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Fluorine in PDB 5xmv: Plasmodium Vivax Shmt Bound with Plp-Glycine and GS362

Enzymatic activity of Plasmodium Vivax Shmt Bound with Plp-Glycine and GS362

All present enzymatic activity of Plasmodium Vivax Shmt Bound with Plp-Glycine and GS362:
2.1.2.1;

Protein crystallography data

The structure of Plasmodium Vivax Shmt Bound with Plp-Glycine and GS362, PDB code: 5xmv 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 / 2.16
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 101.674, 58.843, 234.899, 90.00, 90.14, 90.00
R / Rfree (%) 24.2 / 30.6

Other elements in 5xmv:

The structure of Plasmodium Vivax Shmt Bound with Plp-Glycine and GS362 also contains other interesting chemical elements:

Chlorine (Cl) 5 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Plasmodium Vivax Shmt Bound with Plp-Glycine and GS362 (pdb code 5xmv). 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 GS362, PDB code: 5xmv:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Fluorine binding site 1 out of 9 in 5xmv

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Fluorine binding site 1 out of 9 in the Plasmodium Vivax Shmt Bound with Plp-Glycine and GS362


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 GS362 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F502

b:34.2
occ:1.00
 F32 A:8AU502 0.0 34.2 1.0
C23 A:8AU502 1.3 32.5 1.0
F30 A:8AU502 2.1 34.8 1.0
F31 A:8AU502 2.2 29.5 1.0
C18 A:8AU502 2.3 30.1 1.0
C19 A:8AU502 3.0 29.3 1.0
CD A:LYS355 3.2 37.5 1.0
NZ A:LYS355 3.3 40.0 1.0
C17 A:8AU502 3.3 29.7 1.0
CG A:LYS355 3.4 35.2 1.0
O A:HOH712 3.6 41.6 1.0
CE A:LYS355 3.8 39.6 1.0
CD2 B:TYR63 4.0 28.0 1.0
CE2 B:TYR63 4.1 25.3 1.0
C20 A:8AU502 4.3 29.0 1.0
CG A:PRO367 4.4 40.5 1.0
C16 A:8AU502 4.6 28.7 1.0
CB A:LYS355 4.6 31.6 1.0
O A:LYS355 4.6 29.0 1.0
O A:CYS364 4.7 76.3 1.0
C21 A:8AU502 4.9 28.4 1.0
CD A:PRO367 4.9 40.6 1.0
C A:LYS355 4.9 28.1 1.0

Fluorine binding site 2 out of 9 in 5xmv

Go back to Fluorine Binding Sites List in 5xmv
Fluorine binding site 2 out of 9 in the Plasmodium Vivax Shmt Bound with Plp-Glycine and GS362


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 GS362 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F502

b:29.5
occ:1.00
 F31 A:8AU502 0.0 29.5 1.0
C23 A:8AU502 1.3 32.5 1.0
F32 A:8AU502 2.2 34.2 1.0
F30 A:8AU502 2.2 34.8 1.0
C18 A:8AU502 2.4 30.1 1.0
C17 A:8AU502 2.8 29.7 1.0
O A:LYS355 3.3 29.0 1.0
C A:LYS355 3.6 28.1 1.0
CG A:LYS355 3.6 35.2 1.0
C19 A:8AU502 3.6 29.3 1.0
CG A:PRO367 3.6 40.5 1.0
N A:ASN356 3.8 27.6 1.0
CB A:PRO367 3.9 41.2 1.0
CA A:ASN356 3.9 27.3 1.0
CD A:LYS355 4.0 37.5 1.0
CB A:LYS355 4.2 31.6 1.0
C16 A:8AU502 4.2 28.7 1.0
N A:THR357 4.3 29.6 1.0
C A:ASN356 4.3 29.2 1.0
N9 A:8AU502 4.4 34.7 1.0
CA A:LYS355 4.5 27.3 1.0
CD A:PRO367 4.6 40.6 1.0
C20 A:8AU502 4.8 29.0 1.0
C8 A:8AU502 4.8 32.5 1.0
CG2 A:THR357 4.9 34.6 1.0

Fluorine binding site 3 out of 9 in 5xmv

Go back to Fluorine Binding Sites List in 5xmv
Fluorine binding site 3 out of 9 in the Plasmodium Vivax Shmt Bound with Plp-Glycine and GS362


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 GS362 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F502

b:34.8
occ:1.00
 F30 A:8AU502 0.0 34.8 1.0
C23 A:8AU502 1.3 32.5 1.0
F32 A:8AU502 2.1 34.2 1.0
F31 A:8AU502 2.2 29.5 1.0
C18 A:8AU502 2.3 30.1 1.0
C19 A:8AU502 2.8 29.3 1.0
O A:CYS364 3.2 76.3 1.0
C17 A:8AU502 3.6 29.7 1.0
SG A:CYS364 3.6 70.9 1.0
CB A:CYS364 4.0 72.2 1.0
CG A:PRO367 4.0 40.5 1.0
C A:CYS364 4.1 74.9 1.0
C20 A:8AU502 4.2 29.0 1.0
O A:HOH712 4.2 41.6 1.0
CD A:PRO367 4.3 40.6 1.0
CA A:CYS364 4.3 75.2 1.0
CB A:PRO367 4.3 41.2 1.0
CD A:LYS355 4.6 37.5 1.0
CG2 A:THR357 4.7 34.6 1.0
C16 A:8AU502 4.7 28.7 1.0
C21 A:8AU502 4.9 28.4 1.0
CG A:LYS355 4.9 35.2 1.0

Fluorine binding site 4 out of 9 in 5xmv

Go back to Fluorine Binding Sites List in 5xmv
Fluorine binding site 4 out of 9 in the Plasmodium Vivax Shmt Bound with Plp-Glycine and GS362


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 GS362 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F502

b:32.1
occ:1.00
 F32 B:8AU502 0.0 32.1 1.0
C23 B:8AU502 1.3 30.8 1.0
F30 B:8AU502 2.1 33.1 1.0
F31 B:8AU502 2.2 27.7 1.0
C18 B:8AU502 2.3 30.2 1.0
C19 B:8AU502 3.1 29.6 1.0
C17 B:8AU502 3.3 30.6 1.0
CD B:LYS355 3.3 33.6 1.0
NZ B:LYS355 3.3 36.2 1.0
CG B:LYS355 3.5 32.4 1.0
CE B:LYS355 3.8 35.6 1.0
CD2 A:TYR63 4.1 25.2 1.0
CG B:PRO367 4.3 40.4 1.0
CE2 A:TYR63 4.3 24.0 1.0
C20 B:8AU502 4.3 29.8 1.0
C16 B:8AU502 4.5 30.5 1.0
O B:LYS355 4.6 32.0 1.0
CB B:LYS355 4.7 29.0 1.0
CD B:PRO367 4.8 40.3 1.0
C B:LYS355 4.9 27.8 1.0
C21 B:8AU502 4.9 29.5 1.0

Fluorine binding site 5 out of 9 in 5xmv

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Fluorine binding site 5 out of 9 in the Plasmodium Vivax Shmt Bound with Plp-Glycine and GS362


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 GS362 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F502

b:27.7
occ:1.00
 F31 B:8AU502 0.0 27.7 1.0
C23 B:8AU502 1.3 30.8 1.0
F30 B:8AU502 2.1 33.1 1.0
F32 B:8AU502 2.2 32.1 1.0
C18 B:8AU502 2.3 30.2 1.0
C17 B:8AU502 2.7 30.6 1.0
CG B:PRO367 3.5 40.4 1.0
O B:LYS355 3.6 32.0 1.0
C19 B:8AU502 3.6 29.6 1.0
C B:LYS355 3.8 27.8 1.0
CA B:ASN356 3.8 26.6 1.0
CB B:PRO367 3.8 39.3 1.0
N B:ASN356 3.9 27.8 1.0
CG B:LYS355 3.9 32.4 1.0
N9 B:8AU502 4.1 35.2 1.0
CD B:LYS355 4.1 33.6 1.0
N B:THR357 4.1 29.8 1.0
C16 B:8AU502 4.1 30.5 1.0
C B:ASN356 4.3 28.0 1.0
CD B:PRO367 4.5 40.3 1.0
CB B:LYS355 4.5 29.0 1.0
C8 B:8AU502 4.6 34.8 1.0
CG2 B:THR357 4.6 34.4 1.0
C20 B:8AU502 4.7 29.8 1.0
CA B:LYS355 4.8 26.6 1.0
SG B:CYS364 4.9 71.1 1.0
O B:CYS364 4.9 66.0 1.0
C21 B:8AU502 4.9 29.5 1.0

Fluorine binding site 6 out of 9 in 5xmv

Go back to Fluorine Binding Sites List in 5xmv
Fluorine binding site 6 out of 9 in the Plasmodium Vivax Shmt Bound with Plp-Glycine and GS362


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 GS362 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F502

b:33.1
occ:1.00
 F30 B:8AU502 0.0 33.1 1.0
C23 B:8AU502 1.3 30.8 1.0
F32 B:8AU502 2.1 32.1 1.0
F31 B:8AU502 2.1 27.7 1.0
C18 B:8AU502 2.3 30.2 1.0
C19 B:8AU502 2.8 29.6 1.0
O B:CYS364 3.2 66.0 1.0
C17 B:8AU502 3.6 30.6 1.0
SG B:CYS364 3.7 71.1 1.0
CG B:PRO367 3.9 40.4 1.0
CD B:PRO367 4.1 40.3 1.0
C20 B:8AU502 4.1 29.8 1.0
C B:CYS364 4.3 66.6 1.0
CB B:PRO367 4.4 39.3 1.0
CB B:CYS364 4.5 68.0 1.0
CD B:LYS355 4.6 33.6 1.0
C16 B:8AU502 4.7 30.5 1.0
CA B:CYS364 4.8 68.7 1.0
CG2 B:THR357 4.8 34.4 1.0
O A:HOH622 4.9 27.1 1.0
C21 B:8AU502 4.9 29.5 1.0
C29 B:8AU502 5.0 31.2 1.0
C22 B:8AU502 5.0 30.4 1.0

Fluorine binding site 7 out of 9 in 5xmv

Go back to Fluorine Binding Sites List in 5xmv
Fluorine binding site 7 out of 9 in the Plasmodium Vivax Shmt Bound with Plp-Glycine and GS362


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 GS362 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F502

b:30.7
occ:1.00
 F32 C:8AU502 0.0 30.7 1.0
C23 C:8AU502 1.3 32.0 1.0
F30 C:8AU502 2.1 31.6 1.0
F31 C:8AU502 2.2 29.4 1.0
C18 C:8AU502 2.4 30.5 1.0
C19 C:8AU502 3.1 30.2 1.0
CG C:LYS355 3.2 32.4 1.0
CE C:LYS355 3.3 36.1 1.0
C17 C:8AU502 3.3 29.2 1.0
NZ C:LYS355 3.4 37.8 1.0
CD C:LYS355 3.5 35.5 1.0
CG C:PRO367 4.3 38.7 1.0
C20 C:8AU502 4.4 29.5 1.0
C16 C:8AU502 4.6 28.9 1.0
O C:LYS355 4.7 29.0 1.0
CB C:LYS355 4.7 29.8 1.0
O C:CYS364 4.7 74.7 1.0
CD C:PRO367 4.8 38.8 1.0
C C:LYS355 5.0 27.8 1.0
C21 C:8AU502 5.0 28.8 1.0

Fluorine binding site 8 out of 9 in 5xmv

Go back to Fluorine Binding Sites List in 5xmv
Fluorine binding site 8 out of 9 in the Plasmodium Vivax Shmt Bound with Plp-Glycine and GS362


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 GS362 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F502

b:29.4
occ:1.00
 F31 C:8AU502 0.0 29.4 1.0
C23 C:8AU502 1.3 32.0 1.0
F30 C:8AU502 2.1 31.6 1.0
F32 C:8AU502 2.2 30.7 1.0
C18 C:8AU502 2.3 30.5 1.0
C17 C:8AU502 2.8 29.2 1.0
CG C:LYS355 3.5 32.4 1.0
CG C:PRO367 3.5 38.7 1.0
O C:LYS355 3.6 29.0 1.0
C19 C:8AU502 3.6 30.2 1.0
CB C:PRO367 3.8 38.7 1.0
C C:LYS355 3.8 27.8 1.0
CA C:ASN356 3.9 27.6 1.0
N C:ASN356 3.9 28.0 1.0
N9 C:8AU502 4.1 30.9 1.0
C16 C:8AU502 4.2 28.9 1.0
N C:THR357 4.2 29.1 1.0
C C:ASN356 4.3 28.2 1.0
CB C:LYS355 4.5 29.8 1.0
CD C:PRO367 4.5 38.8 1.0
CD C:LYS355 4.6 35.5 1.0
C8 C:8AU502 4.6 30.9 1.0
C20 C:8AU502 4.7 29.5 1.0
O C:CYS364 4.7 74.7 1.0
CE C:LYS355 4.8 36.1 1.0
CA C:LYS355 4.8 26.6 1.0
C21 C:8AU502 5.0 28.8 1.0

Fluorine binding site 9 out of 9 in 5xmv

Go back to Fluorine Binding Sites List in 5xmv
Fluorine binding site 9 out of 9 in the Plasmodium Vivax Shmt Bound with Plp-Glycine and GS362


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 GS362 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F502

b:31.6
occ:1.00
 F30 C:8AU502 0.0 31.6 1.0
C23 C:8AU502 1.3 32.0 1.0
F32 C:8AU502 2.1 30.7 1.0
F31 C:8AU502 2.1 29.4 1.0
C18 C:8AU502 2.3 30.5 1.0
C19 C:8AU502 2.8 30.2 1.0
O C:CYS364 2.9 74.7 1.0
C17 C:8AU502 3.6 29.2 1.0
CG C:PRO367 3.9 38.7 1.0
C C:CYS364 4.0 77.1 1.0
SG C:CYS364 4.0 70.6 1.0
C20 C:8AU502 4.1 29.5 1.0
CD C:PRO367 4.2 38.8 1.0
CB C:CYS364 4.2 74.5 1.0
CA C:CYS364 4.4 77.8 1.0
CB C:PRO367 4.4 38.7 1.0
CG C:LYS355 4.7 32.4 1.0
C16 C:8AU502 4.8 28.9 1.0
CE C:LYS355 4.9 36.1 1.0
C21 C:8AU502 4.9 28.8 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 17:00:25 2024

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