Fluorine in PDB 3nks: Structure of Human Protoporphyrinogen IX Oxidase

All present enzymatic activity of Structure of Human Protoporphyrinogen IX Oxidase:
1.3.3.4;

The structure of Structure of Human Protoporphyrinogen IX Oxidase, PDB code: 3nks was solved by Y.Shen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.71 / 1.90
Space group	H 3 2
Cell size a, b, c (Å), α, β, γ (°)	136.702, 136.702, 158.877, 90.00, 90.00, 120.00
R / Rfree (%)	20.6 / 23.2

The structure of Structure of Human Protoporphyrinogen IX Oxidase also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Fluorine atom in the Structure of Human Protoporphyrinogen IX Oxidase (pdb code 3nks). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the Structure of Human Protoporphyrinogen IX Oxidase, PDB code: 3nks:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in the Structure of Human Protoporphyrinogen IX Oxidase


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Structure of Human Protoporphyrinogen IX Oxidase within 5.0Å range: probe atom residue distance (Å) B Occ A:F478 b:28.1 occ:1.00 F1 A:ACJ478 0.0 28.1 1.0 C1 A:ACJ478 1.3 26.7 1.0 F3 A:ACJ478 2.1 32.8 1.0 F2 A:ACJ478 2.2 29.4 1.0 C2 A:ACJ478 2.3 24.8 1.0 C3 A:ACJ478 2.7 20.3 1.0 N A:ALA172 3.2 17.8 1.0 CB A:ALA172 3.2 17.4 1.0 CD1 A:ILE419 3.2 26.5 1.0 O A:ARG168 3.5 18.2 1.0 C5 A:ACJ478 3.6 22.4 1.0 CA A:ALA172 3.6 18.4 1.0 O A:VAL170 3.7 19.3 1.0 O A:GLY169 3.7 20.7 1.0 C A:PHE171 3.8 17.1 1.0 C A:VAL170 3.8 20.2 1.0 N A:PHE171 4.0 18.6 1.0 C4 A:ACJ478 4.1 19.1 1.0 C A:GLY169 4.1 21.5 1.0 CA A:PHE171 4.2 18.5 1.0 N A:VAL170 4.4 20.6 1.0 O A:PHE171 4.5 16.4 1.0 CA A:VAL170 4.5 21.4 1.0 C A:ARG168 4.6 19.2 1.0 C6 A:ACJ478 4.7 21.4 1.0 CG1 A:ILE419 4.7 19.1 1.0 CA A:GLY169 4.8 20.0 1.0 CG2 A:VAL314 4.9 16.9 1.0 O A:HOH538 4.9 40.4 1.0 C7 A:ACJ478 4.9 19.0 1.0

Fluorine binding site 2 out of 3 in the Structure of Human Protoporphyrinogen IX Oxidase


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Structure of Human Protoporphyrinogen IX Oxidase within 5.0Å range: probe atom residue distance (Å) B Occ A:F478 b:29.4 occ:1.00 F2 A:ACJ478 0.0 29.4 1.0 C1 A:ACJ478 1.3 26.7 1.0 F3 A:ACJ478 2.2 32.8 1.0 F1 A:ACJ478 2.2 28.1 1.0 C2 A:ACJ478 2.3 24.8 1.0 C5 A:ACJ478 2.7 22.4 1.0 CD1 A:ILE419 3.4 26.5 1.0 O A:HOH538 3.4 40.4 1.0 C3 A:ACJ478 3.5 20.3 1.0 O A:VAL170 3.6 19.3 1.0 C5X A:FAD479 3.6 19.9 1.0 C6 A:FAD479 3.7 17.6 1.0 O A:HOH537 3.7 33.6 1.0 O A:GLY169 3.8 20.7 1.0 C9A A:FAD479 3.9 20.0 1.0 N5 A:FAD479 4.0 24.3 1.0 C6 A:ACJ478 4.1 21.4 1.0 C7 A:FAD479 4.1 19.9 1.0 C A:VAL170 4.2 20.2 1.0 C9 A:FAD479 4.3 20.3 1.0 C8 A:FAD479 4.4 22.1 1.0 N10 A:FAD479 4.5 16.8 1.0 C4X A:FAD479 4.5 23.7 1.0 C A:GLY169 4.6 21.5 1.0 C4 A:ACJ478 4.7 19.1 1.0 CA A:VAL170 4.7 21.4 1.0 CG1 A:ILE419 4.7 19.1 1.0 C10 A:FAD479 4.8 21.5 1.0 C7 A:ACJ478 4.9 19.0 1.0 N A:PHE171 4.9 18.6 1.0

Fluorine binding site 3 out of 3 in the Structure of Human Protoporphyrinogen IX Oxidase


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Structure of Human Protoporphyrinogen IX Oxidase within 5.0Å range: probe atom residue distance (Å) B Occ A:F478 b:32.8 occ:1.00 F3 A:ACJ478 0.0 32.8 1.0 C1 A:ACJ478 1.3 26.7 1.0 F1 A:ACJ478 2.1 28.1 1.0 F2 A:ACJ478 2.2 29.4 1.0 C2 A:ACJ478 2.3 24.8 1.0 CD1 A:ILE419 3.1 26.5 1.0 C5 A:ACJ478 3.2 22.4 1.0 C3 A:ACJ478 3.2 20.3 1.0 C7 A:FAD479 3.4 19.9 1.0 C6 A:FAD479 3.6 17.6 1.0 C8 A:FAD479 3.9 22.1 1.0 C7M A:FAD479 4.0 19.9 1.0 CG2 A:VAL314 4.1 16.9 1.0 CB A:ALA172 4.2 17.4 1.0 C5X A:FAD479 4.2 19.9 1.0 C6 A:ACJ478 4.4 21.4 1.0 C4 A:ACJ478 4.4 19.1 1.0 CG1 A:ILE419 4.4 19.1 1.0 CG1 A:VAL314 4.4 17.0 1.0 C9 A:FAD479 4.5 20.3 1.0 C9A A:FAD479 4.6 20.0 1.0 CB A:VAL314 4.7 16.4 1.0 C7 A:ACJ478 4.9 19.0 1.0 C8M A:FAD479 4.9 19.3 1.0

X.Qin, Y.Tan, L.Wang, Z.Wang, B.Wang, X.Wen, G.Yang, Z.Xi, Y.Shen. Structural Insight Into Human Variegate Porphyria Disease Faseb J. V. 25 653 2011.
ISSN: ISSN 0892-6638
PubMed: 21048046
DOI: 10.1096/FJ.10-170811