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Fluorine in PDB 5xmr: Plasmodium Vivax Shmt(C346A) Bound with Plp-Glycine and GS395

Enzymatic activity of Plasmodium Vivax Shmt(C346A) Bound with Plp-Glycine and GS395

All present enzymatic activity of Plasmodium Vivax Shmt(C346A) Bound with Plp-Glycine and GS395:
2.1.2.1;

Protein crystallography data

The structure of Plasmodium Vivax Shmt(C346A) Bound with Plp-Glycine and GS395, PDB code: 5xmr 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 (°) 101.425, 58.537, 234.912, 90.00, 90.08, 90.00
R / Rfree (%) 20.9 / 28.3

Other elements in 5xmr:

The structure of Plasmodium Vivax Shmt(C346A) Bound with Plp-Glycine and GS395 also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Plasmodium Vivax Shmt(C346A) Bound with Plp-Glycine and GS395 (pdb code 5xmr). 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(C346A) Bound with Plp-Glycine and GS395, PDB code: 5xmr:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Fluorine binding site 1 out of 9 in 5xmr

Go back to Fluorine Binding Sites List in 5xmr
Fluorine binding site 1 out of 9 in the Plasmodium Vivax Shmt(C346A) Bound with Plp-Glycine and GS395


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(C346A) Bound with Plp-Glycine and GS395 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F502

b:36.8
occ:1.00
 F49 A:8AO502 0.0 36.8 1.0
C33 A:8AO502 1.3 40.2 1.0
F48 A:8AO502 2.1 39.8 1.0
F47 A:8AO502 2.2 39.9 1.0
C17 A:8AO502 2.4 41.1 1.0
C16 A:8AO502 2.8 41.4 1.0
O A:LYS355 3.1 21.3 1.0
C A:LYS355 3.4 22.0 1.0
CG A:PRO367 3.5 30.3 1.0
CD A:LYS355 3.6 26.4 1.0
C18 A:8AO502 3.6 41.4 1.0
N A:ASN356 3.6 22.0 1.0
CB A:PRO367 3.7 30.6 1.0
CA A:ASN356 3.7 22.9 1.0
CG A:LYS355 3.9 25.4 1.0
CB A:LYS355 4.0 24.4 1.0
C15 A:8AO502 4.2 41.6 1.0
C A:ASN356 4.3 24.4 1.0
CA A:LYS355 4.3 22.5 1.0
N A:THR357 4.4 25.0 1.0
CD A:PRO367 4.4 31.4 1.0
N9 A:8AO502 4.4 35.2 1.0
O A:ALA364 4.6 56.5 1.0
C14 A:8AO502 4.7 41.6 1.0
CE A:LYS355 4.7 28.5 1.0
NZ A:LYS355 4.7 29.7 1.0
C19 A:8AO502 4.8 43.3 1.0
C8 A:8AO502 4.8 38.9 1.0
CG2 A:THR357 4.9 29.9 1.0
C13 A:8AO502 4.9 40.4 1.0
C20 A:8AO502 5.0 43.4 1.0

Fluorine binding site 2 out of 9 in 5xmr

Go back to Fluorine Binding Sites List in 5xmr
Fluorine binding site 2 out of 9 in the Plasmodium Vivax Shmt(C346A) Bound with Plp-Glycine and GS395


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(C346A) Bound with Plp-Glycine and GS395 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F502

b:39.8
occ:1.00
 F48 A:8AO502 0.0 39.8 1.0
C33 A:8AO502 1.3 40.2 1.0
F49 A:8AO502 2.1 36.8 1.0
F47 A:8AO502 2.2 39.9 1.0
C17 A:8AO502 2.2 41.1 1.0
O A:ALA364 2.9 56.5 1.0
C18 A:8AO502 3.0 41.4 1.0
C16 A:8AO502 3.2 41.4 1.0
CG2 A:THR357 3.4 29.9 1.0
CB A:PRO367 3.6 30.6 1.0
CG A:PRO367 3.7 30.3 1.0
C A:ALA364 3.9 60.7 1.0
CD A:PRO367 4.1 31.4 1.0
CA A:ALA364 4.1 61.8 1.0
C19 A:8AO502 4.2 43.3 1.0
CB A:ALA364 4.2 60.4 1.0
N A:THR357 4.3 25.0 1.0
N9 A:8AO502 4.3 35.2 1.0
C15 A:8AO502 4.4 41.6 1.0
CB A:THR357 4.6 29.0 1.0
CA A:PRO367 4.7 31.5 1.0
C A:ASN356 4.7 24.4 1.0
C20 A:8AO502 4.8 43.4 1.0
N A:PRO367 4.8 33.8 1.0
CA A:ASN356 4.8 22.9 1.0
CA A:THR357 4.8 27.4 1.0
C8 A:8AO502 4.9 38.9 1.0

Fluorine binding site 3 out of 9 in 5xmr

Go back to Fluorine Binding Sites List in 5xmr
Fluorine binding site 3 out of 9 in the Plasmodium Vivax Shmt(C346A) Bound with Plp-Glycine and GS395


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(C346A) Bound with Plp-Glycine and GS395 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F502

b:39.9
occ:1.00
 F47 A:8AO502 0.0 39.9 1.0
C33 A:8AO502 1.3 40.2 1.0
F48 A:8AO502 2.2 39.8 1.0
F49 A:8AO502 2.2 36.8 1.0
C17 A:8AO502 2.3 41.1 1.0
C18 A:8AO502 2.8 41.4 1.0
O A:ALA364 3.2 56.5 1.0
C16 A:8AO502 3.5 41.4 1.0
CD A:LYS355 3.5 26.4 1.0
NZ A:LYS355 3.6 29.7 1.0
CG A:PRO367 3.8 30.3 1.0
CD A:PRO367 3.9 31.4 1.0
C19 A:8AO502 4.1 43.3 1.0
CE A:LYS355 4.2 28.5 1.0
C A:ALA364 4.3 60.7 1.0
CB A:PRO367 4.4 30.6 1.0
CG A:LYS355 4.5 25.4 1.0
C15 A:8AO502 4.7 41.6 1.0
CD1 B:TYR63 4.8 32.0 1.0
CE1 B:TYR63 4.9 32.3 1.0
C20 A:8AO502 4.9 43.4 1.0

Fluorine binding site 4 out of 9 in 5xmr

Go back to Fluorine Binding Sites List in 5xmr
Fluorine binding site 4 out of 9 in the Plasmodium Vivax Shmt(C346A) Bound with Plp-Glycine and GS395


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(C346A) Bound with Plp-Glycine and GS395 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F502

b:40.7
occ:1.00
 F49 B:8AO502 0.0 40.7 1.0
C33 B:8AO502 1.3 41.0 1.0
F48 B:8AO502 2.1 38.0 1.0
F47 B:8AO502 2.2 40.9 1.0
C17 B:8AO502 2.4 41.5 1.0
C16 B:8AO502 2.8 40.9 1.0
O B:LYS355 2.9 26.2 1.0
C B:LYS355 3.3 24.1 1.0
CG B:PRO367 3.5 31.5 1.0
CD B:LYS355 3.6 31.9 1.0
C18 B:8AO502 3.6 40.7 1.0
CG B:LYS355 3.8 28.7 1.0
N B:ASN356 3.8 23.5 1.0
CB B:LYS355 3.9 26.4 1.0
CB B:PRO367 3.9 32.2 1.0
CA B:ASN356 3.9 23.6 1.0
CE B:LYS355 4.1 35.6 1.0
C15 B:8AO502 4.2 39.5 1.0
CA B:LYS355 4.2 24.4 1.0
C B:ASN356 4.4 25.1 1.0
N B:THR357 4.4 24.9 1.0
N9 B:8AO502 4.5 35.2 1.0
CD B:PRO367 4.5 32.4 1.0
C14 B:8AO502 4.7 38.2 1.0
C19 B:8AO502 4.8 41.3 1.0
O B:ALA364 4.8 58.5 1.0
C8 B:8AO502 4.9 37.4 1.0
N B:LYS355 4.9 22.7 1.0
CG2 B:THR357 4.9 27.8 1.0
C13 B:8AO502 4.9 38.1 1.0
C20 B:8AO502 5.0 40.8 1.0

Fluorine binding site 5 out of 9 in 5xmr

Go back to Fluorine Binding Sites List in 5xmr
Fluorine binding site 5 out of 9 in the Plasmodium Vivax Shmt(C346A) Bound with Plp-Glycine and GS395


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(C346A) Bound with Plp-Glycine and GS395 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F502

b:38.0
occ:1.00
 F48 B:8AO502 0.0 38.0 1.0
C33 B:8AO502 1.3 41.0 1.0
F49 B:8AO502 2.1 40.7 1.0
F47 B:8AO502 2.1 40.9 1.0
C17 B:8AO502 2.3 41.5 1.0
O B:ALA364 3.1 58.5 1.0
C18 B:8AO502 3.1 40.7 1.0
C16 B:8AO502 3.3 40.9 1.0
CB B:PRO367 3.4 32.2 1.0
CG B:PRO367 3.4 31.5 1.0
CG2 B:THR357 3.4 27.8 1.0
CD B:PRO367 3.9 32.4 1.0
C B:ALA364 4.0 61.1 1.0
CB B:ALA364 4.1 61.2 1.0
CA B:ALA364 4.1 62.2 1.0
N B:THR357 4.3 24.9 1.0
C19 B:8AO502 4.4 41.3 1.0
C15 B:8AO502 4.6 39.5 1.0
CA B:PRO367 4.6 32.3 1.0
N9 B:8AO502 4.6 35.2 1.0
N B:PRO367 4.7 34.4 1.0
CB B:THR357 4.7 27.4 1.0
CD B:LYS355 4.8 31.9 1.0
O B:LYS355 4.8 26.2 1.0
C B:ASN356 4.8 25.1 1.0
CA B:THR357 4.9 26.7 1.0
CA B:ASN356 4.9 23.6 1.0
C20 B:8AO502 5.0 40.8 1.0

Fluorine binding site 6 out of 9 in 5xmr

Go back to Fluorine Binding Sites List in 5xmr
Fluorine binding site 6 out of 9 in the Plasmodium Vivax Shmt(C346A) Bound with Plp-Glycine and GS395


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(C346A) Bound with Plp-Glycine and GS395 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F502

b:40.9
occ:1.00
 F47 B:8AO502 0.0 40.9 1.0
C33 B:8AO502 1.3 41.0 1.0
F48 B:8AO502 2.1 38.0 1.0
F49 B:8AO502 2.2 40.7 1.0
C17 B:8AO502 2.3 41.5 1.0
C18 B:8AO502 2.8 40.7 1.0
CE B:LYS355 3.3 35.6 1.0
O B:ALA364 3.5 58.5 1.0
CD B:LYS355 3.5 31.9 1.0
C16 B:8AO502 3.5 40.9 1.0
CG B:PRO367 3.9 31.5 1.0
NZ B:LYS355 4.0 38.2 1.0
C19 B:8AO502 4.1 41.3 1.0
CD B:PRO367 4.2 32.4 1.0
CE2 A:TYR63 4.3 29.8 1.0
CG B:LYS355 4.4 28.7 1.0
CD2 A:TYR63 4.4 29.0 1.0
C B:ALA364 4.6 61.1 1.0
CB B:PRO367 4.7 32.2 1.0
C15 B:8AO502 4.7 39.5 1.0
O B:LYS355 4.8 26.2 1.0
C20 B:8AO502 4.9 40.8 1.0
CB B:LYS355 5.0 26.4 1.0
C32 B:8AO502 5.0 41.3 1.0

Fluorine binding site 7 out of 9 in 5xmr

Go back to Fluorine Binding Sites List in 5xmr
Fluorine binding site 7 out of 9 in the Plasmodium Vivax Shmt(C346A) Bound with Plp-Glycine and GS395


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(C346A) Bound with Plp-Glycine and GS395 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F502

b:37.0
occ:1.00
 F49 C:8AO502 0.0 37.0 1.0
C33 C:8AO502 1.3 40.5 1.0
F48 C:8AO502 2.1 41.3 1.0
F47 C:8AO502 2.2 41.9 1.0
C17 C:8AO502 2.4 40.8 1.0
C16 C:8AO502 2.8 39.9 1.0
O C:LYS355 3.0 24.8 1.0
CG C:PRO367 3.4 30.6 1.0
C C:LYS355 3.5 23.8 1.0
C18 C:8AO502 3.7 40.4 1.0
CB C:PRO367 3.8 30.7 1.0
CD C:LYS355 3.8 30.0 1.0
N C:ASN356 3.8 23.2 1.0
CA C:ASN356 3.8 23.6 1.0
CB C:LYS355 4.1 26.4 1.0
C15 C:8AO502 4.2 40.0 1.0
CG C:LYS355 4.2 28.0 1.0
N9 C:8AO502 4.2 35.5 1.0
C C:ASN356 4.3 25.4 1.0
CD C:PRO367 4.3 31.4 1.0
N C:THR357 4.3 26.6 1.0
CA C:LYS355 4.4 23.6 1.0
O C:ALA364 4.5 61.0 1.0
CG2 C:THR357 4.5 29.5 1.0
CE C:LYS355 4.6 32.6 1.0
C8 C:8AO502 4.7 38.2 1.0
C19 C:8AO502 4.8 40.2 1.0
C14 C:8AO502 4.8 40.8 1.0
C13 C:8AO502 4.9 40.7 1.0

Fluorine binding site 8 out of 9 in 5xmr

Go back to Fluorine Binding Sites List in 5xmr
Fluorine binding site 8 out of 9 in the Plasmodium Vivax Shmt(C346A) Bound with Plp-Glycine and GS395


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(C346A) Bound with Plp-Glycine and GS395 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F502

b:41.3
occ:1.00
 F48 C:8AO502 0.0 41.3 1.0
C33 C:8AO502 1.3 40.5 1.0
F49 C:8AO502 2.1 37.0 1.0
F47 C:8AO502 2.2 41.9 1.0
C17 C:8AO502 2.3 40.8 1.0
O C:ALA364 2.9 61.0 1.0
C18 C:8AO502 3.0 40.4 1.0
C16 C:8AO502 3.2 39.9 1.0
CG2 C:THR357 3.3 29.5 1.0
C C:ALA364 3.7 61.5 1.0
CA C:ALA364 3.7 61.9 1.0
CG C:PRO367 3.7 30.6 1.0
CB C:PRO367 3.7 30.7 1.0
CB C:ALA364 3.9 61.5 1.0
CD C:PRO367 4.0 31.4 1.0
C19 C:8AO502 4.2 40.2 1.0
N9 C:8AO502 4.3 35.5 1.0
C15 C:8AO502 4.4 40.0 1.0
N C:THR357 4.5 26.6 1.0
CB C:THR357 4.6 29.0 1.0
CA C:PRO367 4.8 31.2 1.0
C20 C:8AO502 4.8 39.6 1.0
N C:PRO367 4.8 34.1 1.0
C C:ASN356 4.9 25.4 1.0
C8 C:8AO502 4.9 38.2 1.0
CA C:THR357 4.9 28.3 1.0
N C:VAL365 5.0 61.4 1.0
OG1 C:THR357 5.0 34.0 1.0

Fluorine binding site 9 out of 9 in 5xmr

Go back to Fluorine Binding Sites List in 5xmr
Fluorine binding site 9 out of 9 in the Plasmodium Vivax Shmt(C346A) Bound with Plp-Glycine and GS395


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(C346A) Bound with Plp-Glycine and GS395 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F502

b:41.9
occ:1.00
 F47 C:8AO502 0.0 41.9 1.0
C33 C:8AO502 1.3 40.5 1.0
F48 C:8AO502 2.2 41.3 1.0
F49 C:8AO502 2.2 37.0 1.0
C17 C:8AO502 2.3 40.8 1.0
C18 C:8AO502 2.8 40.4 1.0
O C:ALA364 3.0 61.0 1.0
C16 C:8AO502 3.5 39.9 1.0
CD C:LYS355 3.6 30.0 1.0
NZ C:LYS355 3.7 35.5 1.0
CG C:PRO367 3.9 30.6 1.0
CE C:LYS355 3.9 32.6 1.0
CD C:PRO367 4.1 31.4 1.0
C19 C:8AO502 4.1 40.2 1.0
C C:ALA364 4.2 61.5 1.0
C15 C:8AO502 4.6 40.0 1.0
CB C:PRO367 4.7 30.7 1.0
CG C:LYS355 4.7 28.0 1.0
CA C:ALA364 4.9 61.9 1.0
C20 C:8AO502 4.9 39.6 1.0
O C:LYS355 4.9 24.8 1.0
CB C:ALA364 4.9 61.5 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: Thu Aug 1 16:56:37 2024

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