Fluorine in PDB 5yfy: Plasmodium Vivax Shmt Bound with Plp-Glycine and GS625

All present enzymatic activity of Plasmodium Vivax Shmt Bound with Plp-Glycine and GS625:
2.1.2.1;

The structure of Plasmodium Vivax Shmt Bound with Plp-Glycine and GS625, PDB code: 5yfy was solved by P.Chitnumsub, A.Jaruwat, U.Leartsakulpanich, G.Schwertz, F.Diederich, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 2.30
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	101.647, 58.804, 235.489, 90.00, 90.01, 90.00
R / Rfree (%)	21.8 / 27.6

The structure of Plasmodium Vivax Shmt Bound with Plp-Glycine and GS625 also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Fluorine atom in the Plasmodium Vivax Shmt Bound with Plp-Glycine and GS625 (pdb code 5yfy). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the Plasmodium Vivax Shmt Bound with Plp-Glycine and GS625, PDB code: 5yfy:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in the Plasmodium Vivax Shmt Bound with Plp-Glycine and GS625


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Plasmodium Vivax Shmt Bound with Plp-Glycine and GS625 within 5.0Å range: probe atom residue distance (Å) B Occ A:F502 b:38.1 occ:1.00 F21 A:8UL502 0.0 38.1 1.0 C18 A:8UL502 1.3 38.5 1.0 C17 A:8UL502 2.3 38.6 1.0 C30 A:8UL502 2.4 39.1 1.0 CE A:LYS355 3.4 30.6 1.0 CD A:LYS355 3.5 28.4 1.0 C16 A:8UL502 3.6 37.5 1.0 C19 A:8UL502 3.7 37.6 1.0 O A:LYS355 3.8 24.6 1.0 CG A:LYS355 3.9 26.9 1.0 CG A:PRO367 3.9 34.4 1.0 C20 A:8UL502 4.1 37.9 1.0 NZ A:LYS355 4.3 32.5 1.0 C A:LYS355 4.3 24.0 1.0 O A:CYS364 4.5 63.1 1.0 N9 A:8UL502 4.6 34.7 1.0 CB A:LYS355 4.6 24.1 1.0 N A:ASN356 4.7 23.2 1.0 CD A:PRO367 4.7 34.2 1.0 CB A:PRO367 4.7 33.3 1.0 CA A:ASN356 4.9 23.6 1.0 N23 A:8UL502 4.9 38.1 1.0 C8 A:8UL502 4.9 36.1 1.0 C4 A:8UL502 4.9 34.9 1.0 C15 A:8UL502 4.9 36.1 1.0 CD2 B:TYR63 5.0 40.9 1.0

Fluorine binding site 2 out of 3 in the Plasmodium Vivax Shmt Bound with Plp-Glycine and GS625


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Plasmodium Vivax Shmt Bound with Plp-Glycine and GS625 within 5.0Å range: probe atom residue distance (Å) B Occ B:F502 b:41.7 occ:1.00 F21 B:8UL502 0.0 41.7 1.0 C18 B:8UL502 1.3 41.5 1.0 C17 B:8UL502 2.3 40.9 1.0 C30 B:8UL502 2.4 41.0 1.0 CE B:LYS355 3.4 34.8 1.0 CD B:LYS355 3.5 32.0 1.0 CG B:LYS355 3.5 29.1 1.0 C16 B:8UL502 3.6 39.9 1.0 C19 B:8UL502 3.7 40.8 1.0 O B:LYS355 3.8 25.5 1.0 CG B:PRO367 4.0 32.9 1.0 C20 B:8UL502 4.1 41.1 1.0 C B:LYS355 4.3 24.9 1.0 NZ B:LYS355 4.3 36.7 1.0 CB B:LYS355 4.4 26.3 1.0 CB B:PRO367 4.7 32.4 1.0 N9 B:8UL502 4.8 36.0 1.0 CD2 A:TYR63 4.8 42.4 1.0 N B:ASN356 4.8 23.7 1.0 O B:CYS364 4.8 61.1 1.0 CD B:PRO367 4.8 32.8 1.0 N23 B:8UL502 4.9 42.0 1.0 C4 B:8UL502 4.9 36.3 1.0 C8 B:8UL502 4.9 37.9 1.0 C15 B:8UL502 5.0 36.6 1.0 CA B:LYS355 5.0 24.6 1.0

Fluorine binding site 3 out of 3 in the Plasmodium Vivax Shmt Bound with Plp-Glycine and GS625


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Plasmodium Vivax Shmt Bound with Plp-Glycine and GS625 within 5.0Å range: probe atom residue distance (Å) B Occ C:F502 b:39.9 occ:1.00 F21 C:8UL502 0.0 39.9 1.0 C18 C:8UL502 1.3 38.4 1.0 C17 C:8UL502 2.3 37.4 1.0 C30 C:8UL502 2.4 38.5 1.0 CD C:LYS355 3.2 28.2 1.0 CE C:LYS355 3.3 30.9 1.0 C19 C:8UL502 3.6 37.6 1.0 C16 C:8UL502 3.6 36.6 1.0 CG C:LYS355 3.7 26.3 1.0 O C:LYS355 3.8 23.6 1.0 CG C:PRO367 4.0 33.5 1.0 C20 C:8UL502 4.1 37.8 1.0 NZ C:LYS355 4.1 32.9 1.0 C C:LYS355 4.3 23.7 1.0 CB C:LYS355 4.5 24.7 1.0 CD C:PRO367 4.8 33.9 1.0 N9 C:8UL502 4.8 32.6 1.0 N C:ASN356 4.8 22.6 1.0 O C:CYS364 4.8 61.8 1.0 N23 C:8UL502 4.8 37.6 1.0 C15 C:8UL502 4.9 35.4 1.0 C4 C:8UL502 4.9 35.1 1.0 CB C:PRO367 4.9 32.6 1.0

P.Chitnumsub, A.Jaruwat. To Be Published To Be Published.