Atomistry » Fluorine » PDB 5g48-5he1 » 5gvp
Atomistry »
  Fluorine »
    PDB 5g48-5he1 »
      5gvp »

Fluorine in PDB 5gvp: Plasmodium Vivax Shmt Bound with Plp-Glycine and GS654

Protein crystallography data

The structure of Plasmodium Vivax Shmt Bound with Plp-Glycine and GS654, PDB code: 5gvp was solved by P.Chitnumsub, A.Jaruwat, U.Leartsakulpanich, G.Schwertz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.01 / 2.26
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 102.075, 58.928, 234.830, 90.00, 90.06, 90.00
R / Rfree (%) 25 / 31.2

Other elements in 5gvp:

The structure of Plasmodium Vivax Shmt Bound with Plp-Glycine and GS654 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 GS654 (pdb code 5gvp). 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 GS654, PDB code: 5gvp:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Fluorine binding site 1 out of 9 in 5gvp

Go back to Fluorine Binding Sites List in 5gvp
Fluorine binding site 1 out of 9 in the Plasmodium Vivax Shmt Bound with Plp-Glycine and GS654


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 GS654 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F502

b:27.9
occ:1.00
 F48 A:GCF502 0.0 27.9 1.0
C35 A:GCF502 1.3 29.1 1.0
F46 A:GCF502 2.2 31.9 1.0
F47 A:GCF502 2.2 29.2 1.0
C18 A:GCF502 2.4 26.4 1.0
C17 A:GCF502 2.8 25.4 1.0
O A:LYS355 3.5 25.8 1.0
CG A:PRO367 3.6 37.2 1.0
CB A:PRO367 3.6 37.1 1.0
C19 A:GCF502 3.7 25.6 1.0
C A:LYS355 3.7 25.1 1.0
CA A:ASN356 3.8 24.2 1.0
N A:ASN356 3.8 24.8 1.0
CD A:LYS355 4.0 31.2 1.0
N A:THR357 4.1 26.1 1.0
CG A:LYS355 4.1 29.1 1.0
C16 A:GCF502 4.2 24.3 1.0
N9 A:GCF502 4.2 26.6 1.0
C A:ASN356 4.2 24.9 1.0
CB A:LYS355 4.4 26.2 1.0
CD A:PRO367 4.4 38.1 1.0
CG2 A:THR357 4.5 29.9 1.0
CA A:LYS355 4.7 24.8 1.0
C8 A:GCF502 4.7 26.6 1.0
C20 A:GCF502 4.8 25.0 1.0
SG A:CYS364 4.8 59.1 1.0
CE A:LYS355 4.8 32.4 1.0

Fluorine binding site 2 out of 9 in 5gvp

Go back to Fluorine Binding Sites List in 5gvp
Fluorine binding site 2 out of 9 in the Plasmodium Vivax Shmt Bound with Plp-Glycine and GS654


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 GS654 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F502

b:29.2
occ:1.00
 F47 A:GCF502 0.0 29.2 1.0
C35 A:GCF502 1.3 29.1 1.0
F46 A:GCF502 2.1 31.9 1.0
F48 A:GCF502 2.2 27.9 1.0
C18 A:GCF502 2.3 26.4 1.0
C19 A:GCF502 2.9 25.6 1.0
CD A:LYS355 3.4 31.2 1.0
NZ A:LYS355 3.4 34.2 1.0
C17 A:GCF502 3.4 25.4 1.0
CE A:LYS355 3.6 32.4 1.0
CE2 B:TYR63 4.0 20.9 1.0
CD2 B:TYR63 4.1 22.1 1.0
CG A:LYS355 4.1 29.1 1.0
CG A:PRO367 4.1 37.2 1.0
C20 A:GCF502 4.2 25.0 1.0
CD A:PRO367 4.5 38.1 1.0
C16 A:GCF502 4.6 24.3 1.0
CB A:PRO367 4.8 37.1 1.0
O A:CYS364 4.8 63.7 1.0
SG A:CYS364 4.9 59.1 1.0
C21 A:GCF502 4.9 25.1 1.0
O A:LYS355 4.9 25.8 1.0
CB A:LYS355 5.0 26.2 1.0

Fluorine binding site 3 out of 9 in 5gvp

Go back to Fluorine Binding Sites List in 5gvp
Fluorine binding site 3 out of 9 in the Plasmodium Vivax Shmt Bound with Plp-Glycine and GS654


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 GS654 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F502

b:31.9
occ:1.00
 F46 A:GCF502 0.0 31.9 1.0
C35 A:GCF502 1.3 29.1 1.0
F47 A:GCF502 2.1 29.2 1.0
F48 A:GCF502 2.2 27.9 1.0
C18 A:GCF502 2.3 26.4 1.0
C19 A:GCF502 2.9 25.6 1.0
SG A:CYS364 2.9 59.1 1.0
C17 A:GCF502 3.4 25.4 1.0
O A:CYS364 3.5 63.7 1.0
CG2 A:THR357 4.0 29.9 1.0
CG A:PRO367 4.1 37.2 1.0
CD A:PRO367 4.1 38.1 1.0
C20 A:GCF502 4.2 25.0 1.0
CB A:PRO367 4.2 37.1 1.0
CB A:CYS364 4.4 59.6 1.0
C A:CYS364 4.5 61.7 1.0
C16 A:GCF502 4.6 24.3 1.0
CA A:CYS364 4.7 60.4 1.0
N9 A:GCF502 4.8 26.6 1.0
C21 A:GCF502 4.9 25.1 1.0
N A:PRO367 5.0 39.9 1.0

Fluorine binding site 4 out of 9 in 5gvp

Go back to Fluorine Binding Sites List in 5gvp
Fluorine binding site 4 out of 9 in the Plasmodium Vivax Shmt Bound with Plp-Glycine and GS654


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 GS654 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F503

b:28.2
occ:1.00
 F48 A:GCF503 0.0 28.2 1.0
C35 A:GCF503 1.3 29.0 1.0
F46 A:GCF503 2.2 31.1 1.0
F47 A:GCF503 2.2 28.3 1.0
C18 A:GCF503 2.4 26.1 1.0
C17 A:GCF503 2.8 25.3 1.0
CG B:PRO367 3.4 37.9 1.0
O B:LYS355 3.5 26.5 1.0
CB B:PRO367 3.6 37.9 1.0
C19 A:GCF503 3.7 25.2 1.0
C B:LYS355 3.7 25.7 1.0
N B:ASN356 3.8 24.9 1.0
CA B:ASN356 3.9 24.2 1.0
CD B:LYS355 4.0 32.5 1.0
N B:THR357 4.1 26.6 1.0
CG B:LYS355 4.2 30.9 1.0
N9 A:GCF503 4.2 24.8 1.0
C16 A:GCF503 4.2 24.5 1.0
C B:ASN356 4.2 25.4 1.0
CD B:PRO367 4.2 38.3 1.0
CB B:LYS355 4.3 28.1 1.0
CG2 B:THR357 4.6 28.5 1.0
CA B:LYS355 4.7 25.8 1.0
C8 A:GCF503 4.7 24.8 1.0
C20 A:GCF503 4.8 24.7 1.0
SG B:CYS364 4.8 56.8 1.0
O B:CYS364 5.0 64.7 1.0
CA B:PRO367 5.0 38.1 1.0

Fluorine binding site 5 out of 9 in 5gvp

Go back to Fluorine Binding Sites List in 5gvp
Fluorine binding site 5 out of 9 in the Plasmodium Vivax Shmt Bound with Plp-Glycine and GS654


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 GS654 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F503

b:28.3
occ:1.00
 F47 A:GCF503 0.0 28.3 1.0
C35 A:GCF503 1.3 29.0 1.0
F48 A:GCF503 2.2 28.2 1.0
F46 A:GCF503 2.2 31.1 1.0
C18 A:GCF503 2.3 26.1 1.0
C19 A:GCF503 2.9 25.2 1.0
C17 A:GCF503 3.5 25.3 1.0
NZ B:LYS355 3.5 34.8 1.0
CD B:LYS355 3.5 32.5 1.0
CE B:LYS355 4.1 34.1 1.0
CG B:PRO367 4.1 37.9 1.0
CE2 A:TYR63 4.1 21.4 1.0
O B:CYS364 4.1 64.7 1.0
C20 A:GCF503 4.2 24.7 1.0
CD2 A:TYR63 4.2 23.1 1.0
CG B:LYS355 4.3 30.9 1.0
CD B:PRO367 4.3 38.3 1.0
C16 A:GCF503 4.6 24.5 1.0
CB B:PRO367 4.8 37.9 1.0
C21 A:GCF503 4.9 24.9 1.0
SG B:CYS364 5.0 56.8 1.0
CB B:LYS355 5.0 28.1 1.0

Fluorine binding site 6 out of 9 in 5gvp

Go back to Fluorine Binding Sites List in 5gvp
Fluorine binding site 6 out of 9 in the Plasmodium Vivax Shmt Bound with Plp-Glycine and GS654


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 GS654 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F503

b:31.1
occ:1.00
 F46 A:GCF503 0.0 31.1 1.0
C35 A:GCF503 1.3 29.0 1.0
F48 A:GCF503 2.2 28.2 1.0
F47 A:GCF503 2.2 28.3 1.0
C18 A:GCF503 2.3 26.1 1.0
C19 A:GCF503 2.9 25.2 1.0
SG B:CYS364 3.0 56.8 1.0
O B:CYS364 3.1 64.7 1.0
C17 A:GCF503 3.3 25.3 1.0
CB B:CYS364 3.8 57.1 1.0
C B:CYS364 4.0 62.3 1.0
CG2 B:THR357 4.0 28.5 1.0
CG B:PRO367 4.1 37.9 1.0
CA B:CYS364 4.1 59.6 1.0
CD B:PRO367 4.1 38.3 1.0
C20 A:GCF503 4.2 24.7 1.0
CB B:PRO367 4.2 37.9 1.0
C16 A:GCF503 4.5 24.5 1.0
N9 A:GCF503 4.7 24.8 1.0
C21 A:GCF503 4.8 24.9 1.0
N B:THR357 4.9 26.6 1.0
N B:PRO367 5.0 40.3 1.0

Fluorine binding site 7 out of 9 in 5gvp

Go back to Fluorine Binding Sites List in 5gvp
Fluorine binding site 7 out of 9 in the Plasmodium Vivax Shmt Bound with Plp-Glycine and GS654


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 GS654 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F502

b:29.2
occ:1.00
 F48 C:GCF502 0.0 29.2 1.0
C35 C:GCF502 1.3 30.4 1.0
F46 C:GCF502 2.1 33.4 1.0
F47 C:GCF502 2.2 30.4 1.0
C18 C:GCF502 2.4 28.4 1.0
C17 C:GCF502 2.8 27.3 1.0
O C:LYS355 3.5 24.6 1.0
CG C:PRO367 3.6 37.2 1.0
C19 C:GCF502 3.6 27.7 1.0
C C:LYS355 3.7 24.3 1.0
CB C:PRO367 3.7 37.6 1.0
CG C:LYS355 3.8 29.2 1.0
N C:ASN356 3.8 24.4 1.0
CA C:ASN356 3.9 22.8 1.0
CD C:LYS355 4.0 31.5 1.0
N C:THR357 4.2 26.3 1.0
CB C:LYS355 4.2 26.6 1.0
C16 C:GCF502 4.2 26.0 1.0
C C:ASN356 4.3 24.4 1.0
N9 C:GCF502 4.3 25.2 1.0
CD C:PRO367 4.4 37.6 1.0
CG2 C:THR357 4.6 30.1 1.0
CA C:LYS355 4.6 24.1 1.0
C8 C:GCF502 4.8 25.4 1.0
C20 C:GCF502 4.8 26.7 1.0
SG C:CYS364 4.8 64.3 1.0
C21 C:GCF502 5.0 27.1 1.0

Fluorine binding site 8 out of 9 in 5gvp

Go back to Fluorine Binding Sites List in 5gvp
Fluorine binding site 8 out of 9 in the Plasmodium Vivax Shmt Bound with Plp-Glycine and GS654


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 GS654 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F502

b:30.4
occ:1.00
 F47 C:GCF502 0.0 30.4 1.0
C35 C:GCF502 1.3 30.4 1.0
F46 C:GCF502 2.1 33.4 1.0
F48 C:GCF502 2.2 29.2 1.0
C18 C:GCF502 2.3 28.4 1.0
C19 C:GCF502 2.9 27.7 1.0
CD C:LYS355 3.4 31.5 1.0
C17 C:GCF502 3.4 27.3 1.0
NZ C:LYS355 3.6 34.4 1.0
CG C:LYS355 3.9 29.2 1.0
CE C:LYS355 3.9 32.9 1.0
CG C:PRO367 4.1 37.2 1.0
C20 C:GCF502 4.2 26.7 1.0
O C:CYS364 4.5 63.5 1.0
CD C:PRO367 4.5 37.6 1.0
C16 C:GCF502 4.6 26.0 1.0
CB C:LYS355 4.9 26.6 1.0
SG C:CYS364 4.9 64.3 1.0
C21 C:GCF502 4.9 27.1 1.0
CB C:PRO367 4.9 37.6 1.0

Fluorine binding site 9 out of 9 in 5gvp

Go back to Fluorine Binding Sites List in 5gvp
Fluorine binding site 9 out of 9 in the Plasmodium Vivax Shmt Bound with Plp-Glycine and GS654


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 GS654 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F502

b:33.4
occ:1.00
 F46 C:GCF502 0.0 33.4 1.0
C35 C:GCF502 1.3 30.4 1.0
F47 C:GCF502 2.1 30.4 1.0
F48 C:GCF502 2.1 29.2 1.0
C18 C:GCF502 2.3 28.4 1.0
C19 C:GCF502 2.9 27.7 1.0
SG C:CYS364 3.0 64.3 1.0
O C:CYS364 3.3 63.5 1.0
C17 C:GCF502 3.4 27.3 1.0
CG C:PRO367 3.9 37.2 1.0
CG2 C:THR357 4.0 30.1 1.0
CD C:PRO367 4.0 37.6 1.0
CB C:CYS364 4.1 62.9 1.0
CB C:PRO367 4.2 37.6 1.0
C20 C:GCF502 4.2 26.7 1.0
C C:CYS364 4.2 63.0 1.0
CA C:CYS364 4.4 63.5 1.0
C16 C:GCF502 4.6 26.0 1.0
N9 C:GCF502 4.9 25.2 1.0
C21 C:GCF502 4.9 27.1 1.0
N C:PRO367 5.0 39.6 1.0

Reference:

G.Schwertz, M.C.Witschel, M.Rottmann, R.Bonnert, U.Leartsakulpanich, P.Chitnumsub, A.Jaruwat, W.Ittarat, A.Schafer, R.A.Aponte, S.A.Charman, K.L.White, A.Kundu, S.Sadhukhan, M.Lloyd, G.M.Freiberg, M.Srikumaran, M.Siggel, A.Zwyssig, P.Chaiyen, F.Diederich. Antimalarial Inhibitors Targeting Serine Hydroxymethyltransferase (Shmt) with in Vivo Efficacy and Analysis of Their Binding Mode Based on X-Ray Cocrystal Structures J. Med. Chem. V. 60 4840 2017.
ISSN: ISSN 1520-4804
PubMed: 28537728
DOI: 10.1021/ACS.JMEDCHEM.7B00008
Page generated: Thu Aug 1 09:41:40 2024

Last articles

Zn in 9J0N
Zn in 9J0O
Zn in 9J0P
Zn in 9FJX
Zn in 9EKB
Zn in 9C0F
Zn in 9CAH
Zn in 9CH0
Zn in 9CH3
Zn in 9CH1
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy