Atomistry » Fluorine » PDB 5y6m-5zc5 » 5yg0
Atomistry »
  Fluorine »
    PDB 5y6m-5zc5 »
      5yg0 »

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

Go back to Fluorine Binding Sites List in 5yg0
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

Go back to Fluorine Binding Sites List in 5yg0
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

Go back to Fluorine Binding Sites List in 5yg0
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

Go back to Fluorine Binding Sites List in 5yg0
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

Go back to Fluorine Binding Sites List in 5yg0
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

Go back to Fluorine Binding Sites List in 5yg0
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

Go back to Fluorine Binding Sites List in 5yg0
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: Tue Jul 15 09:27:34 2025

Last articles

Fe in 9ERB
Fe in 9ERC
Fe in 9ER7
Fe in 9ERA
Fe in 9ER6
Fe in 9ER5
Fe in 9EQL
Fe in 9EQI
Fe in 9EQA
Fe in 9EQC
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy