Chlorine in PDB 5gvm: Plasmodium Vivax Shmt Bound with Plp-Glycine and GS557

The structure of Plasmodium Vivax Shmt Bound with Plp-Glycine and GS557, PDB code: 5gvm 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 / 2.24
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	101.858, 58.790, 234.062, 90.00, 90.03, 90.00
R / Rfree (%)	24 / 29.7

The structure of Plasmodium Vivax Shmt Bound with Plp-Glycine and GS557 also contains other interesting chemical elements:

Fluorine

(F)

9 atoms

The binding sites of Chlorine atom in the Plasmodium Vivax Shmt Bound with Plp-Glycine and GS557 (pdb code 5gvm). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 2 binding sites of Chlorine where determined in the Plasmodium Vivax Shmt Bound with Plp-Glycine and GS557, PDB code: 5gvm:
Jump to Chlorine binding site number: 1; 2;

Chlorine binding site 1 out of 2 in the Plasmodium Vivax Shmt Bound with Plp-Glycine and GS557


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Plasmodium Vivax Shmt Bound with Plp-Glycine and GS557 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl503 b:29.3 occ:1.00 NZ B:LYS277 3.2 17.5 1.0 ND2 B:ASN276 3.2 19.4 1.0 NZ A:LYS277 3.2 16.9 1.0 ND2 A:ASN276 3.2 19.9 1.0 CE B:LYS277 3.9 17.4 1.0 CE A:LYS277 3.9 16.9 1.0 CG A:LYS277 4.2 16.6 1.0 CG B:LYS277 4.2 16.8 1.0 CG B:ASN276 4.2 18.2 1.0 CG A:ASN276 4.2 18.9 1.0 O B:HOH676 4.3 43.5 1.0 O A:HOH681 4.3 46.4 1.0 CD2 B:LEU46 4.3 24.5 1.0 OD1 A:ASN276 4.4 19.4 1.0 CD2 A:LEU46 4.5 23.9 1.0 OD1 B:ASN276 4.5 17.9 1.0 CD B:LYS277 4.7 17.6 1.0 CD A:LYS277 4.7 17.1 1.0

Chlorine binding site 2 out of 2 in the Plasmodium Vivax Shmt Bound with Plp-Glycine and GS557


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Plasmodium Vivax Shmt Bound with Plp-Glycine and GS557 within 5.0Å range: probe atom residue distance (Å) B Occ C:Cl503 b:13.1 occ:0.50 ND2 C:ASN276 3.0 21.0 1.0 NZ C:LYS277 4.0 17.5 1.0 CG C:ASN276 4.0 21.0 1.0 OD1 C:ASN276 4.2 21.0 1.0 CE C:LYS277 4.3 17.4 1.0 CG C:LYS277 4.5 17.2 1.0 ND1 C:HIS274 4.9 18.9 1.0 CD2 C:LEU46 4.9 25.1 1.0 O C:HOH675 4.9 37.3 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