Fluorine in PDB 5yg2: Plasmodium Vivax Shmt Bound with Plp-Glycine and GS705

All present enzymatic activity of Plasmodium Vivax Shmt Bound with Plp-Glycine and GS705:
2.1.2.1;

The structure of Plasmodium Vivax Shmt Bound with Plp-Glycine and GS705, PDB code: 5yg2 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 / 2.20
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	101.644, 58.682, 234.758, 90.00, 90.01, 90.00
R / Rfree (%)	24.9 / 30.6

The structure of Plasmodium Vivax Shmt Bound with Plp-Glycine and GS705 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 GS705 (pdb code 5yg2). 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 GS705, PDB code: 5yg2:
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 GS705


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 GS705 within 5.0Å range: probe atom residue distance (Å) B Occ A:F502 b:42.9 occ:1.00 F21 A:N05502 0.0 42.9 1.0 C18 A:N05502 1.3 39.8 1.0 C17 A:N05502 2.3 38.3 1.0 C34 A:N05502 2.3 41.3 1.0 CE A:LYS355 3.3 31.3 1.0 CG A:LYS355 3.5 29.2 1.0 CG A:PRO367 3.6 34.5 1.0 C16 A:N05502 3.6 36.5 1.0 C19 A:N05502 3.6 38.6 1.0 CD A:LYS355 3.7 30.4 1.0 O A:LYS355 3.7 28.1 1.0 C20 A:N05502 4.1 37.2 1.0 C A:LYS355 4.1 25.5 1.0 CB A:PRO367 4.3 33.5 1.0 N A:ASN356 4.4 25.6 1.0 NZ A:LYS355 4.4 33.1 1.0 CD A:PRO367 4.4 35.4 1.0 CB A:LYS355 4.4 25.9 1.0 N9 A:N05502 4.5 31.5 1.0 CA A:ASN356 4.5 24.9 1.0 O A:CYS364 4.8 65.1 1.0 C8 A:N05502 4.8 35.6 1.0 N23 A:N05502 4.8 40.2 1.0 C4 A:N05502 4.9 33.5 1.0 CA A:LYS355 4.9 25.1 1.0 N A:THR357 5.0 27.6 1.0

Fluorine binding site 2 out of 3 in the Plasmodium Vivax Shmt Bound with Plp-Glycine and GS705


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 GS705 within 5.0Å range: probe atom residue distance (Å) B Occ B:F502 b:42.0 occ:1.00 F21 B:N05502 0.0 42.0 1.0 C18 B:N05502 1.3 40.0 1.0 C17 B:N05502 2.3 39.4 1.0 C34 B:N05502 2.4 39.8 1.0 CE B:LYS355 3.4 31.7 1.0 CG B:LYS355 3.5 28.9 1.0 CG B:PRO367 3.6 38.4 1.0 C16 B:N05502 3.6 37.3 1.0 C19 B:N05502 3.7 38.7 1.0 CD B:LYS355 3.8 30.3 1.0 O B:LYS355 3.8 29.2 1.0 CB B:PRO367 4.1 37.0 1.0 C20 B:N05502 4.1 37.9 1.0 C B:LYS355 4.2 26.7 1.0 CB B:LYS355 4.5 26.8 1.0 CD B:PRO367 4.5 38.6 1.0 N B:ASN356 4.5 26.3 1.0 N9 B:N05502 4.5 32.8 1.0 NZ B:LYS355 4.6 34.0 1.0 CA B:ASN356 4.6 25.5 1.0 C8 B:N05502 4.7 35.6 1.0 O B:CYS364 4.7 61.7 1.0 N23 B:N05502 4.8 40.5 1.0 C4 B:N05502 4.9 35.4 1.0 N B:THR357 4.9 27.2 1.0 CA B:LYS355 4.9 26.2 1.0

Fluorine binding site 3 out of 3 in the Plasmodium Vivax Shmt Bound with Plp-Glycine and GS705


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 GS705 within 5.0Å range: probe atom residue distance (Å) B Occ C:F502 b:40.6 occ:1.00 F21 C:N05502 0.0 40.6 1.0 C18 C:N05502 1.3 39.5 1.0 C17 C:N05502 2.3 38.5 1.0 C34 C:N05502 2.3 40.7 1.0 CE C:LYS355 3.2 30.1 1.0 CG C:PRO367 3.6 35.8 1.0 CG C:LYS355 3.6 27.9 1.0 C16 C:N05502 3.6 36.7 1.0 C19 C:N05502 3.6 39.3 1.0 CD C:LYS355 3.7 28.9 1.0 O C:LYS355 3.9 27.8 1.0 C20 C:N05502 4.1 37.8 1.0 C C:LYS355 4.2 26.7 1.0 CB C:PRO367 4.3 34.3 1.0 O C:CYS364 4.3 76.9 1.0 CD C:PRO367 4.3 36.2 1.0 NZ C:LYS355 4.3 32.4 1.0 N C:ASN356 4.5 28.2 1.0 CB C:LYS355 4.5 25.4 1.0 N9 C:N05502 4.5 34.5 1.0 CA C:ASN356 4.6 27.4 1.0 N23 C:N05502 4.8 40.2 1.0 C8 C:N05502 4.8 37.1 1.0 C4 C:N05502 4.9 34.6 1.0 CA C:LYS355 5.0 25.2 1.0

G.Schwertz, M.C.Witschel, M.Rottmann, U.Leartsakulpanich, P.Chitnumsub, A.Jaruwat, W.Amornwatcharapong, W.Ittarat, A.Schafer, R.A.Aponte, N.Trapp, P.Chaiyen, F.Diederich. Potent Inhibitors of Plasmodial Serine Hydroxymethyltransferase (Shmt) Featuring A Spirocyclic Scaffold Chemmedchem V. 13 931 2018.
ISSN: ESSN 1860-7187
PubMed: 29655285
DOI: 10.1002/CMDC.201800053