Iron in the structure of Crystal Structure of Tryptophanyl-Trna Synthetase From Hyperthermophilic Archaeon, Aeropyrum Pernix K1 (pdb 3a04)

The binding sites of Iron atom in the structure of Crystal Structure of Tryptophanyl-Trna Synthetase From Hyperthermophilic Archaeon, Aeropyrum Pernix K1 (pdb code 3a04). This binding sites where shown with 5.0 Angstroms radius around Iron atom. The 3a04 structure was solved by W.TSUCHIYA, Z.FUJIMOTO, T.HASEGAWA, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 32.5-2.0 Space group C2221 a (A) 98.709 b (A) 103.194 c (A) 97.806 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 17.8 Rfree (%) 23.5 Iron Binding Sites: Iron binding site 1 out of 4 in 3a04 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Iron in the PDB 3a04. 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: Cys303, A: Val305, A: Ile323, A: Cys327, A: Cys334, A: Cys337, A: Sf4373, conact list: Atom Atom Distance (A) Fe SG A:Cys303 4.68 Fe CG1 A:Val305 4.80 Fe CG2 A:Ile323 4.60 Fe CB A:Cys327 4.78 Fe SG A:Cys327 4.76 Fe SG A:Cys334 4.81 Fe CA A:Cys334 4.77 Fe CB A:Cys337 3.00 Fe SG A:Cys337 2.28 Fe C A:Cys337 4.99 Fe CA A:Cys337 4.43 Fe S1 A:Sf4373 3.85 Fe FE1 A:Sf4373 0.00 Fe FE3 A:Sf4373 2.72 Fe S4 A:Sf4373 2.37 Fe FE2 A:Sf4373 2.75 Fe S2 A:Sf4373 2.25 Fe FE4 A:Sf4373 2.62 Fe S3 A:Sf4373 2.29 interactive model: Iron binding site 2 out of 4 in 3a04 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Iron in the PDB 3a04. 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: Gln293, A: Gly298, A: Val299, A: Pro300, A: Cys327, A: Ile332, A: Cys334, A: Cys337, A: Sf4373, conact list: Atom Atom Distance (A) Fe NE2 A:Gln293 4.38 Fe C A:Gly298 4.89 Fe CA A:Gly298 4.52 Fe N A:Val299 4.83 Fe N A:Pro300 4.92 Fe CD A:Pro300 4.87 Fe CG A:Pro300 4.50 Fe CB A:Cys327 3.06 Fe SG A:Cys327 2.23 Fe CA A:Cys327 4.29 Fe CG2 A:Ile332 4.99 Fe SG A:Cys334 4.82 Fe SG A:Cys337 4.80 Fe S1 A:Sf4373 2.26 Fe FE1 A:Sf4373 2.75 Fe FE3 A:Sf4373 2.75 Fe S4 A:Sf4373 2.30 Fe FE2 A:Sf4373 0.00 Fe S2 A:Sf4373 3.94 Fe FE4 A:Sf4373 2.78 Fe S3 A:Sf4373 2.35 interactive model: Iron binding site 3 out of 4 in 3a04 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Iron in the PDB 3a04. 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: Thr284, A: Gly286, A: Gln293, A: Cys303, A: Cys327, A: Leu333, A: Cys334, A: Cys337, A: Sf4373, conact list: Atom Atom Distance (A) Fe CB A:Thr284 4.14 Fe CG2 A:Thr284 4.51 Fe OG1 A:Thr284 4.58 Fe N A:Gly286 4.59 Fe CA A:Gly286 4.63 Fe NE2 A:Gln293 4.51 Fe SG A:Cys303 4.67 Fe SG A:Cys327 4.73 Fe C A:Leu333 4.70 Fe N A:Cys334 4.03 Fe CB A:Cys334 3.42 Fe SG A:Cys334 2.27 Fe C A:Cys334 4.86 Fe CA A:Cys334 3.55 Fe CB A:Cys337 4.54 Fe SG A:Cys337 4.73 Fe S1 A:Sf4373 2.29 Fe FE1 A:Sf4373 2.72 Fe FE3 A:Sf4373 0.00 Fe S4 A:Sf4373 2.33 Fe FE2 A:Sf4373 2.75 Fe S2 A:Sf4373 2.31 Fe FE4 A:Sf4373 2.74 Fe S3 A:Sf4373 3.91 interactive model: Iron binding site 4 out of 4 in 3a04 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Iron in the PDB 3a04. 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: Thr284, A: Gly285, A: Pro300, A: Cys303, A: Val305, A: Tyr306, A: Cys327, A: Cys334, A: Cys337, A: Sf4373, conact list: Atom Atom Distance (A) Fe CB A:Thr284 4.22 Fe CG2 A:Thr284 4.64 Fe CA A:Thr284 4.71 Fe N A:Gly285 4.28 Fe CA A:Pro300 4.96 Fe CB A:Cys303 3.22 Fe SG A:Cys303 2.35 Fe CA A:Cys303 4.64 Fe CB A:Val305 4.44 Fe N A:Tyr306 4.44 Fe CB A:Tyr306 4.42 Fe CA A:Tyr306 4.98 Fe SG A:Cys327 4.82 Fe SG A:Cys334 4.67 Fe SG A:Cys337 4.65 Fe S1 A:Sf4373 2.39 Fe FE1 A:Sf4373 2.62 Fe FE3 A:Sf4373 2.74 Fe S4 A:Sf4373 3.92 Fe FE2 A:Sf4373 2.78 Fe S2 A:Sf4373 2.27 Fe FE4 A:Sf4373 0.00 Fe S3 A:Sf4373 2.23 interactive model: