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Fluorine in PDB 5yg0: Plasmodium Vivax Shmt Bound with Plp-Glycine and GS657

Enzymatic activity of Plasmodium Vivax Shmt Bound with Plp-Glycine and GS657

All present enzymatic activity of Plasmodium Vivax Shmt Bound with Plp-Glycine and GS657:
2.1.2.1;

Protein crystallography data

The structure of Plasmodium Vivax Shmt Bound with Plp-Glycine and GS657, PDB code: 5yg0 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 / 2.33
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 101.561, 58.615, 233.052, 90.00, 90.02, 90.00
R / Rfree (%) 24.1 / 31.1

Other elements in 5yg0:

The structure of Plasmodium Vivax Shmt Bound with Plp-Glycine and GS657 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 GS657 (pdb code 5yg0). 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 GS657, PDB code: 5yg0:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Fluorine binding site 1 out of 9 in 5yg0

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Fluorine binding site 1 out of 9 in the Plasmodium Vivax Shmt Bound with Plp-Glycine and GS657


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 GS657 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F502

b:29.6
occ:1.00
 F35 A:8UR502 0.0 29.6 1.0
C31 A:8UR502 1.3 30.5 1.0
F33 A:8UR502 2.1 30.2 1.0
F34 A:8UR502 2.2 30.1 1.0
C28 A:8UR502 2.4 32.2 1.0
C27 A:8UR502 2.8 31.8 1.0
N A:ASN356 3.4 24.5 1.0
C A:LYS355 3.4 24.0 1.0
O A:LYS355 3.4 24.4 1.0
CA A:ASN356 3.4 23.3 1.0
CG A:PRO367 3.5 42.2 1.0
CB A:PRO367 3.5 41.0 1.0
C36 A:8UR502 3.6 32.5 1.0
C A:ASN356 3.8 25.2 1.0
N A:THR357 3.8 27.3 1.0
CB A:LYS355 3.9 25.2 1.0
CD A:LYS355 4.0 31.4 1.0
CG A:LYS355 4.2 28.9 1.0
C26 A:8UR502 4.2 31.7 1.0
N19 A:8UR502 4.2 28.8 1.0
CA A:LYS355 4.3 23.5 1.0
CG2 A:THR357 4.5 28.6 1.0
O A:ASN356 4.6 26.7 1.0
O A:CYS364 4.6 99.0 1.0
CD A:PRO367 4.6 43.3 1.0
C18 A:8UR502 4.7 30.5 1.0
C29 A:8UR502 4.8 33.7 1.0
CB A:ASN356 4.9 21.2 1.0
CA A:THR357 4.9 28.6 1.0
CA A:PRO367 5.0 41.2 1.0
C30 A:8UR502 5.0 33.6 1.0

Fluorine binding site 2 out of 9 in 5yg0

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Fluorine binding site 2 out of 9 in the Plasmodium Vivax Shmt Bound with Plp-Glycine and GS657


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 GS657 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F502

b:30.2
occ:1.00
 F33 A:8UR502 0.0 30.2 1.0
C31 A:8UR502 1.3 30.5 1.0
F34 A:8UR502 2.1 30.1 1.0
F35 A:8UR502 2.1 29.6 1.0
C28 A:8UR502 2.3 32.2 1.0
C36 A:8UR502 2.9 32.5 1.0
O A:CYS364 2.9 99.0 1.0
C27 A:8UR502 3.4 31.8 1.0
CB A:PRO367 3.4 41.0 1.0
CG2 A:THR357 3.5 28.6 1.0
CA A:CYS364 3.6 96.8 1.0
CG A:PRO367 3.6 42.2 1.0
C A:CYS364 3.7 95.5 1.0
CB A:CYS364 3.7 97.4 1.0
C29 A:8UR502 4.2 33.7 1.0
CD A:PRO367 4.2 43.3 1.0
N A:THR357 4.3 27.3 1.0
CA A:PRO367 4.6 41.2 1.0
C26 A:8UR502 4.6 31.7 1.0
SG A:CYS364 4.7 0.9 1.0
N19 A:8UR502 4.7 28.8 1.0
CB A:THR357 4.7 28.9 1.0
C A:ASN356 4.8 25.2 1.0
N A:PRO367 4.8 44.8 1.0
CA A:THR357 4.8 28.6 1.0
C30 A:8UR502 4.9 33.6 1.0
N A:VAL365 5.0 92.0 1.0
CA A:ASN356 5.0 23.3 1.0

Fluorine binding site 3 out of 9 in 5yg0

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Fluorine binding site 3 out of 9 in the Plasmodium Vivax Shmt Bound with Plp-Glycine and GS657


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 GS657 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F502

b:30.1
occ:1.00
 F34 A:8UR502 0.0 30.1 1.0
C31 A:8UR502 1.3 30.5 1.0
F33 A:8UR502 2.1 30.2 1.0
F35 A:8UR502 2.2 29.6 1.0
C28 A:8UR502 2.3 32.2 1.0
C36 A:8UR502 2.8 32.5 1.0
O A:CYS364 3.2 99.0 1.0
CD A:LYS355 3.4 31.4 1.0
C27 A:8UR502 3.5 31.8 1.0
CG A:PRO367 3.7 42.2 1.0
NZ A:LYS355 4.0 36.6 1.0
CE2 B:TYR63 4.0 24.8 1.0
CD2 B:TYR63 4.1 24.8 1.0
C29 A:8UR502 4.1 33.7 1.0
CD A:PRO367 4.2 43.3 1.0
CB A:PRO367 4.2 41.0 1.0
CG A:LYS355 4.3 28.9 1.0
CE A:LYS355 4.3 33.8 1.0
C A:CYS364 4.4 95.5 1.0
C26 A:8UR502 4.6 31.7 1.0
CB A:LYS355 4.7 25.2 1.0
CB A:CYS364 4.8 97.4 1.0
C30 A:8UR502 4.9 33.6 1.0
CA A:CYS364 4.9 96.8 1.0

Fluorine binding site 4 out of 9 in 5yg0

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Fluorine binding site 4 out of 9 in the Plasmodium Vivax Shmt Bound with Plp-Glycine and GS657


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 GS657 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F502

b:32.5
occ:1.00
 F35 B:8UR502 0.0 32.5 1.0
C31 B:8UR502 1.3 31.6 1.0
F33 B:8UR502 2.1 31.1 1.0
F34 B:8UR502 2.2 32.4 1.0
C28 B:8UR502 2.4 32.6 1.0
C27 B:8UR502 2.8 31.9 1.0
O B:LYS355 3.2 24.9 1.0
C B:LYS355 3.3 24.9 1.0
N B:ASN356 3.3 25.6 1.0
CA B:ASN356 3.4 23.5 1.0
CB B:PRO367 3.5 42.0 1.0
CG B:PRO367 3.5 43.5 1.0
C36 B:8UR502 3.6 32.5 1.0
CB B:LYS355 3.7 26.0 1.0
C B:ASN356 3.8 25.6 1.0
N B:THR357 3.8 27.3 1.0
CD B:LYS355 3.9 32.9 1.0
CG B:LYS355 4.0 29.6 1.0
N19 B:8UR502 4.1 27.8 1.0
CA B:LYS355 4.1 24.6 1.0
C26 B:8UR502 4.2 31.2 1.0
O B:ASN356 4.6 27.6 1.0
O B:CYS364 4.6 97.2 1.0
C18 B:8UR502 4.6 30.9 1.0
CD B:PRO367 4.7 44.5 1.0
CG2 B:THR357 4.7 29.7 1.0
CB B:ASN356 4.8 21.8 1.0
C29 B:8UR502 4.8 33.8 1.0
CA B:THR357 4.9 28.8 1.0
CA B:PRO367 5.0 42.6 1.0

Fluorine binding site 5 out of 9 in 5yg0

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Fluorine binding site 5 out of 9 in the Plasmodium Vivax Shmt Bound with Plp-Glycine and GS657


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 GS657 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F502

b:31.1
occ:1.00
 F33 B:8UR502 0.0 31.1 1.0
C31 B:8UR502 1.3 31.6 1.0
F34 B:8UR502 2.1 32.4 1.0
F35 B:8UR502 2.1 32.5 1.0
C28 B:8UR502 2.3 32.6 1.0
O B:CYS364 2.9 97.2 1.0
C36 B:8UR502 2.9 32.5 1.0
C27 B:8UR502 3.4 31.9 1.0
CB B:PRO367 3.4 42.0 1.0
CG2 B:THR357 3.5 29.7 1.0
CG B:PRO367 3.7 43.5 1.0
C B:CYS364 3.7 95.4 1.0
CA B:CYS364 3.7 95.4 1.0
CB B:CYS364 3.9 94.5 1.0
N B:THR357 4.2 27.3 1.0
CD B:PRO367 4.2 44.5 1.0
C29 B:8UR502 4.2 33.8 1.0
N19 B:8UR502 4.5 27.8 1.0
CA B:PRO367 4.5 42.6 1.0
C26 B:8UR502 4.6 31.2 1.0
C B:ASN356 4.6 25.6 1.0
CB B:THR357 4.7 29.9 1.0
CA B:THR357 4.8 28.8 1.0
N B:PRO367 4.8 46.4 1.0
CA B:ASN356 4.8 23.5 1.0
C30 B:8UR502 4.9 32.7 1.0
SG B:CYS364 4.9 97.3 1.0
CD B:LYS355 5.0 32.9 1.0
N B:VAL365 5.0 91.4 1.0

Fluorine binding site 6 out of 9 in 5yg0

Go back to Fluorine Binding Sites List in 5yg0
Fluorine binding site 6 out of 9 in the Plasmodium Vivax Shmt Bound with Plp-Glycine and GS657


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 GS657 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F502

b:32.4
occ:1.00
 F34 B:8UR502 0.0 32.4 1.0
C31 B:8UR502 1.3 31.6 1.0
F33 B:8UR502 2.1 31.1 1.0
F35 B:8UR502 2.2 32.5 1.0
C28 B:8UR502 2.3 32.6 1.0
C36 B:8UR502 2.8 32.5 1.0
O B:CYS364 3.2 97.2 1.0
CD B:LYS355 3.3 32.9 1.0
C27 B:8UR502 3.5 31.9 1.0
CG B:PRO367 3.7 43.5 1.0
NZ B:LYS355 3.9 35.4 1.0
CE2 A:TYR63 4.0 23.4 1.0
CD2 A:TYR63 4.1 23.0 1.0
C29 B:8UR502 4.1 33.8 1.0
CG B:LYS355 4.2 29.6 1.0
CD B:PRO367 4.2 44.5 1.0
CE B:LYS355 4.2 34.7 1.0
CB B:PRO367 4.2 42.0 1.0
C B:CYS364 4.3 95.4 1.0
CB B:LYS355 4.6 26.0 1.0
C26 B:8UR502 4.6 31.2 1.0
C30 B:8UR502 4.9 32.7 1.0
CA B:CYS364 4.9 95.4 1.0
CB B:CYS364 5.0 94.5 1.0
O B:LYS355 5.0 24.9 1.0

Fluorine binding site 7 out of 9 in 5yg0

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Fluorine binding site 7 out of 9 in the Plasmodium Vivax Shmt Bound with Plp-Glycine and GS657


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 GS657 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F502

b:27.6
occ:1.00
 F35 C:8UR502 0.0 27.6 1.0
C31 C:8UR502 1.3 29.0 1.0
F33 C:8UR502 2.1 28.3 1.0
F34 C:8UR502 2.2 28.3 1.0
C28 C:8UR502 2.4 30.8 1.0
C27 C:8UR502 2.8 30.1 1.0
O C:LYS355 3.1 28.0 1.0
C C:LYS355 3.2 26.3 1.0
N C:ASN356 3.3 26.7 1.0
CA C:ASN356 3.4 24.8 1.0
CG C:LYS355 3.5 30.1 1.0
CG C:PRO367 3.6 44.5 1.0
C36 C:8UR502 3.6 32.4 1.0
CB C:PRO367 3.7 43.5 1.0
CB C:LYS355 3.8 26.8 1.0
C C:ASN356 3.9 26.8 1.0
N C:THR357 3.9 29.1 1.0
CA C:LYS355 4.2 25.6 1.0
N19 C:8UR502 4.2 26.8 1.0
C26 C:8UR502 4.2 29.7 1.0
CE C:LYS355 4.4 34.6 1.0
CD C:LYS355 4.4 32.3 1.0
O C:ASN356 4.7 27.4 1.0
C18 C:8UR502 4.7 27.7 1.0
CG2 C:THR357 4.7 32.2 1.0
CD C:PRO367 4.8 45.6 1.0
O C:CYS364 4.8 96.4 1.0
C29 C:8UR502 4.8 34.4 1.0
CB C:ASN356 4.8 22.3 1.0

Fluorine binding site 8 out of 9 in 5yg0

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Fluorine binding site 8 out of 9 in the Plasmodium Vivax Shmt Bound with Plp-Glycine and GS657


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 GS657 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F502

b:28.3
occ:1.00
 F33 C:8UR502 0.0 28.3 1.0
C31 C:8UR502 1.3 29.0 1.0
F34 C:8UR502 2.1 28.3 1.0
F35 C:8UR502 2.1 27.6 1.0
C28 C:8UR502 2.3 30.8 1.0
C36 C:8UR502 2.9 32.4 1.0
O C:CYS364 3.1 96.4 1.0
C27 C:8UR502 3.3 30.1 1.0
CB C:PRO367 3.5 43.5 1.0
CG2 C:THR357 3.6 32.2 1.0
CG C:PRO367 3.7 44.5 1.0
C C:CYS364 4.0 94.9 1.0
CA C:CYS364 4.0 97.5 1.0
CB C:CYS364 4.1 96.8 1.0
C29 C:8UR502 4.2 34.4 1.0
CD C:PRO367 4.3 45.6 1.0
N C:THR357 4.3 29.1 1.0
N19 C:8UR502 4.5 26.8 1.0
C26 C:8UR502 4.6 29.7 1.0
C C:ASN356 4.7 26.8 1.0
CA C:PRO367 4.7 44.5 1.0
CB C:THR357 4.7 31.7 1.0
SG C:CYS364 4.7 96.7 1.0
CA C:ASN356 4.8 24.8 1.0
CA C:THR357 4.9 30.0 1.0
C30 C:8UR502 4.9 32.4 1.0
N C:PRO367 5.0 48.5 1.0

Fluorine binding site 9 out of 9 in 5yg0

Go back to Fluorine Binding Sites List in 5yg0
Fluorine binding site 9 out of 9 in the Plasmodium Vivax Shmt Bound with Plp-Glycine and GS657


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 GS657 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F502

b:28.3
occ:1.00
 F34 C:8UR502 0.0 28.3 1.0
C31 C:8UR502 1.3 29.0 1.0
F33 C:8UR502 2.1 28.3 1.0
F35 C:8UR502 2.2 27.6 1.0
C28 C:8UR502 2.3 30.8 1.0
C36 C:8UR502 2.8 32.4 1.0
CE C:LYS355 3.2 34.6 1.0
O C:CYS364 3.4 96.4 1.0
C27 C:8UR502 3.5 30.1 1.0
CG C:LYS355 3.8 30.1 1.0
CG C:PRO367 3.9 44.5 1.0
CD C:LYS355 4.0 32.3 1.0
C29 C:8UR502 4.1 34.4 1.0
CD C:PRO367 4.4 45.6 1.0
CB C:PRO367 4.4 43.5 1.0
NZ C:LYS355 4.5 35.5 1.0
C C:CYS364 4.6 94.9 1.0
C26 C:8UR502 4.7 29.7 1.0
CB C:LYS355 4.7 26.8 1.0
C30 C:8UR502 4.9 32.4 1.0
O C:LYS355 4.9 28.0 1.0
N1 C:8UR502 5.0 37.8 1.0

Reference:

P.Chitnumsub, A.Jaruwat. To Be Published To Be Published.
Page generated: Thu Aug 1 17:15:08 2024

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