Fluorine in PDB 5yg4: Plasmodium Vivax Shmt Bound with Plp-Glycine and S-GS849

Enzymatic activity of Plasmodium Vivax Shmt Bound with Plp-Glycine and S-GS849

All present enzymatic activity of Plasmodium Vivax Shmt Bound with Plp-Glycine and S-GS849:
2.1.2.1;

Protein crystallography data

The structure of Plasmodium Vivax Shmt Bound with Plp-Glycine and S-GS849, PDB code: 5yg4 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 (°) 100.848, 58.207, 234.497, 90.00, 89.99, 90.00
R / Rfree (%) 21.5 / 27.8

Other elements in 5yg4:

The structure of Plasmodium Vivax Shmt Bound with Plp-Glycine and S-GS849 also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Plasmodium Vivax Shmt Bound with Plp-Glycine and S-GS849 (pdb code 5yg4). 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 S-GS849, PDB code: 5yg4:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in 5yg4

Go back to Fluorine Binding Sites List in 5yg4
Fluorine binding site 1 out of 3 in the Plasmodium Vivax Shmt Bound with Plp-Glycine and S-GS849


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 S-GS849 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F502

b:33.3
occ:1.00
F29 A:8UF502 0.0 33.3 1.0
C18 A:8UF502 1.3 34.5 1.0
C17 A:8UF502 2.3 33.0 1.0
C41 A:8UF502 2.4 36.5 1.0
C44 A:8UF502 2.9 32.9 1.0
O A:HOH704 3.1 37.2 1.0
CE A:LYS355 3.2 25.4 1.0
C16 A:8UF502 3.6 31.5 1.0
CG A:LYS355 3.7 23.6 1.0
C19 A:8UF502 3.7 34.5 1.0
CD A:LYS355 3.8 24.2 1.0
O A:LYS355 3.8 22.4 1.0
CD2 B:TYR63 4.0 50.4 1.0
C20 A:8UF502 4.1 34.5 1.0
C14 A:8UF502 4.3 31.5 1.0
CB B:TYR63 4.5 42.9 1.0
C A:LYS355 4.5 22.4 1.0
NZ A:LYS355 4.5 27.3 1.0
C4 A:8UF502 4.7 29.4 1.0
O B:TYR63 4.7 35.5 1.0
CG B:TYR63 4.8 47.3 1.0
C15 A:8UF502 4.8 31.8 1.0
CB A:LYS355 4.8 22.4 1.0
N35 A:8UF502 4.9 37.9 1.0
N9 A:8UF502 4.9 26.0 1.0
CE2 B:TYR63 5.0 53.5 1.0
C8 A:8UF502 5.0 28.6 1.0

Fluorine binding site 2 out of 3 in 5yg4

Go back to Fluorine Binding Sites List in 5yg4
Fluorine binding site 2 out of 3 in the Plasmodium Vivax Shmt Bound with Plp-Glycine and S-GS849


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 S-GS849 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F502

b:35.4
occ:1.00
F29 B:8UF502 0.0 35.4 1.0
C18 B:8UF502 1.3 35.6 1.0
C17 B:8UF502 2.4 33.7 1.0
C41 B:8UF502 2.4 36.2 1.0
C44 B:8UF502 3.0 33.6 1.0
CE B:LYS355 3.2 28.3 1.0
CD B:LYS355 3.5 26.7 1.0
CG B:LYS355 3.6 26.2 1.0
C16 B:8UF502 3.6 32.8 1.0
C19 B:8UF502 3.7 35.1 1.0
O B:LYS355 3.8 22.7 1.0
CD2 A:TYR63 4.0 44.7 1.0
C20 B:8UF502 4.2 34.3 1.0
C14 B:8UF502 4.4 32.6 1.0
CB A:TYR63 4.5 40.1 1.0
C B:LYS355 4.5 22.4 1.0
NZ B:LYS355 4.6 29.8 1.0
CG A:TYR63 4.7 42.0 1.0
C4 B:8UF502 4.7 30.6 1.0
CB B:LYS355 4.8 24.2 1.0
C15 B:8UF502 4.8 32.9 1.0
O A:TYR63 4.8 37.5 1.0
N35 B:8UF502 4.8 36.7 1.0
CE2 A:TYR63 4.9 46.0 1.0

Fluorine binding site 3 out of 3 in 5yg4

Go back to Fluorine Binding Sites List in 5yg4
Fluorine binding site 3 out of 3 in the Plasmodium Vivax Shmt Bound with Plp-Glycine and S-GS849


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 S-GS849 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F502

b:34.4
occ:1.00
F29 C:8UF502 0.0 34.4 1.0
C18 C:8UF502 1.4 36.0 1.0
C17 C:8UF502 2.4 34.3 1.0
C41 C:8UF502 2.4 36.5 1.0
C44 C:8UF502 3.0 33.5 1.0
CE C:LYS355 3.1 26.8 1.0
CG C:LYS355 3.5 24.3 1.0
C16 C:8UF502 3.6 33.2 1.0
O C:LYS355 3.7 21.5 1.0
CD C:LYS355 3.7 24.9 1.0
C19 C:8UF502 3.7 35.2 1.0
C20 C:8UF502 4.2 34.9 1.0
C14 C:8UF502 4.4 32.0 1.0
NZ C:LYS355 4.4 29.1 1.0
C C:LYS355 4.4 21.3 1.0
CB C:LYS355 4.6 22.3 1.0
C4 C:8UF502 4.7 31.7 1.0
C15 C:8UF502 4.8 31.6 1.0
N35 C:8UF502 4.8 35.1 1.0
CA C:LYS355 4.9 21.3 1.0

Reference:

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
Page generated: Sun Dec 13 12:43:28 2020

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