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 |
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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:
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