Iron in the structure of Structure of Catechol 2,3-Dioxygenase (Metapyrocatechase) From Pseudomonas Putida Mt-2 (pdb 1mpy)
The binding sites of Iron atom in the structure of Structure of Catechol 2,3-Dioxygenase (Metapyrocatechase) From Pseudomonas Putida Mt-2 (pdb code 1mpy). This binding sites where shown with 5.0 Angstroms radius around Iron atom. The 1mpy structure was solved by A.KITA, S.KITA, I.FUJISAWA, K.INAKA, T.ISHIDA, K.HORIIKE, M.NOZAKI, K.MIKI, with X-Ray Crystallography technique, brief refinement statistics is given in the table below:
Resolution (A) | 10.0-2.8 | Space group | P42212 | a (A) | 264.000 | b (A) | 264.000 | c (A) | 59.800 | alpha (°) | 90.00 | beta (°) | 90.00 | gamma (°) | 90.00 | Rfactor (%) | 20 | Rfree (%) | 28 |
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Iron Binding Sites:Iron binding site 1 out of 4 in 1mpy
|  Click to enlarge |  Click to enlarge | Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Iron in the PDB 1mpy. 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: His153, A: His199, A: His214, A: Ser216, A: His246, A: Tyr255, A: Glu265, A: Acn309, A: Hoh5109, | conact list:
Atom | Atom | Distance (A) | Fe | NE2 A:His153 | 2.39 | Fe | ND1 A:His153 | 4.52 | Fe | CD2 A:His153 | 3.46 | Fe | CE1 A:His153 | 3.33 | Fe | CG A:His153 | 4.61 | Fe | NE2 A:His199 | 4.00 | Fe | CE1 A:His199 | 4.17 | Fe | NE2 A:His214 | 2.50 | Fe | ND1 A:His214 | 4.45 | Fe | CD2 A:His214 | 3.68 | Fe | CE1 A:His214 | 3.21 | Fe | CG A:His214 | 4.70 | Fe | CB A:Ser216 | 4.71 | Fe | OG A:Ser216 | 3.61 | Fe | NE2 A:His246 | 4.73 | Fe | CZ A:Tyr255 | 4.81 | Fe | CE1 A:Tyr255 | 4.77 | Fe | OH A:Tyr255 | 3.82 | Fe | OE1 A:Glu265 | 2.29 | Fe | CB A:Glu265 | 4.91 | Fe | OE2 A:Glu265 | 3.32 | Fe | CD A:Glu265 | 3.14 | Fe | CG A:Glu265 | 4.51 | Fe | O A:Acn309 | 2.70 | Fe | C A:Acn309 | 3.98 | Fe | C1 A:Acn309 | 4.87 | Fe | O A:Hoh5109 | 4.05 |
| interactive model:
| Iron binding site 2 out of 4 in 1mpy
|  Click to enlarge |  Click to enlarge | Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Iron in the PDB 1mpy. 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: B: His153, B: His199, B: His214, B: Ser216, B: His246, B: Tyr255, B: Glu265, B: Acn309, B: Hoh5110, | conact list:
Atom | Atom | Distance (A) | Fe | NE2 B:His153 | 2.47 | Fe | ND1 B:His153 | 4.57 | Fe | CD2 B:His153 | 3.54 | Fe | CE1 B:His153 | 3.38 | Fe | CG B:His153 | 4.67 | Fe | NE2 B:His199 | 4.15 | Fe | CE1 B:His199 | 4.48 | Fe | NE2 B:His214 | 2.43 | Fe | ND1 B:His214 | 4.26 | Fe | CD2 B:His214 | 3.61 | Fe | CE1 B:His214 | 3.05 | Fe | CG B:His214 | 4.56 | Fe | CB B:Ser216 | 4.78 | Fe | OG B:Ser216 | 3.42 | Fe | NE2 B:His246 | 4.62 | Fe | CZ B:Tyr255 | 4.71 | Fe | CE1 B:Tyr255 | 4.69 | Fe | OH B:Tyr255 | 3.69 | Fe | OE1 B:Glu265 | 2.17 | Fe | CB B:Glu265 | 4.64 | Fe | OE2 B:Glu265 | 3.12 | Fe | CD B:Glu265 | 2.94 | Fe | CG B:Glu265 | 4.30 | Fe | O B:Acn309 | 2.44 | Fe | C B:Acn309 | 3.70 | Fe | C2 B:Acn309 | 4.76 | Fe | C1 B:Acn309 | 4.59 | Fe | O B:Hoh5110 | 4.54 |
| interactive model:
| Iron binding site 3 out of 4 in 1mpy
|  Click to enlarge |  Click to enlarge | Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Iron in the PDB 1mpy. 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: C: His153, C: His199, C: His214, C: Ser216, C: His246, C: Tyr255, C: Glu265, C: Acn309, C: Hoh5112, | conact list:
Atom | Atom | Distance (A) | Fe | NE2 C:His153 | 2.60 | Fe | ND1 C:His153 | 4.72 | Fe | CD2 C:His153 | 3.71 | Fe | CE1 C:His153 | 3.50 | Fe | CG C:His153 | 4.84 | Fe | NE2 C:His199 | 4.17 | Fe | CE1 C:His199 | 4.61 | Fe | NE2 C:His214 | 2.49 | Fe | ND1 C:His214 | 4.07 | Fe | CD2 C:His214 | 3.78 | Fe | CE1 C:His214 | 2.81 | Fe | CG C:His214 | 4.57 | Fe | CB C:Ser216 | 4.74 | Fe | OG C:Ser216 | 3.56 | Fe | NE2 C:His246 | 4.83 | Fe | CZ C:Tyr255 | 4.63 | Fe | CE1 C:Tyr255 | 4.52 | Fe | OH C:Tyr255 | 3.73 | Fe | OE1 C:Glu265 | 2.19 | Fe | CB C:Glu265 | 4.75 | Fe | OE2 C:Glu265 | 3.11 | Fe | CD C:Glu265 | 2.97 | Fe | CG C:Glu265 | 4.39 | Fe | O C:Acn309 | 2.42 | Fe | C C:Acn309 | 3.66 | Fe | C2 C:Acn309 | 4.59 | Fe | C1 C:Acn309 | 4.69 | Fe | O C:Hoh5112 | 3.99 |
| interactive model:
| Iron binding site 4 out of 4 in 1mpy
|  Click to enlarge |  Click to enlarge | Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Iron in the PDB 1mpy. 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: D: His153, D: Leu155, D: His199, D: His214, D: Ser216, D: Tyr255, D: Glu265, D: Acn309, | conact list:
Atom | Atom | Distance (A) | Fe | NE2 D:His153 | 2.43 | Fe | ND1 D:His153 | 4.61 | Fe | CD2 D:His153 | 3.35 | Fe | CE1 D:His153 | 3.49 | Fe | CG D:His153 | 4.56 | Fe | CB D:Leu155 | 4.68 | Fe | CD1 D:Leu155 | 4.67 | Fe | NE2 D:His199 | 3.96 | Fe | CE1 D:His199 | 4.42 | Fe | NE2 D:His214 | 2.19 | Fe | ND1 D:His214 | 4.28 | Fe | CD2 D:His214 | 3.33 | Fe | CE1 D:His214 | 3.06 | Fe | CG D:His214 | 4.43 | Fe | CB D:Ser216 | 4.49 | Fe | OG D:Ser216 | 3.29 | Fe | CZ D:Tyr255 | 4.95 | Fe | CE1 D:Tyr255 | 4.88 | Fe | OH D:Tyr255 | 4.06 | Fe | OE1 D:Glu265 | 2.36 | Fe | CB D:Glu265 | 4.90 | Fe | OE2 D:Glu265 | 3.77 | Fe | CD D:Glu265 | 3.42 | Fe | CG D:Glu265 | 4.70 | Fe | O D:Acn309 | 2.86 | Fe | C D:Acn309 | 4.17 |
| interactive model:
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