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

Enzymatic activity of 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;

Protein crystallography data

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

Other elements in 5yg2:

The structure of Plasmodium Vivax Shmt Bound with Plp-Glycine and GS705 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 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 5yg2

Go back to Fluorine Binding Sites List in 5yg2
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 5yg2

Go back to Fluorine Binding Sites List in 5yg2
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 5yg2

Go back to Fluorine Binding Sites List in 5yg2
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

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 12:43:25 2020

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