Fluorine in PDB 5xmu: Plasmodium Vivax Shmt Bound with Plp-Glycine and GS363

Enzymatic activity of Plasmodium Vivax Shmt Bound with Plp-Glycine and GS363

All present enzymatic activity of Plasmodium Vivax Shmt Bound with Plp-Glycine and GS363:
2.1.2.1;

Protein crystallography data

The structure of Plasmodium Vivax Shmt Bound with Plp-Glycine and GS363, PDB code: 5xmu 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 / 2.39
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 101.534, 58.618, 233.875, 90.00, 90.04, 90.00
R / Rfree (%) 23.2 / 31.8

Other elements in 5xmu:

The structure of Plasmodium Vivax Shmt Bound with Plp-Glycine and GS363 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 GS363 (pdb code 5xmu). 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 GS363, PDB code: 5xmu:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Fluorine binding site 1 out of 9 in 5xmu

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Fluorine binding site 1 out of 9 in the Plasmodium Vivax Shmt Bound with Plp-Glycine and GS363


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 GS363 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F502

b:27.6
occ:1.00
 F48 A:8A0502 0.0 27.6 1.0
C33 A:8A0502 1.3 30.6 1.0
F47 A:8A0502 2.1 31.7 1.0
F46 A:8A0502 2.2 29.1 1.0
C17 A:8A0502 2.4 30.5 1.0
C16 A:8A0502 2.8 31.5 1.0
CB A:PRO367 3.4 42.7 1.0
O A:LYS355 3.5 32.6 1.0
CG A:PRO367 3.5 43.9 1.0
C18 A:8A0502 3.7 28.8 1.0
C A:LYS355 3.8 31.3 1.0
N A:ASN356 3.9 30.9 1.0
CA A:ASN356 3.9 31.7 1.0
CD A:LYS355 4.0 41.7 1.0
CG A:LYS355 4.2 36.8 1.0
CB A:LYS355 4.2 32.7 1.0
N A:THR357 4.2 33.4 1.0
CG2 A:THR357 4.2 36.7 1.0
C15 A:8A0502 4.3 30.7 1.0
C A:ASN356 4.3 33.6 1.0
CD A:PRO367 4.3 43.6 1.0
N9 A:8A0502 4.4 30.7 1.0
CA A:LYS355 4.6 29.4 1.0
CA A:PRO367 4.7 44.4 1.0
C19 A:8A0502 4.8 28.2 1.0
C8 A:8A0502 4.8 32.3 1.0
C14 A:8A0502 5.0 33.1 1.0

Fluorine binding site 2 out of 9 in 5xmu

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Fluorine binding site 2 out of 9 in the Plasmodium Vivax Shmt Bound with Plp-Glycine and GS363


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 GS363 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F502

b:29.1
occ:1.00
 F46 A:8A0502 0.0 29.1 1.0
C33 A:8A0502 1.3 30.6 1.0
F47 A:8A0502 2.1 31.7 1.0
F48 A:8A0502 2.2 27.6 1.0
C17 A:8A0502 2.4 30.5 1.0
C18 A:8A0502 3.0 28.8 1.0
CD A:LYS355 3.3 41.7 1.0
C16 A:8A0502 3.4 31.5 1.0
NZ A:LYS355 3.7 47.6 1.0
CE A:LYS355 3.9 45.0 1.0
CD2 B:TYR63 3.9 34.1 1.0
CE2 B:TYR63 3.9 31.5 1.0
CG A:LYS355 4.2 36.8 1.0
CG A:PRO367 4.2 43.9 1.0
C19 A:8A0502 4.3 28.2 1.0
CD A:PRO367 4.5 43.6 1.0
C15 A:8A0502 4.6 30.7 1.0
CB A:PRO367 4.7 42.7 1.0
CB A:LYS355 4.8 32.7 1.0
O A:LYS355 4.8 32.6 1.0
C20 A:8A0502 4.9 29.4 1.0

Fluorine binding site 3 out of 9 in 5xmu

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Fluorine binding site 3 out of 9 in the Plasmodium Vivax Shmt Bound with Plp-Glycine and GS363


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 GS363 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F502

b:31.7
occ:1.00
 F47 A:8A0502 0.0 31.7 1.0
C33 A:8A0502 1.3 30.6 1.0
F46 A:8A0502 2.1 29.1 1.0
F48 A:8A0502 2.1 27.6 1.0
C17 A:8A0502 2.3 30.5 1.0
C18 A:8A0502 2.9 28.8 1.0
C16 A:8A0502 3.5 31.5 1.0
O A:CYS364 3.6 81.1 1.0
CG2 A:THR357 4.0 36.7 1.0
CB A:PRO367 4.0 42.7 1.0
CG A:PRO367 4.0 43.9 1.0
CD A:PRO367 4.0 43.6 1.0
SG A:CYS364 4.2 92.6 1.0
C19 A:8A0502 4.2 28.2 1.0
CB A:CYS364 4.5 90.8 1.0
C50 A:8A0502 4.6 29.6 1.0
C A:CYS364 4.6 87.3 1.0
C15 A:8A0502 4.7 30.7 1.0
N A:PRO367 4.7 48.6 1.0
CA A:CYS364 4.8 89.7 1.0
CA A:PRO367 4.9 44.4 1.0
C20 A:8A0502 4.9 29.4 1.0
CD A:LYS355 5.0 41.7 1.0

Fluorine binding site 4 out of 9 in 5xmu

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Fluorine binding site 4 out of 9 in the Plasmodium Vivax Shmt Bound with Plp-Glycine and GS363


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 GS363 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F502

b:30.1
occ:1.00
 F48 B:8A0502 0.0 30.1 1.0
C33 B:8A0502 1.3 33.4 1.0
F47 B:8A0502 2.1 34.5 1.0
F46 B:8A0502 2.2 32.4 1.0
C17 B:8A0502 2.4 33.5 1.0
C16 B:8A0502 2.7 33.6 1.0
O B:LYS355 3.2 29.7 1.0
C B:LYS355 3.6 28.6 1.0
CG B:PRO367 3.6 41.6 1.0
CB B:PRO367 3.6 39.8 1.0
C18 B:8A0502 3.6 30.7 1.0
N B:ASN356 3.8 28.7 1.0
CA B:ASN356 3.9 28.2 1.0
CD B:LYS355 3.9 35.0 1.0
CG B:LYS355 4.0 32.2 1.0
CB B:LYS355 4.1 29.1 1.0
C15 B:8A0502 4.2 32.0 1.0
N B:THR357 4.2 31.1 1.0
C B:ASN356 4.3 29.9 1.0
N9 B:8A0502 4.3 34.6 1.0
CA B:LYS355 4.5 27.4 1.0
CD B:PRO367 4.6 43.3 1.0
CE B:LYS355 4.6 37.7 1.0
CG2 B:THR357 4.6 33.4 1.0
C8 B:8A0502 4.7 35.7 1.0
C19 B:8A0502 4.8 30.6 1.0
C14 B:8A0502 4.9 31.5 1.0
C13 B:8A0502 5.0 31.6 1.0
C20 B:8A0502 5.0 32.1 1.0

Fluorine binding site 5 out of 9 in 5xmu

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Fluorine binding site 5 out of 9 in the Plasmodium Vivax Shmt Bound with Plp-Glycine and GS363


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 GS363 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F502

b:32.4
occ:1.00
 F46 B:8A0502 0.0 32.4 1.0
C33 B:8A0502 1.3 33.4 1.0
F47 B:8A0502 2.1 34.5 1.0
F48 B:8A0502 2.2 30.1 1.0
C17 B:8A0502 2.4 33.5 1.0
C18 B:8A0502 2.9 30.7 1.0
CD B:LYS355 3.4 35.0 1.0
C16 B:8A0502 3.5 33.6 1.0
CE B:LYS355 3.6 37.7 1.0
NZ B:LYS355 3.8 37.5 1.0
CG B:PRO367 4.0 41.6 1.0
CE2 A:TYR63 4.0 30.6 1.0
C19 B:8A0502 4.2 30.6 1.0
O B:CYS364 4.2 87.4 1.0
CD2 A:TYR63 4.2 32.5 1.0
CG B:LYS355 4.3 32.2 1.0
CD B:PRO367 4.4 43.3 1.0
CB B:PRO367 4.6 39.8 1.0
C15 B:8A0502 4.7 32.0 1.0
CB B:LYS355 4.9 29.1 1.0
C20 B:8A0502 4.9 32.1 1.0
O B:LYS355 4.9 29.7 1.0

Fluorine binding site 6 out of 9 in 5xmu

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Fluorine binding site 6 out of 9 in the Plasmodium Vivax Shmt Bound with Plp-Glycine and GS363


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 GS363 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F502

b:34.5
occ:1.00
 F47 B:8A0502 0.0 34.5 1.0
C33 B:8A0502 1.3 33.4 1.0
F48 B:8A0502 2.1 30.1 1.0
F46 B:8A0502 2.1 32.4 1.0
C17 B:8A0502 2.3 33.5 1.0
C18 B:8A0502 3.0 30.7 1.0
O B:CYS364 3.2 87.4 1.0
C16 B:8A0502 3.4 33.6 1.0
CG B:PRO367 3.7 41.6 1.0
CB B:PRO367 3.7 39.8 1.0
CG2 B:THR357 3.7 33.4 1.0
CB B:CYS364 3.8 86.2 1.0
CD B:PRO367 4.0 43.3 1.0
C B:CYS364 4.1 89.0 1.0
CA B:CYS364 4.1 88.5 1.0
C19 B:8A0502 4.2 30.6 1.0
C15 B:8A0502 4.6 32.0 1.0
C50 B:8A0502 4.6 35.9 1.0
CA B:PRO367 4.7 40.8 1.0
N B:PRO367 4.7 46.4 1.0
N9 B:8A0502 4.8 34.6 1.0
N B:THR357 4.8 31.1 1.0
C20 B:8A0502 4.9 32.1 1.0
CD B:LYS355 5.0 35.0 1.0

Fluorine binding site 7 out of 9 in 5xmu

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Fluorine binding site 7 out of 9 in the Plasmodium Vivax Shmt Bound with Plp-Glycine and GS363


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 GS363 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F502

b:28.6
occ:1.00
 F48 C:8A0502 0.0 28.6 1.0
C33 C:8A0502 1.3 33.6 1.0
F47 C:8A0502 2.1 38.1 1.0
F46 C:8A0502 2.2 33.3 1.0
C17 C:8A0502 2.4 32.7 1.0
C16 C:8A0502 2.8 33.3 1.0
O C:LYS355 3.6 33.4 1.0
CB C:PRO367 3.6 42.8 1.0
C18 C:8A0502 3.6 32.2 1.0
CG C:PRO367 3.7 43.2 1.0
C C:LYS355 3.8 32.1 1.0
CA C:ASN356 3.8 30.8 1.0
N C:ASN356 3.9 32.8 1.0
CD C:LYS355 4.0 37.0 1.0
N C:THR357 4.1 34.3 1.0
C C:ASN356 4.1 33.6 1.0
C15 C:8A0502 4.2 33.5 1.0
CB C:LYS355 4.3 31.6 1.0
CG2 C:THR357 4.3 39.0 1.0
N9 C:8A0502 4.3 37.5 1.0
CG C:LYS355 4.4 34.3 1.0
CD C:PRO367 4.6 44.2 1.0
CA C:LYS355 4.7 30.4 1.0
C8 C:8A0502 4.7 36.7 1.0
C19 C:8A0502 4.8 33.3 1.0
C14 C:8A0502 4.9 32.2 1.0
O C:ASN356 4.9 34.6 1.0
CA C:THR357 5.0 36.6 1.0
C20 C:8A0502 5.0 34.2 1.0

Fluorine binding site 8 out of 9 in 5xmu

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Fluorine binding site 8 out of 9 in the Plasmodium Vivax Shmt Bound with Plp-Glycine and GS363


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 GS363 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F502

b:33.3
occ:1.00
 F46 C:8A0502 0.0 33.3 1.0
C33 C:8A0502 1.3 33.6 1.0
F48 C:8A0502 2.2 28.6 1.0
F47 C:8A0502 2.2 38.1 1.0
C17 C:8A0502 2.3 32.7 1.0
C18 C:8A0502 2.9 32.2 1.0
CD C:LYS355 3.3 37.0 1.0
C16 C:8A0502 3.4 33.3 1.0
NZ C:LYS355 3.5 41.9 1.0
CE C:LYS355 3.9 39.7 1.0
CG C:PRO367 4.2 43.2 1.0
C19 C:8A0502 4.2 33.3 1.0
CG C:LYS355 4.3 34.3 1.0
O C:CYS364 4.5 83.9 1.0
C15 C:8A0502 4.6 33.5 1.0
CD C:PRO367 4.6 44.2 1.0
CB C:PRO367 4.8 42.8 1.0
CB C:LYS355 4.8 31.6 1.0
C20 C:8A0502 4.9 34.2 1.0
O C:LYS355 5.0 33.4 1.0

Fluorine binding site 9 out of 9 in 5xmu

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Fluorine binding site 9 out of 9 in the Plasmodium Vivax Shmt Bound with Plp-Glycine and GS363


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 GS363 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F502

b:38.1
occ:1.00
 F47 C:8A0502 0.0 38.1 1.0
C33 C:8A0502 1.3 33.6 1.0
F48 C:8A0502 2.1 28.6 1.0
F46 C:8A0502 2.2 33.3 1.0
C17 C:8A0502 2.3 32.7 1.0
C18 C:8A0502 2.9 32.2 1.0
CB C:CYS364 3.4 84.9 1.0
C16 C:8A0502 3.4 33.3 1.0
O C:CYS364 3.5 83.9 1.0
CG2 C:THR357 3.8 39.0 1.0
SG C:CYS364 3.9 84.5 1.0
CA C:CYS364 3.9 85.3 1.0
CG C:PRO367 4.0 43.2 1.0
CB C:PRO367 4.0 42.8 1.0
C C:CYS364 4.1 86.8 1.0
C19 C:8A0502 4.2 33.3 1.0
CD C:PRO367 4.2 44.2 1.0
C50 C:8A0502 4.6 36.5 1.0
C15 C:8A0502 4.6 33.5 1.0
C20 C:8A0502 4.9 34.2 1.0
N9 C:8A0502 5.0 37.5 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: Sun Dec 13 12:42:49 2020

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