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

The binding sites of Iron atom in the structure of Assimilatory Nitrite Reductase (NII3) - NO2 Complex From Tobbaco Leaf Analysed With Low X-Ray Dose (pdb code 3vkp). This binding sites where shown with 5.0 Angstroms radius around Iron atom. The 3vkp 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) 29.2-1.4 Space group P4212 a (A) 133.107 b (A) 133.107 c (A) 77.796 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 17.5 Rfree (%) 18.9 Iron Binding Sites: Iron binding site 1 out of 5 in 3vkp Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Iron in the PDB 3vkp. 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 4.84 Fe NZ A:Lys224 4.41 Fe N A:Cys485 4.99 Fe CB A:Cys485 3.41 Fe SG A:Cys485 2.36 Fe CA A:Cys485 4.24 Fe C2D A:Srm601 4.30 Fe NA A:Srm601 2.03 Fe CAB A:Srm601 4.98 Fe CHA A:Srm601 3.38 Fe CDB A:Srm601 4.89 Fe C2A A:Srm601 4.29 Fe C1D A:Srm601 3.02 Fe C4A A:Srm601 3.00 Fe C4B A:Srm601 3.03 Fe C3A A:Srm601 4.29 Fe C1C A:Srm601 3.02 Fe C2C A:Srm601 4.30 Fe NB A:Srm601 2.02 Fe FE A:Srm601 0.00 Fe C3B A:Srm601 4.28 Fe C4D A:Srm601 3.02 Fe NC A:Srm601 2.04 Fe CHB A:Srm601 3.34 Fe CHC A:Srm601 3.37 Fe C3D A:Srm601 4.28 Fe C4C A:Srm601 3.03 Fe C2B A:Srm601 4.30 Fe CHD A:Srm601 3.37 Fe ND A:Srm601 2.02 Fe C1B A:Srm601 3.01 Fe C3C A:Srm601 4.30 Fe C1A A:Srm601 3.03 Fe CMA A:Srm601 4.78 Fe FE4 A:Sf4602 4.14 Fe O1 A:No2606 3.11 Fe O2 A:No2606 2.84 Fe N A:No2606 1.92 Fe O A:Hoh1054 4.35 interactive model: Iron binding site 2 out of 5 in 3vkp Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Iron in the PDB 3vkp. 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 4.88 Fe SG A:Cys446 4.52 Fe O A:Gln448 4.93 Fe CB A:Gln448 4.67 Fe C A:Gln448 4.80 Fe N A:Ala449 4.73 Fe CA A:Ala449 4.73 Fe O A:Gly480 4.92 Fe N A:Gly480 4.58 Fe C A:Gly480 4.20 Fe CA A:Gly480 4.59 Fe O A:Cys481 4.18 Fe N A:Cys481 3.57 Fe CB A:Cys481 3.34 Fe SG A:Cys481 2.28 Fe C A:Cys481 4.24 Fe CA A:Cys481 3.89 Fe N A:Asn483 4.62 Fe CB A:Asn483 4.09 Fe ND2 A:Asn483 4.31 Fe CG A:Asn483 4.65 Fe CA A:Asn483 4.85 Fe N A:Thr484 4.98 Fe SG A:Cys485 4.67 Fe S1 A:Sf4602 3.94 Fe FE1 A:Sf4602 0.00 Fe FE3 A:Sf4602 2.70 Fe S4 A:Sf4602 2.33 Fe FE2 A:Sf4602 2.75 Fe S2 A:Sf4602 2.33 Fe FE4 A:Sf4602 2.73 Fe S3 A:Sf4602 2.27 interactive model: Iron binding site 3 out of 5 in 3vkp Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Iron in the PDB 3vkp. 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 3.25 Fe SG A:Cys440 2.30 Fe C A:Cys440 4.72 Fe CA A:Cys440 4.58 Fe N A:Thr441 4.53 Fe N A:Gly442 4.08 Fe CA A:Gly442 4.60 Fe SG A:Cys446 4.84 Fe OG1 A:Thr479 4.26 Fe C A:Thr479 4.76 Fe CA A:Thr479 4.97 Fe N A:Gly480 3.65 Fe C A:Gly480 4.67 Fe CA A:Gly480 4.12 Fe N A:Cys481 4.51 Fe SG A:Cys481 4.94 Fe CB A:Cys485 4.49 Fe SG A:Cys485 4.55 Fe S1 A:Sf4602 2.30 Fe FE1 A:Sf4602 2.75 Fe FE3 A:Sf4602 2.70 Fe S4 A:Sf4602 2.26 Fe FE2 A:Sf4602 0.00 Fe S2 A:Sf4602 3.88 Fe FE4 A:Sf4602 2.63 Fe S3 A:Sf4602 2.32 interactive model: Iron binding site 4 out of 5 in 3vkp Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Iron in the PDB 3vkp. 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 4.74 Fe N A:Gly442 4.77 Fe CB A:Cys446 3.20 Fe SG A:Cys446 2.26 Fe CA A:Cys446 4.63 Fe CB A:Gln448 4.80 Fe N A:Ala449 4.47 Fe CB A:Ala449 4.65 Fe CA A:Ala449 4.77 Fe SG A:Cys481 4.63 Fe SG A:Cys485 4.93 Fe C4A A:Srm601 4.57 Fe C3A A:Srm601 4.30 Fe CBA A:Srm601 4.37 Fe S1 A:Sf4602 2.26 Fe FE1 A:Sf4602 2.70 Fe FE3 A:Sf4602 0.00 Fe S4 A:Sf4602 2.32 Fe FE2 A:Sf4602 2.70 Fe S2 A:Sf4602 2.32 Fe FE4 A:Sf4602 2.71 Fe S3 A:Sf4602 3.91 interactive model: Iron binding site 5 out of 5 in 3vkp Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Iron in the PDB 3vkp. 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 4.74 Fe SG A:Cys440 4.62 Fe SG A:Cys446 4.74 Fe SG A:Cys481 4.71 Fe CB A:Asn483 4.28 Fe ND2 A:Asn483 4.86 Fe N A:Cys485 4.20 Fe CB A:Cys485 3.16 Fe SG A:Cys485 2.30 Fe CA A:Cys485 4.30 Fe NA A:Srm601 3.73 Fe CHA A:Srm601 4.78 Fe C4A A:Srm601 3.73 Fe C3A A:Srm601 4.33 Fe NB A:Srm601 4.64 Fe FE A:Srm601 4.14 Fe C4D A:Srm601 4.77 Fe CHB A:Srm601 4.05 Fe ND A:Srm601 4.51 Fe C1B A:Srm601 4.53 Fe C1A A:Srm601 4.32 Fe S1 A:Sf4602 2.32 Fe FE1 A:Sf4602 2.73 Fe FE3 A:Sf4602 2.71 Fe S4 A:Sf4602 3.87 Fe FE2 A:Sf4602 2.63 Fe S2 A:Sf4602 2.26 Fe FE4 A:Sf4602 0.00 Fe S3 A:Sf4602 2.34 interactive model: