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Fluorine in PDB 5xmt: Plasmodium Vivax Shmt Bound with Plp-Glycine and GS380

Enzymatic activity of Plasmodium Vivax Shmt Bound with Plp-Glycine and GS380

All present enzymatic activity of Plasmodium Vivax Shmt Bound with Plp-Glycine and GS380:
2.1.2.1;

Protein crystallography data

The structure of Plasmodium Vivax Shmt Bound with Plp-Glycine and GS380, PDB code: 5xmt 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 / 2.55
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 101.578, 58.613, 236.371, 90.00, 89.97, 90.00
R / Rfree (%) 19.5 / 27.2

Other elements in 5xmt:

The structure of Plasmodium Vivax Shmt Bound with Plp-Glycine and GS380 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 GS380 (pdb code 5xmt). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 9 binding sites of Fluorine where determined in the Plasmodium Vivax Shmt Bound with Plp-Glycine and GS380, PDB code: 5xmt:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Fluorine binding site 1 out of 9 in 5xmt

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Fluorine binding site 1 out of 9 in the Plasmodium Vivax Shmt Bound with Plp-Glycine and GS380


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 GS380 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F502

b:40.8
occ:1.00
 F48 A:8B0502 0.0 40.8 1.0
C33 A:8B0502 1.3 42.0 1.0
F46 A:8B0502 2.1 45.2 1.0
F47 A:8B0502 2.2 42.6 1.0
C17 A:8B0502 2.4 38.0 1.0
C18 A:8B0502 2.8 36.2 1.0
O B:CYS364 3.1 67.1 1.0
C16 A:8B0502 3.7 37.4 1.0
C B:CYS364 4.2 64.6 1.0
C19 A:8B0502 4.2 34.6 1.0
CB B:CYS364 4.3 54.8 1.0
CE B:LYS355 4.4 38.6 1.0
CD B:LYS355 4.4 36.1 1.0
CG B:PRO367 4.4 33.4 1.0
CD B:PRO367 4.5 35.2 1.0
CE1 A:TYR63 4.6 25.9 1.0
NZ B:LYS355 4.6 41.1 1.0
CA B:CYS364 4.7 61.8 1.0
N53 A:8B0502 4.7 40.0 1.0
C15 A:8B0502 4.9 37.7 1.0
CD1 A:TYR63 4.9 26.6 1.0
C50 A:8B0502 4.9 36.5 1.0

Fluorine binding site 2 out of 9 in 5xmt

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Fluorine binding site 2 out of 9 in the Plasmodium Vivax Shmt Bound with Plp-Glycine and GS380


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 GS380 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F502

b:42.6
occ:1.00
 F47 A:8B0502 0.0 42.6 1.0
C33 A:8B0502 1.3 42.0 1.0
F46 A:8B0502 2.1 45.2 1.0
F48 A:8B0502 2.2 40.8 1.0
C17 A:8B0502 2.3 38.0 1.0
C16 A:8B0502 2.9 37.4 1.0
CD B:LYS355 3.3 36.1 1.0
CE B:LYS355 3.4 38.6 1.0
C18 A:8B0502 3.5 36.2 1.0
CG B:LYS355 3.7 33.5 1.0
O B:LYS355 4.0 31.9 1.0
CG B:PRO367 4.2 33.4 1.0
C15 A:8B0502 4.2 37.7 1.0
NZ B:LYS355 4.3 41.1 1.0
CB B:LYS355 4.3 31.6 1.0
C B:LYS355 4.5 29.4 1.0
CD1 A:TYR63 4.5 26.6 1.0
C14 A:8B0502 4.5 43.2 1.0
C19 A:8B0502 4.6 34.6 1.0
CE1 A:TYR63 4.8 25.9 1.0
CB B:PRO367 4.9 33.0 1.0
C20 A:8B0502 4.9 36.7 1.0
CD B:PRO367 5.0 35.2 1.0
O B:CYS364 5.0 67.1 1.0
CA B:LYS355 5.0 30.0 1.0

Fluorine binding site 3 out of 9 in 5xmt

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Fluorine binding site 3 out of 9 in the Plasmodium Vivax Shmt Bound with Plp-Glycine and GS380


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 GS380 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F502

b:45.2
occ:1.00
 F46 A:8B0502 0.0 45.2 1.0
C33 A:8B0502 1.3 42.0 1.0
F47 A:8B0502 2.1 42.6 1.0
F48 A:8B0502 2.1 40.8 1.0
C17 A:8B0502 2.3 38.0 1.0
C16 A:8B0502 2.9 37.4 1.0
C18 A:8B0502 3.4 36.2 1.0
O B:CYS364 3.8 67.1 1.0
CG B:PRO367 3.8 33.4 1.0
CB B:PRO367 4.0 33.0 1.0
CB B:CYS364 4.1 54.8 1.0
CG2 B:THR357 4.1 34.7 1.0
N9 A:8B0502 4.2 49.7 1.0
C15 A:8B0502 4.2 37.7 1.0
CA B:CYS364 4.4 61.8 1.0
CD B:PRO367 4.4 35.2 1.0
C B:CYS364 4.5 64.6 1.0
SG B:CYS364 4.5 53.4 1.0
C19 A:8B0502 4.6 34.6 1.0
N B:THR357 4.7 30.2 1.0
C8 A:8B0502 4.7 43.4 1.0
O B:LYS355 4.7 31.9 1.0
CD B:LYS355 4.8 36.1 1.0
C20 A:8B0502 4.9 36.7 1.0
CA B:ASN356 5.0 30.3 1.0

Fluorine binding site 4 out of 9 in 5xmt

Go back to Fluorine Binding Sites List in 5xmt
Fluorine binding site 4 out of 9 in the Plasmodium Vivax Shmt Bound with Plp-Glycine and GS380


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Plasmodium Vivax Shmt Bound with Plp-Glycine and GS380 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F502

b:38.0
occ:1.00
 F48 B:8B0502 0.0 38.0 1.0
C33 B:8B0502 1.3 39.6 1.0
F46 B:8B0502 2.1 40.8 1.0
F47 B:8B0502 2.2 38.7 1.0
C17 B:8B0502 2.4 37.3 1.0
C18 B:8B0502 2.8 36.2 1.0
O A:CYS364 3.4 65.5 1.0
NZ A:LYS355 3.5 36.1 1.0
C16 B:8B0502 3.6 38.1 1.0
C19 B:8B0502 4.2 35.1 1.0
CB A:CYS364 4.3 63.9 1.0
CG A:PRO367 4.4 34.4 1.0
C A:CYS364 4.5 67.2 1.0
CD A:LYS355 4.5 32.5 1.0
CE1 B:TYR63 4.6 26.5 1.0
CE A:LYS355 4.6 34.3 1.0
CD A:PRO367 4.7 35.3 1.0
SG A:CYS364 4.7 65.8 1.0
CD1 B:TYR63 4.8 27.8 1.0
C15 B:8B0502 4.8 37.5 1.0
N53 B:8B0502 4.9 38.0 1.0
CA A:CYS364 4.9 67.2 1.0
C50 B:8B0502 5.0 36.6 1.0

Fluorine binding site 5 out of 9 in 5xmt

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Fluorine binding site 5 out of 9 in the Plasmodium Vivax Shmt Bound with Plp-Glycine and GS380


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Plasmodium Vivax Shmt Bound with Plp-Glycine and GS380 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F502

b:38.7
occ:1.00
 F47 B:8B0502 0.0 38.7 1.0
C33 B:8B0502 1.3 39.6 1.0
F48 B:8B0502 2.2 38.0 1.0
F46 B:8B0502 2.2 40.8 1.0
C17 B:8B0502 2.3 37.3 1.0
C16 B:8B0502 2.8 38.1 1.0
NZ A:LYS355 3.5 36.1 1.0
C18 B:8B0502 3.6 36.2 1.0
CD A:LYS355 3.7 32.5 1.0
O A:LYS355 3.9 28.4 1.0
CG A:LYS355 4.0 30.1 1.0
CG A:PRO367 4.1 34.4 1.0
CE A:LYS355 4.1 34.3 1.0
C15 B:8B0502 4.2 37.5 1.0
C A:LYS355 4.3 26.5 1.0
CB A:LYS355 4.4 29.1 1.0
C14 B:8B0502 4.5 38.8 1.0
CB A:PRO367 4.7 33.7 1.0
C19 B:8B0502 4.7 35.1 1.0
N A:ASN356 4.7 27.2 1.0
N9 B:8B0502 4.8 44.4 1.0
C13 B:8B0502 4.8 39.1 1.0
C20 B:8B0502 4.9 37.0 1.0
CD A:PRO367 4.9 35.3 1.0
CA A:LYS355 5.0 27.0 1.0
CD1 B:TYR63 5.0 27.8 1.0

Fluorine binding site 6 out of 9 in 5xmt

Go back to Fluorine Binding Sites List in 5xmt
Fluorine binding site 6 out of 9 in the Plasmodium Vivax Shmt Bound with Plp-Glycine and GS380


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Plasmodium Vivax Shmt Bound with Plp-Glycine and GS380 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F502

b:40.8
occ:1.00
 F46 B:8B0502 0.0 40.8 1.0
C33 B:8B0502 1.3 39.6 1.0
F48 B:8B0502 2.1 38.0 1.0
F47 B:8B0502 2.2 38.7 1.0
C17 B:8B0502 2.3 37.3 1.0
C16 B:8B0502 3.0 38.1 1.0
C18 B:8B0502 3.2 36.2 1.0
SG A:CYS364 3.4 65.8 1.0
CB A:CYS364 3.7 63.9 1.0
O A:CYS364 3.8 65.5 1.0
CG A:PRO367 4.1 34.4 1.0
CA A:CYS364 4.1 67.2 1.0
CB A:PRO367 4.3 33.7 1.0
CG2 A:THR357 4.3 35.4 1.0
C15 B:8B0502 4.3 37.5 1.0
N9 B:8B0502 4.3 44.4 1.0
C A:CYS364 4.4 67.2 1.0
C19 B:8B0502 4.4 35.1 1.0
CD A:PRO367 4.5 35.3 1.0
C8 B:8B0502 4.8 41.0 1.0
C20 B:8B0502 4.8 37.0 1.0
N53 B:8B0502 4.9 38.0 1.0
N A:THR357 4.9 30.8 1.0

Fluorine binding site 7 out of 9 in 5xmt

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Fluorine binding site 7 out of 9 in the Plasmodium Vivax Shmt Bound with Plp-Glycine and GS380


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 7 of Plasmodium Vivax Shmt Bound with Plp-Glycine and GS380 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F502

b:42.0
occ:1.00
 F48 C:8B0502 0.0 42.0 1.0
C33 C:8B0502 1.3 42.1 1.0
F47 C:8B0502 2.1 45.0 1.0
F46 C:8B0502 2.2 45.6 1.0
C17 C:8B0502 2.4 37.2 1.0
C18 C:8B0502 2.8 34.8 1.0
O C:CYS364 3.0 65.2 1.0
C16 C:8B0502 3.6 36.7 1.0
NZ C:LYS355 3.7 34.9 1.0
C C:CYS364 4.2 70.4 1.0
C19 C:8B0502 4.2 32.5 1.0
CB C:CYS364 4.3 64.7 1.0
CG C:PRO367 4.5 37.0 1.0
CE C:LYS355 4.5 32.2 1.0
N53 C:8B0502 4.6 38.0 1.0
CD C:PRO367 4.6 39.0 1.0
CD C:LYS355 4.6 30.4 1.0
CA C:CYS364 4.7 70.0 1.0
C50 C:8B0502 4.8 34.6 1.0
C15 C:8B0502 4.8 36.2 1.0

Fluorine binding site 8 out of 9 in 5xmt

Go back to Fluorine Binding Sites List in 5xmt
Fluorine binding site 8 out of 9 in the Plasmodium Vivax Shmt Bound with Plp-Glycine and GS380


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 8 of Plasmodium Vivax Shmt Bound with Plp-Glycine and GS380 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F502

b:45.0
occ:1.00
 F47 C:8B0502 0.0 45.0 1.0
C33 C:8B0502 1.3 42.1 1.0
F48 C:8B0502 2.1 42.0 1.0
F46 C:8B0502 2.2 45.6 1.0
C17 C:8B0502 2.3 37.2 1.0
C16 C:8B0502 2.9 36.7 1.0
CD C:LYS355 3.4 30.4 1.0
NZ C:LYS355 3.4 34.9 1.0
C18 C:8B0502 3.4 34.8 1.0
CE C:LYS355 3.5 32.2 1.0
CG C:LYS355 4.1 28.7 1.0
O C:LYS355 4.1 29.0 1.0
CG C:PRO367 4.1 37.0 1.0
C15 C:8B0502 4.2 36.2 1.0
C14 C:8B0502 4.4 38.7 1.0
C19 C:8B0502 4.6 32.5 1.0
C C:LYS355 4.7 27.3 1.0
CB C:LYS355 4.7 28.0 1.0
O C:CYS364 4.8 65.2 1.0
CB C:PRO367 4.9 36.4 1.0
CD C:PRO367 4.9 39.0 1.0
C20 C:8B0502 4.9 34.2 1.0

Fluorine binding site 9 out of 9 in 5xmt

Go back to Fluorine Binding Sites List in 5xmt
Fluorine binding site 9 out of 9 in the Plasmodium Vivax Shmt Bound with Plp-Glycine and GS380


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 9 of Plasmodium Vivax Shmt Bound with Plp-Glycine and GS380 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F502

b:45.6
occ:1.00
 F46 C:8B0502 0.0 45.6 1.0
C33 C:8B0502 1.3 42.1 1.0
F48 C:8B0502 2.2 42.0 1.0
F47 C:8B0502 2.2 45.0 1.0
C17 C:8B0502 2.3 37.2 1.0
C16 C:8B0502 2.9 36.7 1.0
C18 C:8B0502 3.4 34.8 1.0
O C:CYS364 3.7 65.2 1.0
CB C:CYS364 4.0 64.7 1.0
CG C:PRO367 4.0 37.0 1.0
SG C:CYS364 4.1 65.5 1.0
N9 C:8B0502 4.1 42.8 1.0
C15 C:8B0502 4.2 36.2 1.0
CB C:PRO367 4.2 36.4 1.0
CG2 C:THR357 4.2 34.8 1.0
CA C:CYS364 4.4 70.0 1.0
C C:CYS364 4.5 70.4 1.0
C19 C:8B0502 4.5 32.5 1.0
CD C:PRO367 4.5 39.0 1.0
C8 C:8B0502 4.6 38.7 1.0
N C:THR357 4.8 31.1 1.0
C20 C:8B0502 4.8 34.2 1.0
O C:LYS355 4.9 29.0 1.0
CD C:LYS355 5.0 30.4 1.0

Reference:

G.Schwertz, M.S.Frei, M.C.Witschel, M.Rottmann, U.Leartsakulpanich, P.Chitnumsub, A.Jaruwat, W.Ittarat, A.Schafer, R.A.Aponte, N.Trapp, K.Mark, P.Chaiyen, F.Diederich. Conformational Aspects in the Design of Inhibitors For Serine Hydroxymethyltransferase (Shmt): Biphenyl, Aryl Sulfonamide, and Aryl Sulfone Motifs Chemistry V. 23 14345 2017.
ISSN: ISSN 1521-3765
PubMed: 28967982
DOI: 10.1002/CHEM.201703244
Page generated: Tue Jul 15 09:16:49 2025

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