Iron in the structure of Three-Dimensional Structure Of the Carbon Monoxide Complex of [Nife]Hydrogenase From Desulufovibrio Vulgaris Miyazaki F (pdb 1ubo)

The binding sites of Iron atom in the structure of Three-Dimensional Structure Of the Carbon Monoxide Complex of [Nife]Hydrogenase From Desulufovibrio Vulgaris Miyazaki F (pdb code 1ubo). This binding sites where shown with 5.0 Angstroms radius around Iron atom. The 1ubo structure was solved by H.OGATA, Y.MIZOGUCHI, N.MIZUNO, K.MIKI, S.ADACHI, N.YASUOKA, T.YAGI, O.YAMAUCHI, S.HIROTA, Y.HIGUCHI, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 20.0-1.4 Space group P212121 a (A) 98.000 b (A) 125.980 c (A) 66.570 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 13.4 Rfree (%) 13.7 Iron Binding Sites: Iron binding site 1 out of 12 in 1ubo Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Iron in the PDB 1ubo. 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: S: Glu16, S: Cys17, S: Thr18, S: Gly19, S: Cys20, S: Cys114, S: Cys150, L: Arg79, L: His235, S: Sf41001, S: Hoh3117, conact list: Atom Atom Distance (A) Fe C S:Glu16 4.89 Fe N S:Cys17 3.75 Fe CB S:Cys17 3.39 Fe SG S:Cys17 2.28 Fe C S:Cys17 4.50 Fe CA S:Cys17 4.05 Fe N S:Thr18 4.50 Fe N S:Gly19 4.20 Fe C S:Gly19 4.96 Fe CA S:Gly19 4.49 Fe N S:Cys20 4.58 Fe SG S:Cys20 4.84 Fe SG S:Cys114 4.65 Fe SG S:Cys150 4.73 Fe CG L:Arg79 4.69 Fe ND1 L:His235 4.86 Fe CE1 L:His235 4.18 Fe S1 S:Sf41001 2.32 Fe FE1 S:Sf41001 0.00 Fe FE3 S:Sf41001 2.67 Fe S4 S:Sf41001 3.85 Fe FE2 S:Sf41001 2.65 Fe S2 S:Sf41001 2.25 Fe FE4 S:Sf41001 2.69 Fe S3 S:Sf41001 2.31 Fe O S:Hoh3117 4.44 interactive model: Iron binding site 2 out of 12 in 1ubo Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Iron in the PDB 1ubo. 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: S: Glu16, S: Cys17, S: Cys20, S: Cys114, S: Cys150, S: Sf41001, S: Hoh3014, S: Hoh3015, S: Hoh3117, conact list: Atom Atom Distance (A) Fe CA S:Glu16 4.98 Fe N S:Cys17 4.87 Fe SG S:Cys17 4.83 Fe SG S:Cys20 4.71 Fe N S:Cys114 4.05 Fe CB S:Cys114 3.25 Fe SG S:Cys114 2.23 Fe CA S:Cys114 4.24 Fe SG S:Cys150 4.51 Fe S1 S:Sf41001 2.28 Fe FE1 S:Sf41001 2.65 Fe FE3 S:Sf41001 2.64 Fe S4 S:Sf41001 2.30 Fe FE2 S:Sf41001 0.00 Fe S2 S:Sf41001 2.29 Fe FE4 S:Sf41001 2.73 Fe S3 S:Sf41001 3.82 Fe O S:Hoh3014 4.01 Fe O S:Hoh3015 4.02 Fe O S:Hoh3117 4.10 interactive model: Iron binding site 3 out of 12 in 1ubo Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Iron in the PDB 1ubo. 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: S: Cys17, S: Cys20, S: Cys114, S: Gly149, S: Cys150, S: Pro151, L: Arg79, L: His235, S: Sf41001, S: Hoh3014, conact list: Atom Atom Distance (A) Fe SG S:Cys17 4.59 Fe SG S:Cys20 4.74 Fe SG S:Cys114 4.35 Fe O S:Gly149 4.69 Fe O S:Cys150 4.22 Fe N S:Cys150 4.78 Fe CB S:Cys150 3.40 Fe SG S:Cys150 2.30 Fe C S:Cys150 3.81 Fe CA S:Cys150 3.44 Fe N S:Pro151 4.33 Fe CA S:Pro151 4.66 Fe CG L:Arg79 4.16 Fe NE L:Arg79 4.68 Fe ND1 L:His235 4.59 Fe CE1 L:His235 4.64 Fe S1 S:Sf41001 3.89 Fe FE1 S:Sf41001 2.67 Fe FE3 S:Sf41001 0.00 Fe S4 S:Sf41001 2.31 Fe FE2 S:Sf41001 2.64 Fe S2 S:Sf41001 2.33 Fe FE4 S:Sf41001 2.73 Fe S3 S:Sf41001 2.22 Fe O S:Hoh3014 3.86 interactive model: Iron binding site 4 out of 12 in 1ubo Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Iron in the PDB 1ubo. 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: S: Cys17, S: Gly19, S: Cys20, S: Glu75, S: Gly112, S: Cys114, S: Gly149, S: Cys150, S: Pro151, S: Sf41001, S: Hoh3015, conact list: Atom Atom Distance (A) Fe SG S:Cys17 4.64 Fe N S:Gly19 4.94 Fe C S:Gly19 4.46 Fe CA S:Gly19 4.85 Fe N S:Cys20 3.62 Fe CB S:Cys20 3.47 Fe SG S:Cys20 2.27 Fe CA S:Cys20 4.05 Fe OE1 S:Glu75 4.69 Fe CG S:Glu75 4.97 Fe CA S:Gly112 4.57 Fe SG S:Cys114 4.85 Fe O S:Gly149 4.78 Fe SG S:Cys150 4.91 Fe CA S:Cys150 4.75 Fe N S:Pro151 4.78 Fe CB S:Pro151 4.36 Fe CA S:Pro151 4.36 Fe S1 S:Sf41001 2.32 Fe FE1 S:Sf41001 2.69 Fe FE3 S:Sf41001 2.73 Fe S4 S:Sf41001 2.28 Fe FE2 S:Sf41001 2.73 Fe S2 S:Sf41001 3.95 Fe FE4 S:Sf41001 0.00 Fe S3 S:Sf41001 2.27 Fe O S:Hoh3015 3.91 interactive model: Iron binding site 5 out of 12 in 1ubo Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Iron in the PDB 1ubo. 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: S: His188, S: Cys191, S: Phe197, S: Cys216, S: Cys222, S: Gly224, S: Pro225, S: Sf41002, conact list: Atom Atom Distance (A) Fe O S:His188 4.49 Fe NE2 S:His188 4.20 Fe CB S:His188 3.67 Fe ND1 S:His188 2.08 Fe CD2 S:His188 4.28 Fe C S:His188 4.68 Fe CE1 S:His188 3.00 Fe CG S:His188 3.18 Fe CA S:His188 3.95 Fe CB S:Cys191 4.46 Fe SG S:Cys191 4.58 Fe CD2 S:Phe197 4.71 Fe SG S:Cys216 4.62 Fe SG S:Cys222 4.73 Fe CA S:Gly224 4.92 Fe N S:Pro225 4.80 Fe CD S:Pro225 4.30 Fe CG S:Pro225 4.36 Fe S1 S:Sf41002 2.26 Fe FE1 S:Sf41002 0.00 Fe FE3 S:Sf41002 2.63 Fe S4 S:Sf41002 3.81 Fe FE2 S:Sf41002 2.67 Fe S2 S:Sf41002 2.28 Fe FE4 S:Sf41002 2.68 Fe S3 S:Sf41002 2.31 interactive model: Iron binding site 6 out of 12 in 1ubo Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 6 of Iron in the PDB 1ubo. 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: S: His188, S: Cys191, S: Cys216, S: Leu217, S: Tyr218, S: Cys222, S: Gly224, S: Pro225, S: Val243, S: Sf41002, conact list: Atom Atom Distance (A) Fe ND1 S:His188 4.62 Fe SG S:Cys191 4.74 Fe SG S:Cys216 4.72 Fe N S:Leu217 4.82 Fe CB S:Leu217 4.86 Fe N S:Tyr218 4.84 Fe CB S:Cys222 3.22 Fe SG S:Cys222 2.31 Fe C S:Cys222 4.85 Fe CA S:Cys222 4.60 Fe N S:Gly224 4.52 Fe CA S:Gly224 4.54 Fe CD S:Pro225 4.65 Fe CG1 S:Val243 4.35 Fe S1 S:Sf41002 2.31 Fe FE1 S:Sf41002 2.67 Fe FE3 S:Sf41002 2.68 Fe S4 S:Sf41002 2.32 Fe FE2 S:Sf41002 0.00 Fe S2 S:Sf41002 2.26 Fe FE4 S:Sf41002 2.77 Fe S3 S:Sf41002 3.90 interactive model: Iron binding site 7 out of 12 in 1ubo Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 7 of Iron in the PDB 1ubo. 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: S: His188, S: Cys191, S: Arg193, S: Leu194, S: Cys216, S: Cys222, S: Val243, S: Sf41002, conact list: Atom Atom Distance (A) Fe ND1 S:His188 4.44 Fe CB S:Cys191 3.15 Fe SG S:Cys191 2.31 Fe CA S:Cys191 4.59 Fe N S:Arg193 4.57 Fe CB S:Arg193 3.94 Fe CD S:Arg193 4.91 Fe C S:Arg193 4.66 Fe CG S:Arg193 4.63 Fe CA S:Arg193 4.61 Fe N S:Leu194 4.73 Fe SG S:Cys216 4.94 Fe SG S:Cys222 4.78 Fe CG2 S:Val243 4.35 Fe CG1 S:Val243 4.58 Fe S1 S:Sf41002 3.87 Fe FE1 S:Sf41002 2.63 Fe FE3 S:Sf41002 0.00 Fe S4 S:Sf41002 2.27 Fe FE2 S:Sf41002 2.68 Fe S2 S:Sf41002 2.33 Fe FE4 S:Sf41002 2.72 Fe S3 S:Sf41002 2.30 interactive model: Iron binding site 8 out of 12 in 1ubo Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 8 of Iron in the PDB 1ubo. 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: S: His188, S: Cys191, S: Arg193, S: Phe197, S: Cys216, S: Leu217, S: Tyr218, S: Cys222, S: Sf41002, conact list: Atom Atom Distance (A) Fe ND1 S:His188 4.40 Fe CE1 S:His188 4.71 Fe SG S:Cys191 4.88 Fe O S:Arg193 4.85 Fe CB S:Arg193 4.44 Fe CB S:Phe197 4.39 Fe CD2 S:Phe197 4.43 Fe CG S:Phe197 4.89 Fe CB S:Cys216 3.44 Fe SG S:Cys216 2.29 Fe C S:Cys216 4.24 Fe CA S:Cys216 3.87 Fe N S:Leu217 3.77 Fe C S:Leu217 4.82 Fe CA S:Leu217 4.76 Fe N S:Tyr218 4.23 Fe CB S:Tyr218 4.66 Fe CA S:Tyr218 4.89 Fe SG S:Cys222 4.87 Fe S1 S:Sf41002 2.34 Fe FE1 S:Sf41002 2.68 Fe FE3 S:Sf41002 2.72 Fe S4 S:Sf41002 2.30 Fe FE2 S:Sf41002 2.77 Fe S2 S:Sf41002 3.94 Fe FE4 S:Sf41002 0.00 Fe S3 S:Sf41002 2.24 interactive model: Iron binding site 9 out of 12 in 1ubo Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 9 of Iron in the PDB 1ubo. 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: S: Val187, S: Thr227, S: Cys231, S: Cys249, S: Ile250, S: Gly251, S: Cys252, L: Gln237, S: F3s1003, conact list: Atom Atom Distance (A) Fe CG1 S:Val187 4.67 Fe CG2 S:Thr227 4.61 Fe SG S:Cys231 4.79 Fe N S:Cys249 4.99 Fe CB S:Cys249 3.29 Fe SG S:Cys249 2.34 Fe C S:Cys249 4.31 Fe CA S:Cys249 3.71 Fe N S:Ile250 4.05 Fe N S:Gly251 4.17 Fe CA S:Gly251 4.77 Fe N S:Cys252 4.46 Fe SG S:Cys252 4.81 Fe NE2 L:Gln237 4.82 Fe S1 S:F3s1003 2.25 Fe FE1 S:F3s1003 0.00 Fe FE3 S:F3s1003 2.70 Fe S4 S:F3s1003 3.90 Fe S2 S:F3s1003 2.29 Fe FE4 S:F3s1003 2.69 Fe S3 S:F3s1003 2.30 interactive model: Iron binding site 10 out of 12 in 1ubo Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 10 of Iron in the PDB 1ubo. 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: S: Val187, S: Asn229, S: Cys231, S: Phe236, S: Pro242, S: Cys249, S: Cys252, S: F3s1003, S: Hoh3033, conact list: Atom Atom Distance (A) Fe CG1 S:Val187 4.57 Fe CB S:Asn229 4.64 Fe OD1 S:Asn229 3.89 Fe CG S:Asn229 4.50 Fe CB S:Cys231 3.33 Fe SG S:Cys231 2.30 Fe CA S:Cys231 4.73 Fe CE2 S:Phe236 4.32 Fe CZ S:Phe236 4.49 Fe CD S:Pro242 4.74 Fe CG S:Pro242 4.84 Fe SG S:Cys249 4.81 Fe SG S:Cys252 4.77 Fe S1 S:F3s1003 2.24 Fe FE1 S:F3s1003 2.70 Fe FE3 S:F3s1003 0.00 Fe S4 S:F3s1003 2.26 Fe S2 S:F3s1003 3.96 Fe FE4 S:F3s1003 2.70 Fe S3 S:F3s1003 2.30 Fe O S:Hoh3033 4.37 interactive model: Iron binding site 11 out of 12 in 1ubo Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 11 of Iron in the PDB 1ubo. 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: S: Asn229, S: Cys231, S: Cys249, S: Gly251, S: Cys252, S: Ser253, L: Lys232, S: F3s1003, S: Hoh3033, S: Hoh3148, L: Hoh3021, conact list: Atom Atom Distance (A) Fe OD1 S:Asn229 4.46 Fe SG S:Cys231 4.70 Fe SG S:Cys249 4.77 Fe C S:Gly251 4.94 Fe N S:Cys252 3.79 Fe CB S:Cys252 3.45 Fe SG S:Cys252 2.30 Fe C S:Cys252 4.57 Fe CA S:Cys252 4.08 Fe N S:Ser253 4.67 Fe CE L:Lys232 4.95 Fe S1 S:F3s1003 3.86 Fe FE1 S:F3s1003 2.69 Fe FE3 S:F3s1003 2.70 Fe S4 S:F3s1003 2.25 Fe S2 S:F3s1003 2.29 Fe FE4 S:F3s1003 0.00 Fe S3 S:F3s1003 2.31 Fe O S:Hoh3033 4.07 Fe O S:Hoh3148 4.83 Fe O L:Hoh3021 3.70 interactive model: Iron binding site 12 out of 12 in 1ubo Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 12 of Iron in the PDB 1ubo. 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: L: Cys81, L: Cys84, L: Thr87, L: His88, L: Arg479, L: Val500, L: Pro501, L: Cys546, L: Cys549, L: Fne1004, L: Cmo1006, conact list: Atom Atom Distance (A) Fe CB L:Cys81 4.87 Fe SG L:Cys81 4.71 Fe CB L:Cys84 3.36 Fe SG L:Cys84 2.25 Fe CA L:Cys84 4.75 Fe OG1 L:Thr87 4.71 Fe NE2 L:His88 4.12 Fe CD2 L:His88 4.89 Fe CB L:Arg479 4.94 Fe CD L:Arg479 4.27 Fe NH1 L:Arg479 4.64 Fe CG1 L:Val500 4.31 Fe CD L:Pro501 5.00 Fe CG L:Pro501 4.66 Fe CB L:Cys546 4.36 Fe SG L:Cys546 4.26 Fe CB L:Cys549 3.42 Fe SG L:Cys549 2.28 Fe CA L:Cys549 4.79 Fe NI L:Fne1004 2.62 Fe O2 L:Fne1004 3.11 Fe C1 L:Fne1004 1.96 Fe O1 L:Fne1004 3.11 Fe C3 L:Fne1004 1.78 Fe FE L:Fne1004 0.00 Fe O3 L:Fne1004 2.90 Fe C2 L:Fne1004 1.98 Fe O L:Cmo1006 4.39 Fe C L:Cmo1006 3.45 interactive model: