Iron in the structure of Assimilatory Nitrite Reductase (NII3) - NO2 Complex From Tobbaco Leaf Analysed With Middle X-Ray Dose (pdb 3vkq)

The binding sites of Iron atom in the structure of Assimilatory Nitrite Reductase (NII3) - NO2 Complex From Tobbaco Leaf Analysed With Middle X-Ray Dose (pdb code 3vkq). This binding sites where shown with 5.0 Angstroms radius around Iron atom. The 3vkq structure was solved by S.NAKANO, M.TAKAHASHI, A.SAKAMOTO, H.MORIKAWA, K.KATAYANAGI, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 37.3-1.6 Space group P4212 a (A) 134.150 b (A) 134.150 c (A) 77.994 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 15.2 Rfree (%) 16.8 Iron Binding Sites: Iron binding site 1 out of 5 in 3vkq Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Iron in the PDB 3vkq. 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: Arg109, A: Lys224, A: Cys485, A: Srm601, A: Sf4602, A: No2606, A: Hoh1054, conact list: Atom Atom Distance (A) Fe NH2 A:Arg109 4.85 Fe NZ A:Lys224 4.44 Fe N A:Cys485 4.97 Fe CB A:Cys485 3.38 Fe SG A:Cys485 2.35 Fe CA A:Cys485 4.25 Fe C2D A:Srm601 4.29 Fe NA A:Srm601 2.04 Fe CAB A:Srm601 4.98 Fe CHA A:Srm601 3.40 Fe CDB A:Srm601 4.87 Fe C2A A:Srm601 4.32 Fe C1D A:Srm601 3.01 Fe C4A A:Srm601 3.00 Fe C4B A:Srm601 3.03 Fe C3A A:Srm601 4.30 Fe C1C A:Srm601 3.04 Fe C2C A:Srm601 4.32 Fe NB A:Srm601 2.02 Fe FE A:Srm601 0.00 Fe C3B A:Srm601 4.29 Fe C4D A:Srm601 3.00 Fe NC A:Srm601 2.06 Fe CHB A:Srm601 3.34 Fe CHC A:Srm601 3.38 Fe C3D A:Srm601 4.27 Fe C4C A:Srm601 3.04 Fe C2B A:Srm601 4.30 Fe CHD A:Srm601 3.39 Fe ND A:Srm601 2.02 Fe C1B A:Srm601 3.01 Fe C3C A:Srm601 4.32 Fe C1A A:Srm601 3.05 Fe CMA A:Srm601 4.83 Fe FE4 A:Sf4602 4.15 Fe O1 A:No2606 2.98 Fe O2 A:No2606 2.98 Fe N A:No2606 1.92 Fe O A:Hoh1054 4.37 interactive model: Iron binding site 2 out of 5 in 3vkq Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Iron in the PDB 3vkq. 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: Cys440, A: Cys446, A: Gln448, A: Ala449, A: Gly480, A: Cys481, A: Asn483, A: Thr484, A: Cys485, A: Sf4602, conact list: Atom Atom Distance (A) Fe SG A:Cys440 4.91 Fe SG A:Cys446 4.53 Fe O A:Gln448 4.98 Fe CB A:Gln448 4.70 Fe C A:Gln448 4.82 Fe N A:Ala449 4.72 Fe CA A:Ala449 4.72 Fe O A:Gly480 4.95 Fe N A:Gly480 4.58 Fe C A:Gly480 4.22 Fe CA A:Gly480 4.59 Fe O A:Cys481 4.19 Fe N A:Cys481 3.57 Fe CB A:Cys481 3.39 Fe SG A:Cys481 2.28 Fe C A:Cys481 4.25 Fe CA A:Cys481 3.91 Fe N A:Asn483 4.64 Fe CB A:Asn483 4.14 Fe ND2 A:Asn483 4.32 Fe CG A:Asn483 4.68 Fe CA A:Asn483 4.89 Fe N A:Thr484 4.94 Fe SG A:Cys485 4.70 Fe S1 A:Sf4602 3.95 Fe FE1 A:Sf4602 0.00 Fe FE3 A:Sf4602 2.72 Fe S4 A:Sf4602 2.32 Fe FE2 A:Sf4602 2.76 Fe S2 A:Sf4602 2.33 Fe FE4 A:Sf4602 2.74 Fe S3 A:Sf4602 2.28 interactive model: Iron binding site 3 out of 5 in 3vkq Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Iron in the PDB 3vkq. 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: Cys440, A: Thr441, A: Gly442, A: Cys446, A: Thr479, A: Gly480, A: Cys481, A: Cys485, A: Sf4602, conact list: Atom Atom Distance (A) Fe CB A:Cys440 3.26 Fe SG A:Cys440 2.31 Fe C A:Cys440 4.71 Fe CA A:Cys440 4.59 Fe N A:Thr441 4.52 Fe N A:Gly442 4.06 Fe CA A:Gly442 4.61 Fe SG A:Cys446 4.87 Fe OG1 A:Thr479 4.25 Fe C A:Thr479 4.75 Fe CA A:Thr479 4.94 Fe N A:Gly480 3.64 Fe C A:Gly480 4.69 Fe CA A:Gly480 4.12 Fe N A:Cys481 4.53 Fe SG A:Cys481 4.95 Fe CB A:Cys485 4.54 Fe SG A:Cys485 4.57 Fe S1 A:Sf4602 2.31 Fe FE1 A:Sf4602 2.76 Fe FE3 A:Sf4602 2.73 Fe S4 A:Sf4602 2.27 Fe FE2 A:Sf4602 0.00 Fe S2 A:Sf4602 3.89 Fe FE4 A:Sf4602 2.64 Fe S3 A:Sf4602 2.32 interactive model: Iron binding site 4 out of 5 in 3vkq Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Iron in the PDB 3vkq. 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: Cys440, A: Gly442, A: Cys446, A: Gln448, A: Ala449, A: Cys481, A: Cys485, A: Srm601, A: Sf4602, conact list: Atom Atom Distance (A) Fe SG A:Cys440 4.78 Fe N A:Gly442 4.77 Fe CB A:Cys446 3.19 Fe SG A:Cys446 2.25 Fe CA A:Cys446 4.62 Fe CB A:Gln448 4.80 Fe N A:Ala449 4.46 Fe CB A:Ala449 4.63 Fe CA A:Ala449 4.77 Fe SG A:Cys481 4.64 Fe SG A:Cys485 4.95 Fe C4A A:Srm601 4.64 Fe C3A A:Srm601 4.32 Fe CBA A:Srm601 4.39 Fe CDA A:Srm601 5.00 Fe S1 A:Sf4602 2.28 Fe FE1 A:Sf4602 2.72 Fe FE3 A:Sf4602 0.00 Fe S4 A:Sf4602 2.32 Fe FE2 A:Sf4602 2.73 Fe S2 A:Sf4602 2.31 Fe FE4 A:Sf4602 2.72 Fe S3 A:Sf4602 3.93 interactive model: Iron binding site 5 out of 5 in 3vkq Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Iron in the PDB 3vkq. 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: Cys440, A: Cys446, A: Cys481, A: Asn483, A: Cys485, A: Srm601, A: Sf4602, conact list: Atom Atom Distance (A) Fe CB A:Cys440 4.75 Fe SG A:Cys440 4.64 Fe SG A:Cys446 4.75 Fe SG A:Cys481 4.70 Fe CB A:Asn483 4.31 Fe ND2 A:Asn483 4.86 Fe N A:Cys485 4.19 Fe CB A:Cys485 3.20 Fe SG A:Cys485 2.31 Fe CA A:Cys485 4.33 Fe NA A:Srm601 3.75 Fe CHA A:Srm601 4.77 Fe C2A A:Srm601 4.99 Fe C4A A:Srm601 3.81 Fe C3A A:Srm601 4.36 Fe NB A:Srm601 4.68 Fe FE A:Srm601 4.15 Fe C4D A:Srm601 4.84 Fe CHB A:Srm601 4.07 Fe ND A:Srm601 4.52 Fe C1B A:Srm601 4.56 Fe C1A A:Srm601 4.31 Fe S1 A:Sf4602 2.33 Fe FE1 A:Sf4602 2.74 Fe FE3 A:Sf4602 2.72 Fe S4 A:Sf4602 3.87 Fe FE2 A:Sf4602 2.64 Fe S2 A:Sf4602 2.27 Fe FE4 A:Sf4602 0.00 Fe S3 A:Sf4602 2.34 interactive model: