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Fluorine in PDB 5yg1: Plasmodium Vivax Shmt Bound with Plp-Glycine and GS704

Enzymatic activity of Plasmodium Vivax Shmt Bound with Plp-Glycine and GS704

All present enzymatic activity of Plasmodium Vivax Shmt Bound with Plp-Glycine and GS704:
2.1.2.1;

Protein crystallography data

The structure of Plasmodium Vivax Shmt Bound with Plp-Glycine and GS704, PDB code: 5yg1 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 (°) 101.471, 58.632, 234.636, 90.00, 90.00, 90.00
R / Rfree (%) 22.5 / 29.4

Other elements in 5yg1:

The structure of Plasmodium Vivax Shmt Bound with Plp-Glycine and GS704 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 GS704 (pdb code 5yg1). 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 GS704, PDB code: 5yg1:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Fluorine binding site 1 out of 9 in 5yg1

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Fluorine binding site 1 out of 9 in the Plasmodium Vivax Shmt Bound with Plp-Glycine and GS704


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 GS704 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F502

b:28.2
occ:1.00
 F37 A:8UU502 0.0 28.2 1.0
C21 A:8UU502 1.3 31.0 1.0
F35 A:8UU502 2.1 30.1 1.0
F36 A:8UU502 2.3 29.8 1.0
C18 A:8UU502 2.4 31.3 1.0
C17 A:8UU502 2.8 30.8 1.0
O A:LYS355 3.4 27.1 1.0
CG A:PRO367 3.4 37.5 1.0
C A:LYS355 3.5 27.6 1.0
N A:ASN356 3.6 29.1 1.0
C34 A:8UU502 3.6 30.4 1.0
CA A:ASN356 3.6 28.1 1.0
CB A:PRO367 3.7 37.6 1.0
CD A:LYS355 3.9 34.2 1.0
C A:ASN356 4.0 29.3 1.0
CG A:LYS355 4.0 31.9 1.0
N A:THR357 4.0 30.2 1.0
CB A:LYS355 4.1 28.4 1.0
C16 A:8UU502 4.2 29.3 1.0
N9 A:8UU502 4.2 27.3 1.0
CG2 A:THR357 4.3 32.2 1.0
CD A:PRO367 4.4 39.2 1.0
O A:CYS364 4.5 88.0 1.0
CA A:LYS355 4.5 26.5 1.0
CE A:LYS355 4.6 35.1 1.0
O A:ASN356 4.7 31.1 1.0
C8 A:8UU502 4.7 27.8 1.0
C19 A:8UU502 4.8 30.9 1.0
CA A:THR357 5.0 30.6 1.0
C20 A:8UU502 5.0 30.3 1.0

Fluorine binding site 2 out of 9 in 5yg1

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Fluorine binding site 2 out of 9 in the Plasmodium Vivax Shmt Bound with Plp-Glycine and GS704


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 GS704 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F502

b:30.1
occ:1.00
 F35 A:8UU502 0.0 30.1 1.0
C21 A:8UU502 1.3 31.0 1.0
F36 A:8UU502 2.1 29.8 1.0
F37 A:8UU502 2.1 28.2 1.0
C18 A:8UU502 2.3 31.3 1.0
O A:CYS364 2.5 88.0 1.0
C34 A:8UU502 2.9 30.4 1.0
C A:CYS364 3.5 89.0 1.0
C17 A:8UU502 3.5 30.8 1.0
CB A:CYS364 3.7 89.1 1.0
CG A:PRO367 3.7 37.5 1.0
CA A:CYS364 3.7 90.6 1.0
CB A:PRO367 3.9 37.6 1.0
CD A:PRO367 3.9 39.2 1.0
CG2 A:THR357 3.9 32.2 1.0
C19 A:8UU502 4.2 30.9 1.0
SG A:CYS364 4.5 88.8 1.0
CD A:LYS355 4.7 34.2 1.0
C16 A:8UU502 4.7 29.3 1.0
N A:VAL365 4.7 91.2 1.0
N A:PRO367 4.9 42.8 1.0
C20 A:8UU502 4.9 30.3 1.0
CA A:PRO367 5.0 38.8 1.0

Fluorine binding site 3 out of 9 in 5yg1

Go back to Fluorine Binding Sites List in 5yg1
Fluorine binding site 3 out of 9 in the Plasmodium Vivax Shmt Bound with Plp-Glycine and GS704


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 GS704 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F502

b:29.8
occ:1.00
 F36 A:8UU502 0.0 29.8 1.0
C21 A:8UU502 1.3 31.0 1.0
F35 A:8UU502 2.1 30.1 1.0
F37 A:8UU502 2.3 28.2 1.0
C18 A:8UU502 2.3 31.3 1.0
C34 A:8UU502 2.9 30.4 1.0
CE A:LYS355 3.1 35.1 1.0
CD A:LYS355 3.1 34.2 1.0
C17 A:8UU502 3.4 30.8 1.0
NZ A:LYS355 3.5 36.5 1.0
O A:CYS364 3.8 88.0 1.0
CG A:LYS355 3.9 31.9 1.0
CG A:PRO367 4.1 37.5 1.0
C19 A:8UU502 4.2 30.9 1.0
CD2 B:TYR63 4.3 38.0 1.0
CE2 B:TYR63 4.4 37.7 1.0
CD A:PRO367 4.5 39.2 1.0
C16 A:8UU502 4.6 29.3 1.0
CB A:LYS355 4.7 28.4 1.0
O A:LYS355 4.8 27.1 1.0
C20 A:8UU502 4.9 30.3 1.0
CB A:PRO367 4.9 37.6 1.0
C A:CYS364 4.9 89.0 1.0

Fluorine binding site 4 out of 9 in 5yg1

Go back to Fluorine Binding Sites List in 5yg1
Fluorine binding site 4 out of 9 in the Plasmodium Vivax Shmt Bound with Plp-Glycine and GS704


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 GS704 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F502

b:29.1
occ:1.00
 F37 B:8UU502 0.0 29.1 1.0
C21 B:8UU502 1.3 31.5 1.0
F35 B:8UU502 2.1 34.6 1.0
F36 B:8UU502 2.2 29.1 1.0
C18 B:8UU502 2.4 30.1 1.0
C17 B:8UU502 2.8 29.4 1.0
O B:LYS355 3.3 25.2 1.0
C B:LYS355 3.5 26.3 1.0
CG B:PRO367 3.5 35.6 1.0
N B:ASN356 3.6 28.2 1.0
CA B:ASN356 3.6 28.5 1.0
C34 B:8UU502 3.7 29.5 1.0
CB B:PRO367 3.8 36.4 1.0
CD B:LYS355 3.9 34.6 1.0
C B:ASN356 4.0 30.9 1.0
CG B:LYS355 4.0 30.8 1.0
CB B:LYS355 4.0 27.5 1.0
N B:THR357 4.0 31.5 1.0
C16 B:8UU502 4.2 28.2 1.0
N9 B:8UU502 4.3 29.0 1.0
CA B:LYS355 4.4 25.8 1.0
CD B:PRO367 4.5 37.3 1.0
CG2 B:THR357 4.7 37.0 1.0
O B:ASN356 4.8 33.7 1.0
C8 B:8UU502 4.8 29.7 1.0
CE B:LYS355 4.8 37.4 1.0
O B:CYS364 4.8 86.5 1.0
C19 B:8UU502 4.9 29.1 1.0
NZ B:LYS355 5.0 38.7 1.0

Fluorine binding site 5 out of 9 in 5yg1

Go back to Fluorine Binding Sites List in 5yg1
Fluorine binding site 5 out of 9 in the Plasmodium Vivax Shmt Bound with Plp-Glycine and GS704


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 GS704 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F502

b:34.6
occ:1.00
 F35 B:8UU502 0.0 34.6 1.0
C21 B:8UU502 1.3 31.5 1.0
F37 B:8UU502 2.1 29.1 1.0
F36 B:8UU502 2.2 29.1 1.0
C18 B:8UU502 2.3 30.1 1.0
C34 B:8UU502 3.0 29.5 1.0
C17 B:8UU502 3.4 29.4 1.0
O B:CYS364 3.4 86.5 1.0
CA B:CYS364 3.4 86.5 1.0
CG2 B:THR357 3.5 37.0 1.0
CB B:CYS364 3.6 84.4 1.0
CB B:PRO367 3.7 36.4 1.0
CG B:PRO367 3.7 35.6 1.0
C B:CYS364 3.7 85.4 1.0
SG B:CYS364 4.0 84.4 1.0
CD B:PRO367 4.1 37.3 1.0
C19 B:8UU502 4.3 29.1 1.0
N B:THR357 4.4 31.5 1.0
C16 B:8UU502 4.6 28.2 1.0
N9 B:8UU502 4.7 29.0 1.0
CB B:THR357 4.7 35.5 1.0
N B:CYS364 4.7 90.3 1.0
O B:ASP363 4.8 90.0 1.0
C B:ASN356 4.9 30.9 1.0
C20 B:8UU502 4.9 28.9 1.0
CA B:PRO367 4.9 38.4 1.0
OG1 B:THR357 4.9 36.7 1.0
CA B:THR357 5.0 32.5 1.0
N B:VAL365 5.0 85.4 1.0

Fluorine binding site 6 out of 9 in 5yg1

Go back to Fluorine Binding Sites List in 5yg1
Fluorine binding site 6 out of 9 in the Plasmodium Vivax Shmt Bound with Plp-Glycine and GS704


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 GS704 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F502

b:29.1
occ:1.00
 F36 B:8UU502 0.0 29.1 1.0
C21 B:8UU502 1.3 31.5 1.0
F35 B:8UU502 2.2 34.6 1.0
F37 B:8UU502 2.2 29.1 1.0
C18 B:8UU502 2.4 30.1 1.0
C34 B:8UU502 2.8 29.5 1.0
O B:CYS364 3.1 86.5 1.0
NZ B:LYS355 3.4 38.7 1.0
CD B:LYS355 3.5 34.6 1.0
C17 B:8UU502 3.5 29.4 1.0
CE B:LYS355 3.8 37.4 1.0
CG B:PRO367 4.0 35.6 1.0
C B:CYS364 4.1 85.4 1.0
C19 B:8UU502 4.2 29.1 1.0
CD B:PRO367 4.3 37.3 1.0
CG B:LYS355 4.3 30.8 1.0
CA B:CYS364 4.5 86.5 1.0
CD2 A:TYR63 4.6 35.5 1.0
CB B:CYS364 4.6 84.4 1.0
CE2 A:TYR63 4.6 35.3 1.0
CB B:PRO367 4.7 36.4 1.0
C16 B:8UU502 4.7 28.2 1.0
C20 B:8UU502 4.9 28.9 1.0
CB B:LYS355 4.9 27.5 1.0

Fluorine binding site 7 out of 9 in 5yg1

Go back to Fluorine Binding Sites List in 5yg1
Fluorine binding site 7 out of 9 in the Plasmodium Vivax Shmt Bound with Plp-Glycine and GS704


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 GS704 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F502

b:31.5
occ:1.00
 F37 C:8UU502 0.0 31.5 1.0
C21 C:8UU502 1.3 32.8 1.0
F35 C:8UU502 2.0 33.9 1.0
F36 C:8UU502 2.2 31.6 1.0
C18 C:8UU502 2.4 32.9 1.0
C17 C:8UU502 2.9 32.1 1.0
O C:LYS355 3.3 26.8 1.0
C C:LYS355 3.5 26.8 1.0
CG C:PRO367 3.5 35.7 1.0
N C:ASN356 3.6 27.5 1.0
C34 C:8UU502 3.7 33.3 1.0
CA C:ASN356 3.7 26.9 1.0
CD C:LYS355 3.8 33.8 1.0
CG C:LYS355 3.9 31.1 1.0
CB C:PRO367 3.9 35.8 1.0
CB C:LYS355 3.9 28.1 1.0
C C:ASN356 4.1 27.9 1.0
N C:THR357 4.1 28.6 1.0
C16 C:8UU502 4.3 31.0 1.0
CA C:LYS355 4.3 26.4 1.0
N9 C:8UU502 4.4 29.5 1.0
CD C:PRO367 4.6 38.2 1.0
CG2 C:THR357 4.7 32.1 1.0
CE C:LYS355 4.8 34.1 1.0
C8 C:8UU502 4.8 30.2 1.0
O C:ASN356 4.8 30.1 1.0
C19 C:8UU502 4.9 34.2 1.0

Fluorine binding site 8 out of 9 in 5yg1

Go back to Fluorine Binding Sites List in 5yg1
Fluorine binding site 8 out of 9 in the Plasmodium Vivax Shmt Bound with Plp-Glycine and GS704


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 GS704 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F502

b:33.9
occ:1.00
 F35 C:8UU502 0.0 33.9 1.0
C21 C:8UU502 1.3 32.8 1.0
F37 C:8UU502 2.0 31.5 1.0
F36 C:8UU502 2.1 31.6 1.0
C18 C:8UU502 2.3 32.9 1.0
C34 C:8UU502 3.0 33.3 1.0
C17 C:8UU502 3.3 32.1 1.0
CG2 C:THR357 3.5 32.1 1.0
CG C:PRO367 3.6 35.7 1.0
O C:CYS364 3.6 79.0 1.0
CA C:CYS364 3.7 87.5 1.0
CB C:PRO367 3.7 35.8 1.0
CB C:CYS364 3.9 85.3 1.0
C C:CYS364 4.0 83.6 1.0
CD C:PRO367 4.2 38.2 1.0
C19 C:8UU502 4.3 34.2 1.0
N C:THR357 4.4 28.6 1.0
C16 C:8UU502 4.5 31.0 1.0
N9 C:8UU502 4.6 29.5 1.0
CB C:THR357 4.7 30.7 1.0
SG C:CYS364 4.7 81.0 1.0
C C:ASN356 4.8 27.9 1.0
CA C:THR357 4.9 29.6 1.0
C20 C:8UU502 4.9 32.1 1.0
OG1 C:THR357 5.0 33.2 1.0
N C:CYS364 5.0 91.3 1.0
O C:ASP363 5.0 94.7 1.0
CA C:ASN356 5.0 26.9 1.0
CA C:PRO367 5.0 37.7 1.0

Fluorine binding site 9 out of 9 in 5yg1

Go back to Fluorine Binding Sites List in 5yg1
Fluorine binding site 9 out of 9 in the Plasmodium Vivax Shmt Bound with Plp-Glycine and GS704


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 GS704 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F502

b:31.6
occ:1.00
 F36 C:8UU502 0.0 31.6 1.0
C21 C:8UU502 1.3 32.8 1.0
F35 C:8UU502 2.1 33.9 1.0
F37 C:8UU502 2.2 31.5 1.0
C18 C:8UU502 2.4 32.9 1.0
C34 C:8UU502 2.9 33.3 1.0
O C:CYS364 3.3 79.0 1.0
CD C:LYS355 3.5 33.8 1.0
NZ C:LYS355 3.6 36.1 1.0
C17 C:8UU502 3.6 32.1 1.0
CG C:PRO367 3.9 35.7 1.0
CE C:LYS355 3.9 34.1 1.0
C19 C:8UU502 4.2 34.2 1.0
C C:CYS364 4.2 83.6 1.0
CG C:LYS355 4.3 31.1 1.0
CD C:PRO367 4.3 38.2 1.0
CA C:CYS364 4.6 87.5 1.0
CB C:CYS364 4.7 85.3 1.0
CB C:PRO367 4.7 35.8 1.0
C16 C:8UU502 4.7 31.0 1.0
CB C:LYS355 4.9 28.1 1.0
C20 C:8UU502 5.0 32.1 1.0

Reference:

P.Chitnumsub, A.Jaruwat. To Be Published To Be Published.
Page generated: Thu Aug 1 17:16:11 2024

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