Tyr104 4.95 Fe N A:Cys105 4.68 Fe SG A:Cys105 4.65 Fe SG A:Cys137 4.32 Fe N A:Arg138 4.72 Fe C A:Arg138 4.94 Fe N A:Cys139 3.99 Fe CB A:Cys139 3.29 Fe SG A:Cys139 2.31 Fe CA A:Cys139 4.26 Fe S1 A:Fes3907 2.25 Fe S2 A:Fes3907 2.22 Fe FE1 A:Fes3907 0.00 Fe FE2 A:Fes3907 2.69 Fe O B:Hoh3926 3.92 interactive model: Iron binding site 2 out of 8 in 1n62 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Iron in the PDB 1n62. 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: Hoh4009, conact list: Atom Atom Distance (A) Fe SG A:Cys102 4.65 Fe N A:Tyr104 4.90 Fe N A:Cys105 3.98 Fe CB A:Cys105 3.32 Fe SG A:Cys105 2.25 Fe C A:Cys105 4.89 Fe CA A:Cys105 4.22 Fe O A:Leu136 4.88 Fe N A:Cys137 4.94 Fe CB A:Cys137 3.32 Fe SG A:Cys137 2.34 Fe C A:Cys137 4.32 Fe CA A:Cys137 3.68 Fe N A:Arg138 4.07 Fe N A:Cys139 4.22 Fe CB A:Cys139 4.35 Fe SG A:Cys139 4.39 Fe CA A:Cys139 4.88 Fe N A:Thr140 5.00 Fe CG2 A:Thr140 4.67 Fe S1 A:Fes3907 2.19 Fe S2 A:Fes3907 2.22 Fe FE1 A:Fes3907 2.69 Fe FE2 A:Fes3907 0.00 Fe O A:Hoh4009 4.33 interactive model: Iron binding site 3 out of 8 in 1n62 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Iron in the PDB 1n62. 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: Hoh4063, conact list: Atom Atom Distance (A) Fe O A:Gly41 4.93 Fe N A:Gly41 4.08 Fe C A:Gly41 4.14 Fe CA A:Gly41 4.43 Fe O A:Cys42 3.99 Fe N A:Cys42 3.49 Fe CB A:Cys42 3.46 Fe SG A:Cys42 2.31 Fe C A:Cys42 4.15 Fe CA A:Cys42 3.86 Fe N A:Ser45 4.64 Fe C A:Ser45 4.61 Fe CA A:Ser45 4.55 Fe N A:His46 4.33 Fe C A:His46 4.54 Fe N A:Cys47 3.41 Fe CB A:Cys47 3.40 Fe SG A:Cys47 2.27 Fe C A:Cys47 4.19 Fe CA A:Cys47 3.77 Fe N A:Gly48 3.80 Fe CA A:Gly48 4.83 Fe N A:Ala49 4.47 Fe SG A:Cys50 4.61 Fe SG A:Cys62 4.31 Fe S1 A:Fes3908 2.23 Fe S2 A:Fes3908 2.23 Fe FE1 A:Fes3908 0.00 Fe FE2 A:Fes3908 2.70 Fe O A:Hoh4063 3.93 interactive model: Iron binding site 4 out of 8 in 1n62 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Iron in the PDB 1n62. 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: Thr63, A: Fes3908, A: Hoh4063, conact list: Atom Atom Distance (A) Fe SG A:Cys42 4.51 Fe CA A:Ser45 4.74 Fe SG A:Cys47 4.39 Fe N A:Gly48 4.53 Fe CA A:Gly48 4.88 Fe N A:Ala49 4.74 Fe N A:Cys50 4.23 Fe CB A:Cys50 3.36 Fe SG A:Cys50 2.27 Fe CA A:Cys50 4.43 Fe CB A:Lys60 4.37 Fe CD A:Lys60 4.92 Fe CG A:Lys60 4.73 Fe CA A:Lys60 4.95 Fe N A:Cys62 4.19 Fe CB A:Cys62 3.20 Fe SG A:Cys62 2.28 Fe C A:Cys62 4.99 Fe CA A:Cys62 4.27 Fe OG1 A:Thr63 4.95 Fe S1 A:Fes3908 2.17 Fe S2 A:Fes3908 2.17 Fe FE1 A:Fes3908 2.70 Fe FE2 A:Fes3908 0.00 Fe O A:Hoh4063 3.98 interactive model: Iron binding site 5 out of 8 in 1n62 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Iron in the PDB 1n62. 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: Hoh4947, conact list: Atom Atom Distance (A) Fe N D:Gln101 4.76 Fe CB D:Gln101 4.93 Fe C D:Gln101 4.65 Fe N D:Cys102 3.54 Fe CB D:Cys102 3.39 Fe SG D:Cys102 2.27 Fe C D:Cys102 4.23 Fe CA D:Cys102 3.85 Fe N D:Gly103 3.95 Fe C D:Gly103 4.92 Fe CA D:Gly103 4.90 Fe N D:Tyr104 4.10 Fe CB D:Tyr104 4.71 Fe CA D:Tyr104 4.90 Fe N D:Cys105 4.62 Fe SG D:Cys105 4.69 Fe SG D:Cys137 4.33 Fe N D:Arg138 4.73 Fe C D:Arg138 4.88 Fe N D:Cys139 3.93 Fe CB D:Cys139 3.26 Fe SG D:Cys139 2.27 Fe CA D:Cys139 4.21 Fe S1 D:Fes4907 2.25 Fe S2 D:Fes4907 2.24 Fe FE1 D:Fes4907 0.00 Fe FE2 D:Fes4907 2.71 Fe O E:Hoh4947 3.92 interactive model: Iron binding site 6 out of 8 in 1n62 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 6 of Iron in the PDB 1n62. 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: Thr106, D: Leu136, D: Cys137, D: Arg138, D: Cys139, D: Thr140, D: Fes4907, D: Hoh4917, conact list: Atom Atom Distance (A) Fe SG D:Cys102 4.67 Fe N D:Tyr104 4.88 Fe N D:Cys105 3.91 Fe CB D:Cys105 3.30 Fe SG D:Cys105 2.25 Fe C D:Cys105 4.83 Fe CA D:Cys105 4.16 Fe N D:Thr106 4.98 Fe O D:Leu136 4.92 Fe N D:Cys137 4.97 Fe CB D:Cys137 3.35 Fe SG D:Cys137 2.32 Fe C D:Cys137 4.33 Fe CA D:Cys137 3.71 Fe N D:Arg138 4.07 Fe N D:Cys139 4.15 Fe CB D:Cys139 4.34 Fe SG D:Cys139 4.39 Fe CA D:Cys139 4.83 Fe N D:Thr140 4.93 Fe CG2 D:Thr140 4.66 Fe S1 D:Fes4907 2.21 Fe S2 D:Fes4907 2.23 Fe FE1 D:Fes4907 2.71 Fe FE2 D:Fes4907 0.00 Fe O D:Hoh4917 4.33 interactive model: Iron binding site 7 out of 8 in 1n62 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 7 of Iron in the PDB 1n62. 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, D: Hoh4960, conact list: Atom Atom Distance (A) Fe O D:Gly41 4.94 Fe N D:Gly41 4.15 Fe C D:Gly41 4.16 Fe CA D:Gly41 4.46 Fe O D:Cys42 4.00 Fe N D:Cys42 3.50 Fe CB D:Cys42 3.44 Fe SG D:Cys42 2.30 Fe C D:Cys42 4.12 Fe CA D:Cys42 3.85 Fe N D:Ser45 4.66 Fe C D:Ser45 4.63 Fe CA D:Ser45 4.60 Fe N D:His46 4.33 Fe C D:His46 4.54 Fe N D:Cys47 3.42 Fe CB D:Cys47 3.39 Fe SG D:Cys47 2.28 Fe C D:Cys47 4.22 Fe CA D:Cys47 3.81 Fe N D:Gly48 3.84 Fe CA D:Gly48 4.84 Fe N D:Ala49 4.50 Fe SG D:Cys50 4.58 Fe SG D:Cys62 4.27 Fe S1 D:Fes4908 2.24 Fe S2 D:Fes4908 2.22 Fe FE1 D:Fes4908 0.00 Fe FE2 D:Fes4908 2.67 Fe O D:Hoh4960 4.17 interactive model: Iron binding site 8 out of 8 in 1n62 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 8 of Iron in the PDB 1n62. 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, D: Hoh4960, conact list: Atom Atom Distance (A) Fe SG D:Cys42 4.45 Fe CA D:Ser45 4.73 Fe SG D:Cys47 4.36 Fe N D:Gly48 4.53 Fe CA D:Gly48 4.88 Fe N D:Ala49 4.77 Fe N D:Cys50 4.25 Fe CB D:Cys50 3.34 Fe SG D:Cys50 2.27 Fe CA D:Cys50 4.44 Fe CB D:Lys60 4.41 Fe C D:Lys60 5.00 Fe CG D:Lys60 4.79 Fe CA D:Lys60 4.97 Fe N D:Cys62 4.15 Fe CB D:Cys62 3.18 Fe SG D:Cys62 2.29 Fe CA D:Cys62 4.26 Fe S1 D:Fes4908 2.16 Fe S2 D:Fes4908 2.18 Fe FE1 D:Fes4908 2.67 Fe FE2 D:Fes4908 0.00 Fe O D:Hoh4960 4.05 interactive model: