Fluorine in PDB 5gvn: Plasmodium Vivax Shmt Bound with Plp-Glycine and GS653

The structure of Plasmodium Vivax Shmt Bound with Plp-Glycine and GS653, PDB code: 5gvn was solved by P.Chitnumsub, A.Jaruwat, U.Leartsakulpanich, G.Schwertz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.01 / 2.30
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	101.849, 58.799, 235.609, 90.00, 89.97, 90.00
R / Rfree (%)	21.9 / 28.2

The structure of Plasmodium Vivax Shmt Bound with Plp-Glycine and GS653 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 GS653 (pdb code 5gvn). 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 GS653, PDB code: 5gvn:
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 GS653


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 GS653 within 5.0Å range: probe atom residue distance (Å) B Occ A:F502 b:35.0 occ:1.00 F35 A:G6F502 0.0 35.0 1.0 C18 A:G6F502 1.3 34.0 1.0 C17 A:G6F502 2.4 33.5 1.0 C19 A:G6F502 2.4 34.9 1.0 C20 A:G6F502 3.6 34.2 1.0 CG B:PRO367 3.6 35.0 1.0 C16 A:G6F502 3.6 32.2 1.0 CD B:LYS355 3.8 27.6 1.0 NZ B:LYS355 4.0 30.6 1.0 C21 A:G6F502 4.1 33.3 1.0 CG B:LYS355 4.1 26.7 1.0 O B:LYS355 4.2 25.7 1.0 CB B:PRO367 4.3 33.1 1.0 O B:CYS364 4.4 56.0 1.0 CD B:PRO367 4.4 34.6 1.0 CE B:LYS355 4.5 29.6 1.0 C B:LYS355 4.6 24.7 1.0 N9 A:G6F502 4.7 31.4 1.0 CD2 A:TYR63 4.8 27.2 1.0 CB B:LYS355 4.8 24.7 1.0 C8 A:G6F502 4.9 33.1 1.0 N B:ASN356 4.9 24.1 1.0 C4 A:G6F502 4.9 30.8 1.0 C34 A:G6F502 4.9 35.1 1.0 CA B:ASN356 5.0 22.2 1.0 CE2 A:TYR63 5.0 26.9 1.0

Fluorine binding site 2 out of 3 in the Plasmodium Vivax Shmt Bound with Plp-Glycine and GS653


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 GS653 within 5.0Å range: probe atom residue distance (Å) B Occ B:F502 b:33.6 occ:1.00 F35 B:G6F502 0.0 33.6 1.0 C18 B:G6F502 1.3 33.3 1.0 C17 B:G6F502 2.4 33.1 1.0 C19 B:G6F502 2.4 33.5 1.0 C20 B:G6F502 3.6 33.2 1.0 C16 B:G6F502 3.7 32.3 1.0 CG A:PRO367 3.8 32.3 1.0 CD A:LYS355 3.9 26.6 1.0 CG A:LYS355 4.0 26.0 1.0 O A:CYS364 4.1 49.4 1.0 C21 B:G6F502 4.1 32.6 1.0 NZ A:LYS355 4.2 28.3 1.0 CE A:LYS355 4.2 28.2 1.0 O A:LYS355 4.3 24.0 1.0 CB A:PRO367 4.5 31.5 1.0 CD A:PRO367 4.5 32.6 1.0 N9 B:G6F502 4.6 32.8 1.0 C A:LYS355 4.6 23.3 1.0 CD2 B:TYR63 4.8 27.9 1.0 CB A:LYS355 4.8 23.7 1.0 C8 B:G6F502 4.9 34.1 1.0 C34 B:G6F502 4.9 34.9 1.0 C4 B:G6F502 4.9 31.0 1.0 N A:ASN356 4.9 23.1 1.0

Fluorine binding site 3 out of 3 in the Plasmodium Vivax Shmt Bound with Plp-Glycine and GS653


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 GS653 within 5.0Å range: probe atom residue distance (Å) B Occ C:F502 b:31.3 occ:1.00 F35 C:G6F502 0.0 31.3 1.0 C18 C:G6F502 1.3 32.2 1.0 C19 C:G6F502 2.4 32.4 1.0 C17 C:G6F502 2.4 31.2 1.0 C20 C:G6F502 3.6 31.5 1.0 C16 C:G6F502 3.7 30.2 1.0 CG C:PRO367 3.7 33.3 1.0 CD C:LYS355 3.7 28.1 1.0 CG C:LYS355 4.0 27.5 1.0 NZ C:LYS355 4.0 32.0 1.0 CE C:LYS355 4.1 30.4 1.0 C21 C:G6F502 4.1 31.0 1.0 O C:CYS364 4.2 52.7 1.0 O C:LYS355 4.4 23.4 1.0 CD C:PRO367 4.4 32.7 1.0 CB C:PRO367 4.4 32.4 1.0 N9 C:G6F502 4.6 31.9 1.0 C C:LYS355 4.7 24.4 1.0 CB C:LYS355 4.8 25.2 1.0 C8 C:G6F502 4.9 33.1 1.0 C34 C:G6F502 4.9 33.0 1.0 C4 C:G6F502 4.9 30.1 1.0

G.Schwertz, M.C.Witschel, M.Rottmann, R.Bonnert, U.Leartsakulpanich, P.Chitnumsub, A.Jaruwat, W.Ittarat, A.Schafer, R.A.Aponte, S.A.Charman, K.L.White, A.Kundu, S.Sadhukhan, M.Lloyd, G.M.Freiberg, M.Srikumaran, M.Siggel, A.Zwyssig, P.Chaiyen, F.Diederich. Antimalarial Inhibitors Targeting Serine Hydroxymethyltransferase (Shmt) with in Vivo Efficacy and Analysis of Their Binding Mode Based on X-Ray Cocrystal Structures J. Med. Chem. V. 60 4840 2017.
ISSN: ISSN 1520-4804
PubMed: 28537728
DOI: 10.1021/ACS.JMEDCHEM.7B00008