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

Protein crystallography data

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

Other elements in 5gvm:

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

Fluorine (F) 9 atoms

Chlorine Binding Sites:

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 5gvm

Go back to Chlorine Binding Sites List in 5gvm
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 5gvm

Go back to Chlorine Binding Sites List in 5gvm
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

Reference:

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
Page generated: Sat Dec 12 11:47:35 2020

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