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Fluorine in PDB 5xms: Plasmodium Vivax Shmt Bound with Plp-Glycine and GS498

Enzymatic activity of Plasmodium Vivax Shmt Bound with Plp-Glycine and GS498

All present enzymatic activity of Plasmodium Vivax Shmt Bound with Plp-Glycine and GS498:
2.1.2.1;

Protein crystallography data

The structure of Plasmodium Vivax Shmt Bound with Plp-Glycine and GS498, PDB code: 5xms 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 / 2.45
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 101.808, 58.794, 235.131, 90.00, 89.99, 90.00
R / Rfree (%) 21.8 / 28

Other elements in 5xms:

The structure of Plasmodium Vivax Shmt Bound with Plp-Glycine and GS498 also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Fluorine Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Fluorine atom in the Plasmodium Vivax Shmt Bound with Plp-Glycine and GS498 (pdb code 5xms). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 12 binding sites of Fluorine where determined in the Plasmodium Vivax Shmt Bound with Plp-Glycine and GS498, PDB code: 5xms:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Fluorine binding site 1 out of 12 in 5xms

Go back to Fluorine Binding Sites List in 5xms
Fluorine binding site 1 out of 12 in the Plasmodium Vivax Shmt Bound with Plp-Glycine and GS498


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 GS498 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F502

b:26.1
occ:1.00
 F50 A:8B3502 0.0 26.1 1.0
C39 A:8B3502 1.4 24.2 1.0
C32 A:8B3502 2.4 24.5 1.0
C40 A:8B3502 2.4 23.1 1.0
C19 A:8B3502 2.8 26.0 1.0
C20 A:8B3502 2.9 25.8 1.0
CZ B:TYR63 3.3 25.1 1.0
C12 A:8B3502 3.4 27.7 1.0
CE2 B:TYR63 3.5 25.2 1.0
OH B:TYR63 3.6 25.7 1.0
C41 A:8B3502 3.6 23.3 1.0
C43 A:8B3502 3.6 23.1 1.0
CE1 B:TYR63 3.6 25.7 1.0
C10 A:8B3502 3.8 27.6 1.0
C18 A:8B3502 4.0 26.3 1.0
CZ B:PHE266 4.0 24.0 1.0
CD2 B:TYR63 4.0 25.1 1.0
CD2 A:LEU130 4.1 24.8 1.0
C15 A:8B3502 4.1 26.6 1.0
C42 A:8B3502 4.1 23.1 1.0
CD1 B:TYR63 4.1 26.0 1.0
N51 A:8B3502 4.3 29.3 1.0
CG B:TYR63 4.3 27.1 1.0
C5 A:8B3502 4.4 25.9 1.0
CD1 A:LEU130 4.5 24.5 1.0
CE2 B:PHE266 4.7 23.8 1.0
CG A:LEU130 4.8 24.1 1.0
CE1 B:PHE266 4.9 22.2 1.0
C17 A:8B3502 4.9 28.3 1.0
C4 A:8B3502 4.9 24.7 1.0
C16 A:8B3502 4.9 28.7 1.0

Fluorine binding site 2 out of 12 in 5xms

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Fluorine binding site 2 out of 12 in the Plasmodium Vivax Shmt Bound with Plp-Glycine and GS498


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 GS498 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F502

b:33.6
occ:1.00
 F48 A:8B3502 0.0 33.6 1.0
C33 A:8B3502 1.3 30.8 1.0
F46 A:8B3502 2.1 29.7 1.0
F47 A:8B3502 2.1 28.3 1.0
C17 A:8B3502 2.3 28.3 1.0
C18 A:8B3502 3.0 26.3 1.0
O A:CYS364 3.2 76.9 1.0
C16 A:8B3502 3.3 28.7 1.0
CA A:CYS364 3.5 72.6 1.0
CB A:CYS364 3.6 68.4 1.0
C A:CYS364 3.6 74.6 1.0
CG2 A:THR357 3.6 28.7 1.0
CG A:PRO367 3.9 32.5 1.0
CB A:PRO367 4.1 32.5 1.0
CD A:PRO367 4.1 35.1 1.0
SG A:CYS364 4.2 65.6 1.0
C19 A:8B3502 4.3 26.0 1.0
C15 A:8B3502 4.5 26.6 1.0
N A:CYS364 4.8 72.7 1.0
N A:THR357 4.8 27.4 1.0
N A:VAL365 4.8 74.6 1.0
N9 A:8B3502 4.8 23.6 1.0
C20 A:8B3502 4.9 25.8 1.0
O A:ASP363 4.9 73.8 1.0
CB A:THR357 5.0 28.0 1.0

Fluorine binding site 3 out of 12 in 5xms

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Fluorine binding site 3 out of 12 in the Plasmodium Vivax Shmt Bound with Plp-Glycine and GS498


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 GS498 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F502

b:28.3
occ:1.00
 F47 A:8B3502 0.0 28.3 1.0
C33 A:8B3502 1.3 30.8 1.0
F48 A:8B3502 2.1 33.6 1.0
F46 A:8B3502 2.2 29.7 1.0
C17 A:8B3502 2.3 28.3 1.0
C18 A:8B3502 2.8 26.3 1.0
O A:CYS364 3.2 76.9 1.0
NZ A:LYS355 3.4 33.7 1.0
C16 A:8B3502 3.5 28.7 1.0
CD A:LYS355 3.7 30.8 1.0
CE1 B:TYR63 4.0 25.7 1.0
CE A:LYS355 4.1 32.2 1.0
C19 A:8B3502 4.1 26.0 1.0
C A:CYS364 4.2 74.6 1.0
CD1 B:TYR63 4.2 26.0 1.0
CG A:PRO367 4.3 32.5 1.0
CD A:PRO367 4.5 35.1 1.0
CG A:LYS355 4.6 27.7 1.0
CA A:CYS364 4.7 72.6 1.0
CB A:CYS364 4.7 68.4 1.0
C15 A:8B3502 4.7 26.6 1.0
C20 A:8B3502 4.9 25.8 1.0

Fluorine binding site 4 out of 12 in 5xms

Go back to Fluorine Binding Sites List in 5xms
Fluorine binding site 4 out of 12 in the Plasmodium Vivax Shmt Bound with Plp-Glycine and GS498


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 GS498 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F502

b:29.7
occ:1.00
 F46 A:8B3502 0.0 29.7 1.0
C33 A:8B3502 1.3 30.8 1.0
F48 A:8B3502 2.1 33.6 1.0
F47 A:8B3502 2.2 28.3 1.0
C17 A:8B3502 2.4 28.3 1.0
C16 A:8B3502 2.8 28.7 1.0
O A:LYS355 3.3 23.6 1.0
CG A:PRO367 3.6 32.5 1.0
C18 A:8B3502 3.6 26.3 1.0
CD A:LYS355 3.7 30.8 1.0
C A:LYS355 3.8 24.2 1.0
CG A:LYS355 4.0 27.7 1.0
N A:ASN356 4.0 24.8 1.0
CB A:PRO367 4.1 32.5 1.0
CA A:ASN356 4.1 25.5 1.0
C15 A:8B3502 4.2 26.6 1.0
CB A:LYS355 4.2 25.2 1.0
N A:THR357 4.4 27.4 1.0
CD A:PRO367 4.4 35.1 1.0
C A:ASN356 4.4 26.9 1.0
N9 A:8B3502 4.5 23.6 1.0
CG2 A:THR357 4.6 28.7 1.0
CA A:LYS355 4.6 24.6 1.0
CE A:LYS355 4.7 32.2 1.0
O A:CYS364 4.7 76.9 1.0
NZ A:LYS355 4.8 33.7 1.0
C19 A:8B3502 4.8 26.0 1.0
C14 A:8B3502 4.8 26.4 1.0
C8 A:8B3502 4.9 26.2 1.0
C13 A:8B3502 4.9 25.8 1.0
C20 A:8B3502 5.0 25.8 1.0

Fluorine binding site 5 out of 12 in 5xms

Go back to Fluorine Binding Sites List in 5xms
Fluorine binding site 5 out of 12 in the Plasmodium Vivax Shmt Bound with Plp-Glycine and GS498


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 GS498 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F502

b:28.8
occ:1.00
 F50 B:8B3502 0.0 28.8 1.0
C39 B:8B3502 1.4 26.7 1.0
C40 B:8B3502 2.4 25.9 1.0
C32 B:8B3502 2.4 26.3 1.0
C19 B:8B3502 2.8 26.7 1.0
C20 B:8B3502 3.0 27.5 1.0
CZ A:TYR63 3.2 24.6 1.0
C12 B:8B3502 3.4 28.5 1.0
CE2 A:TYR63 3.4 24.4 1.0
OH A:TYR63 3.4 25.0 1.0
CE1 A:TYR63 3.5 24.6 1.0
C41 B:8B3502 3.6 26.0 1.0
C43 B:8B3502 3.6 26.0 1.0
C10 B:8B3502 3.8 28.8 1.0
CZ A:PHE266 3.9 26.5 1.0
CD2 A:TYR63 3.9 24.9 1.0
C18 B:8B3502 4.0 28.2 1.0
CD1 A:TYR63 4.0 24.9 1.0
C42 B:8B3502 4.1 25.8 1.0
C15 B:8B3502 4.1 27.6 1.0
CG A:TYR63 4.2 26.2 1.0
N51 B:8B3502 4.3 29.2 1.0
CD1 B:LEU130 4.3 26.5 1.0
CD2 B:LEU130 4.4 27.2 1.0
C5 B:8B3502 4.5 28.0 1.0
CE2 A:PHE266 4.6 25.9 1.0
CE1 A:PHE266 4.8 25.6 1.0
CG B:LEU130 4.8 26.4 1.0
C17 B:8B3502 4.9 29.2 1.0
C16 B:8B3502 5.0 28.9 1.0
C4 B:8B3502 5.0 26.9 1.0

Fluorine binding site 6 out of 12 in 5xms

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Fluorine binding site 6 out of 12 in the Plasmodium Vivax Shmt Bound with Plp-Glycine and GS498


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 GS498 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F502

b:29.6
occ:1.00
 F48 B:8B3502 0.0 29.6 1.0
C33 B:8B3502 1.3 31.4 1.0
F47 B:8B3502 2.1 32.2 1.0
F46 B:8B3502 2.2 30.4 1.0
C17 B:8B3502 2.3 29.2 1.0
C18 B:8B3502 2.7 28.2 1.0
O B:CYS364 2.8 68.2 1.0
C16 B:8B3502 3.6 28.9 1.0
O B:HOH676 3.6 35.6 1.0
C B:CYS364 3.8 65.8 1.0
NZ B:LYS355 3.8 33.5 1.0
CG B:PRO367 4.1 34.8 1.0
C19 B:8B3502 4.1 26.7 1.0
CD B:LYS355 4.1 29.4 1.0
CB B:CYS364 4.2 63.2 1.0
CD B:PRO367 4.2 36.9 1.0
CA B:CYS364 4.3 65.3 1.0
CE B:LYS355 4.5 31.0 1.0
CE2 A:TYR63 4.5 24.4 1.0
C15 B:8B3502 4.8 27.6 1.0
CB B:PRO367 4.8 35.2 1.0
CD2 A:TYR63 4.8 24.9 1.0
N B:VAL365 4.8 66.8 1.0
C20 B:8B3502 4.9 27.5 1.0
C32 B:8B3502 5.0 26.3 1.0

Fluorine binding site 7 out of 12 in 5xms

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Fluorine binding site 7 out of 12 in the Plasmodium Vivax Shmt Bound with Plp-Glycine and GS498


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 GS498 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F502

b:32.2
occ:1.00
 F47 B:8B3502 0.0 32.2 1.0
C33 B:8B3502 1.3 31.4 1.0
F46 B:8B3502 2.0 30.4 1.0
F48 B:8B3502 2.1 29.6 1.0
C17 B:8B3502 2.4 29.2 1.0
C16 B:8B3502 2.8 28.9 1.0
CD B:LYS355 3.2 29.4 1.0
O B:LYS355 3.4 23.9 1.0
C18 B:8B3502 3.5 28.2 1.0
CG B:LYS355 3.6 26.8 1.0
CG B:PRO367 3.7 34.8 1.0
C B:LYS355 3.8 25.1 1.0
CB B:LYS355 4.0 25.7 1.0
CE B:LYS355 4.0 31.0 1.0
NZ B:LYS355 4.1 33.5 1.0
C15 B:8B3502 4.2 27.6 1.0
N B:ASN356 4.2 24.2 1.0
CB B:PRO367 4.4 35.2 1.0
CA B:ASN356 4.4 24.3 1.0
O B:CYS364 4.4 68.2 1.0
CA B:LYS355 4.5 25.6 1.0
CD B:PRO367 4.5 36.9 1.0
C19 B:8B3502 4.7 26.7 1.0
C14 B:8B3502 4.7 28.9 1.0
O B:HOH676 4.8 35.6 1.0
N9 B:8B3502 4.9 26.4 1.0
C B:ASN356 4.9 26.7 1.0
C20 B:8B3502 4.9 27.5 1.0
CD2 A:TYR63 4.9 24.9 1.0
C13 B:8B3502 5.0 28.5 1.0

Fluorine binding site 8 out of 12 in 5xms

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Fluorine binding site 8 out of 12 in the Plasmodium Vivax Shmt Bound with Plp-Glycine and GS498


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 GS498 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F502

b:30.4
occ:1.00
 F46 B:8B3502 0.0 30.4 1.0
C33 B:8B3502 1.3 31.4 1.0
F47 B:8B3502 2.0 32.2 1.0
F48 B:8B3502 2.2 29.6 1.0
C17 B:8B3502 2.3 29.2 1.0
C16 B:8B3502 3.0 28.9 1.0
C18 B:8B3502 3.4 28.2 1.0
O B:CYS364 3.5 68.2 1.0
CG B:PRO367 3.6 34.8 1.0
CG2 B:THR357 3.6 31.1 1.0
CB B:PRO367 3.7 35.2 1.0
N B:THR357 4.0 28.2 1.0
N9 B:8B3502 4.0 26.4 1.0
CD B:PRO367 4.2 36.9 1.0
C15 B:8B3502 4.3 27.6 1.0
C B:ASN356 4.3 26.7 1.0
C B:CYS364 4.4 65.8 1.0
CA B:CYS364 4.4 65.3 1.0
CA B:ASN356 4.5 24.3 1.0
CB B:CYS364 4.5 63.2 1.0
C19 B:8B3502 4.5 26.7 1.0
CB B:THR357 4.6 29.1 1.0
O B:LYS355 4.6 23.9 1.0
C8 B:8B3502 4.6 27.9 1.0
CA B:THR357 4.6 28.7 1.0
OG1 B:THR357 4.7 31.2 1.0
N B:ASN356 4.8 24.2 1.0
C B:LYS355 4.9 25.1 1.0
C20 B:8B3502 4.9 27.5 1.0
CD B:LYS355 4.9 29.4 1.0

Fluorine binding site 9 out of 12 in 5xms

Go back to Fluorine Binding Sites List in 5xms
Fluorine binding site 9 out of 12 in the Plasmodium Vivax Shmt Bound with Plp-Glycine and GS498


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 GS498 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F502

b:28.8
occ:1.00
 F50 C:8B3502 0.0 28.8 1.0
C39 C:8B3502 1.4 25.6 1.0
C40 C:8B3502 2.4 24.2 1.0
C32 C:8B3502 2.4 24.9 1.0
C19 C:8B3502 2.9 25.6 1.0
C20 C:8B3502 3.0 26.0 1.0
C12 C:8B3502 3.3 28.9 1.0
C41 C:8B3502 3.6 25.1 1.0
C43 C:8B3502 3.7 24.6 1.0
C10 C:8B3502 3.7 28.9 1.0
CD2 C:LEU130 4.0 27.5 1.0
C18 C:8B3502 4.1 26.5 1.0
C42 C:8B3502 4.1 25.0 1.0
C15 C:8B3502 4.2 25.5 1.0
N51 C:8B3502 4.2 29.9 1.0
CD1 C:LEU130 4.2 26.9 1.0
C5 C:8B3502 4.4 27.1 1.0
CG C:LEU130 4.6 26.8 1.0
C4 C:8B3502 4.9 25.1 1.0

Fluorine binding site 10 out of 12 in 5xms

Go back to Fluorine Binding Sites List in 5xms
Fluorine binding site 10 out of 12 in the Plasmodium Vivax Shmt Bound with Plp-Glycine and GS498


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 10 of Plasmodium Vivax Shmt Bound with Plp-Glycine and GS498 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F502

b:28.8
occ:1.00
 F48 C:8B3502 0.0 28.8 1.0
C33 C:8B3502 1.3 29.6 1.0
F46 C:8B3502 2.1 34.7 1.0
F47 C:8B3502 2.2 26.9 1.0
C17 C:8B3502 2.3 27.2 1.0
C18 C:8B3502 2.9 26.5 1.0
NZ C:LYS355 3.4 35.0 1.0
C16 C:8B3502 3.4 27.2 1.0
CD C:LYS355 3.4 34.3 1.0
O C:CYS364 3.6 77.6 1.0
CE C:LYS355 3.8 34.8 1.0
CG C:PRO367 4.2 35.8 1.0
C19 C:8B3502 4.2 25.6 1.0
CG C:LYS355 4.4 31.4 1.0
CD C:PRO367 4.4 37.6 1.0
C15 C:8B3502 4.6 25.5 1.0
C C:CYS364 4.7 73.5 1.0
C20 C:8B3502 4.9 26.0 1.0
CB C:PRO367 5.0 34.5 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 16:56:56 2024

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