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Fluorine in PDB 5jwc: Structure of NDH2 From Plasmodium Falciparum in Complex with Ryl-552

Enzymatic activity of Structure of NDH2 From Plasmodium Falciparum in Complex with Ryl-552

All present enzymatic activity of Structure of NDH2 From Plasmodium Falciparum in Complex with Ryl-552:
1.6.99.3;

Protein crystallography data

The structure of Structure of NDH2 From Plasmodium Falciparum in Complex with Ryl-552, PDB code: 5jwc was solved by Y.Yu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.45 / 2.05
Space group I 41
Cell size a, b, c (Å), α, β, γ (°) 192.603, 192.603, 92.025, 90.00, 90.00, 90.00
R / Rfree (%) 18.7 / 22.1

Other elements in 5jwc:

The structure of Structure of NDH2 From Plasmodium Falciparum in Complex with Ryl-552 also contains other interesting chemical elements:

Magnesium (Mg) 8 atoms

Fluorine Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 16;

Binding sites:

The binding sites of Fluorine atom in the Structure of NDH2 From Plasmodium Falciparum in Complex with Ryl-552 (pdb code 5jwc). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 16 binding sites of Fluorine where determined in the Structure of NDH2 From Plasmodium Falciparum in Complex with Ryl-552, PDB code: 5jwc:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Fluorine binding site 1 out of 16 in 5jwc

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Fluorine binding site 1 out of 16 in the Structure of NDH2 From Plasmodium Falciparum in Complex with Ryl-552


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Structure of NDH2 From Plasmodium Falciparum in Complex with Ryl-552 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F609

b:37.9
occ:1.00
 F1 A:4W0609 0.0 37.9 1.0
C5 A:4W0609 1.3 31.9 1.0
C4 A:4W0609 2.3 32.6 1.0
C6 A:4W0609 2.4 34.6 1.0
O2 A:4W0609 2.6 35.9 1.0
O A:HOH776 2.7 35.1 1.0
C7 A:4W0609 2.8 38.6 1.0
O H:HOH841 3.2 43.9 1.0
CG H:PRO530 3.5 31.4 1.0
C3 A:4W0609 3.6 31.3 1.0
C1 A:4W0609 3.7 34.3 1.0
CB H:SER90 3.7 35.5 1.0
O H:GLY87 3.9 32.7 1.0
O A:HOH797 3.9 43.9 1.0
CA H:SER90 4.0 31.7 1.0
CD H:PRO530 4.0 33.3 1.0
O H:LEU89 4.1 31.3 1.0
C2 A:4W0609 4.1 31.7 1.0
C8 A:4W0609 4.3 36.2 1.0
O H:HOH844 4.3 34.4 1.0
N H:SER90 4.3 30.8 1.0
O H:HOH861 4.3 45.6 1.0
C H:LEU89 4.4 31.5 1.0
C H:GLY87 4.6 32.7 1.0
CA H:GLY87 4.6 34.1 1.0
CB H:PRO530 4.8 32.7 1.0
N A:4W0609 4.8 30.9 1.0
OG H:SER90 4.9 38.1 1.0

Fluorine binding site 2 out of 16 in 5jwc

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Fluorine binding site 2 out of 16 in the Structure of NDH2 From Plasmodium Falciparum in Complex with Ryl-552


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Structure of NDH2 From Plasmodium Falciparum in Complex with Ryl-552 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F609

b:52.5
occ:1.00
 F2 A:4W0609 0.0 52.5 1.0
C24 A:4W0609 1.3 61.3 1.0
F3 A:4W0609 2.2 63.1 1.0
O1 A:4W0609 2.2 50.1 1.0
F4 A:4W0609 2.3 57.2 1.0
C20 A:4W0609 2.6 44.9 1.0
O H:LYS533 2.8 44.6 1.0
O H:HOH899 2.9 54.5 1.0
C19 A:4W0609 3.1 41.8 1.0
C H:LYS533 3.2 43.3 1.0
C21 A:4W0609 3.5 40.5 1.0
O A:HOH893 3.5 41.9 1.0
C18 A:4W0609 4.2 37.4 1.0
CE H:LYS178 4.3 48.7 1.0
C22 A:4W0609 4.5 37.7 1.0
OH A:TYR74 4.6 34.1 1.0
CA H:LYS533 4.7 40.9 1.0
C17 A:4W0609 4.7 39.5 1.0
CE2 A:TYR74 4.8 33.5 1.0
NZ H:LYS178 4.8 45.4 1.0

Fluorine binding site 3 out of 16 in 5jwc

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Fluorine binding site 3 out of 16 in the Structure of NDH2 From Plasmodium Falciparum in Complex with Ryl-552


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Structure of NDH2 From Plasmodium Falciparum in Complex with Ryl-552 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F609

b:63.1
occ:1.00
 F3 A:4W0609 0.0 63.1 1.0
C24 A:4W0609 1.3 61.3 1.0
F4 A:4W0609 2.1 57.2 1.0
F2 A:4W0609 2.2 52.5 1.0
O1 A:4W0609 2.3 50.1 1.0
O H:HOH899 3.2 54.5 1.0
C20 A:4W0609 3.5 44.9 1.0
C21 A:4W0609 4.3 40.5 1.0
C19 A:4W0609 4.4 41.8 1.0
O A:HOH893 4.8 41.9 1.0
O H:LYS533 4.9 44.6 1.0

Fluorine binding site 4 out of 16 in 5jwc

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Fluorine binding site 4 out of 16 in the Structure of NDH2 From Plasmodium Falciparum in Complex with Ryl-552


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Structure of NDH2 From Plasmodium Falciparum in Complex with Ryl-552 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F609

b:57.2
occ:1.00
 F4 A:4W0609 0.0 57.2 1.0
C24 A:4W0609 1.4 61.3 1.0
F3 A:4W0609 2.1 63.1 1.0
F2 A:4W0609 2.3 52.5 1.0
O1 A:4W0609 2.3 50.1 1.0
OH A:TYR74 3.1 34.1 1.0
C20 A:4W0609 3.3 44.9 1.0
C19 A:4W0609 3.5 41.8 1.0
O A:HOH893 3.7 41.9 1.0
CE2 A:TYR74 3.8 33.5 1.0
O H:HOH899 3.8 54.5 1.0
CZ A:TYR74 3.9 34.9 1.0
O A:HOH816 4.4 35.2 1.0
O A:HOH727 4.5 40.8 1.0
C21 A:4W0609 4.6 40.5 1.0
C H:LYS533 4.8 43.3 1.0
O H:LYS533 4.8 44.6 1.0
C18 A:4W0609 4.9 37.4 1.0

Fluorine binding site 5 out of 16 in 5jwc

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Fluorine binding site 5 out of 16 in the Structure of NDH2 From Plasmodium Falciparum in Complex with Ryl-552


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Structure of NDH2 From Plasmodium Falciparum in Complex with Ryl-552 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F610

b:38.4
occ:1.00
 F1 A:4W0610 0.0 38.4 1.0
C5 A:4W0610 1.3 30.2 1.0
C4 A:4W0610 2.4 31.9 1.0
C6 A:4W0610 2.4 33.6 1.0
O2 A:4W0610 2.6 33.9 1.0
O A:HOH806 2.7 34.8 1.0
C7 A:4W0610 2.8 36.5 1.0
O A:HOH822 3.3 46.2 1.0
CG A:PRO530 3.6 31.1 1.0
C3 A:4W0610 3.6 30.2 1.0
C1 A:4W0610 3.7 31.4 1.0
CB A:SER90 3.7 32.7 1.0
CA A:SER90 4.0 31.2 1.0
O A:GLY87 4.0 31.4 1.0
CD A:PRO530 4.1 33.7 1.0
O A:LEU89 4.1 31.6 1.0
C2 A:4W0610 4.2 32.7 1.0
O A:HOH847 4.2 33.9 1.0
C8 A:4W0610 4.3 35.7 1.0
N A:SER90 4.3 27.7 1.0
C A:LEU89 4.4 29.5 1.0
O A:HOH820 4.4 49.0 1.0
CA A:GLY87 4.6 32.2 1.0
C A:GLY87 4.7 34.5 1.0
CB A:PRO530 4.8 32.9 1.0
N A:4W0610 4.8 29.9 1.0
OG A:SER90 4.9 36.2 1.0

Fluorine binding site 6 out of 16 in 5jwc

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Fluorine binding site 6 out of 16 in the Structure of NDH2 From Plasmodium Falciparum in Complex with Ryl-552


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Structure of NDH2 From Plasmodium Falciparum in Complex with Ryl-552 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F610

b:49.1
occ:1.00
 F2 A:4W0610 0.0 49.1 1.0
C24 A:4W0610 1.3 60.5 1.0
F4 A:4W0610 2.2 59.2 1.0
F3 A:4W0610 2.2 61.4 1.0
O1 A:4W0610 2.3 52.2 1.0
O A:LYS533 2.6 47.4 1.0
C20 A:4W0610 2.7 44.1 1.0
O A:HOH780 2.9 47.1 1.0
C19 A:4W0610 3.3 41.7 1.0
C A:LYS533 3.3 41.4 1.0
C21 A:4W0610 3.4 41.5 1.0
O A:HOH804 3.9 44.2 1.0
NZ A:LYS178 4.1 46.2 1.0
O H:HOH785 4.1 45.2 1.0
C18 A:4W0610 4.3 37.5 1.0
CE A:LYS178 4.4 48.7 1.0
C22 A:4W0610 4.4 37.1 1.0
C17 A:4W0610 4.8 39.3 1.0
CA A:LYS533 4.8 38.0 1.0

Fluorine binding site 7 out of 16 in 5jwc

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Fluorine binding site 7 out of 16 in the Structure of NDH2 From Plasmodium Falciparum in Complex with Ryl-552


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 7 of Structure of NDH2 From Plasmodium Falciparum in Complex with Ryl-552 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F610

b:61.4
occ:1.00
 F3 A:4W0610 0.0 61.4 1.0
C24 A:4W0610 1.4 60.5 1.0
F4 A:4W0610 2.2 59.2 1.0
F2 A:4W0610 2.2 49.1 1.0
O1 A:4W0610 2.3 52.2 1.0
O H:HOH785 3.1 45.2 1.0
O A:HOH780 3.2 47.1 1.0
C20 A:4W0610 3.6 44.1 1.0
O H:HOH889 4.0 49.8 1.0
C21 A:4W0610 4.4 41.5 1.0
C19 A:4W0610 4.4 41.7 1.0
O A:HOH804 4.7 44.2 1.0
O A:LYS533 4.8 47.4 1.0

Fluorine binding site 8 out of 16 in 5jwc

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Fluorine binding site 8 out of 16 in the Structure of NDH2 From Plasmodium Falciparum in Complex with Ryl-552


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 8 of Structure of NDH2 From Plasmodium Falciparum in Complex with Ryl-552 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F610

b:59.2
occ:1.00
 F4 A:4W0610 0.0 59.2 1.0
C24 A:4W0610 1.3 60.5 1.0
O H:HOH785 2.0 45.2 1.0
F3 A:4W0610 2.2 61.4 1.0
F2 A:4W0610 2.2 49.1 1.0
O1 A:4W0610 2.3 52.2 1.0
C20 A:4W0610 3.1 44.1 1.0
C19 A:4W0610 3.2 41.7 1.0
OH H:TYR74 3.3 34.5 1.0
O A:HOH804 3.3 44.2 1.0
O H:HOH889 3.5 49.8 1.0
CE2 H:TYR74 3.6 36.1 1.0
O A:HOH780 3.6 47.1 1.0
CZ H:TYR74 3.9 36.5 1.0
O A:LYS533 4.1 47.4 1.0
C A:LYS533 4.2 41.4 1.0
C21 A:4W0610 4.3 41.5 1.0
C18 A:4W0610 4.5 37.5 1.0
O H:HOH712 4.6 41.7 1.0
O H:HOH824 4.7 34.8 1.0
CD2 H:TYR74 4.9 33.5 1.0

Fluorine binding site 9 out of 16 in 5jwc

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Fluorine binding site 9 out of 16 in the Structure of NDH2 From Plasmodium Falciparum in Complex with Ryl-552


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 9 of Structure of NDH2 From Plasmodium Falciparum in Complex with Ryl-552 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F611

b:48.0
occ:1.00
 F1 A:4W0611 0.0 48.0 1.0
C5 A:4W0611 1.3 45.0 1.0
C4 A:4W0611 2.4 44.6 1.0
C6 A:4W0611 2.4 41.1 1.0
O2 A:4W0611 2.5 53.6 1.0
C7 A:4W0611 2.8 51.2 1.0
CE A:LYS501 3.4 39.7 1.0
CE3 A:TRP500 3.6 33.8 1.0
C3 A:4W0611 3.6 44.2 1.0
O A:SER497 3.6 34.6 1.0
C1 A:4W0611 3.7 42.4 1.0
CB A:SER497 3.7 35.6 1.0
CG A:LYS501 4.0 30.6 1.0
CZ3 A:TRP500 4.1 32.2 1.0
CD2 A:TRP500 4.1 31.1 1.0
CA A:SER497 4.1 33.0 1.0
C2 A:4W0611 4.1 45.9 1.0
CZ A:PHE521 4.2 41.2 1.0
C A:SER497 4.3 33.8 1.0
C8 A:4W0611 4.3 52.7 1.0
CE1 A:PHE521 4.3 39.5 1.0
CD A:LYS501 4.3 31.7 1.0
NZ A:LYS501 4.5 53.9 1.0
CG A:TRP500 4.6 31.1 1.0
CB A:TRP500 4.6 25.6 1.0
OG A:SER497 4.7 41.0 1.0
N A:4W0611 4.9 45.3 1.0
CH2 A:TRP500 4.9 32.7 1.0
CE2 A:TRP500 4.9 35.3 1.0

Fluorine binding site 10 out of 16 in 5jwc

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Fluorine binding site 10 out of 16 in the Structure of NDH2 From Plasmodium Falciparum in Complex with Ryl-552


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 10 of Structure of NDH2 From Plasmodium Falciparum in Complex with Ryl-552 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F611

b:81.0
occ:1.00
 F2 A:4W0611 0.0 81.0 1.0
C24 A:4W0611 1.3 79.1 1.0
F3 A:4W0611 2.2 86.9 1.0
F4 A:4W0611 2.2 75.2 1.0
O1 A:4W0611 2.2 72.2 1.0
OD1 A:ASN478 2.7 44.0 1.0
C20 A:4W0611 2.8 64.4 1.0
C19 A:4W0611 3.0 60.2 1.0
CG A:ASN478 3.1 47.8 1.0
ND2 A:ASN478 3.5 41.0 1.0
C21 A:4W0611 3.9 55.4 1.0
CB A:ASN478 4.1 40.0 1.0
C18 A:4W0611 4.2 55.5 1.0
CD2 A:LEU268 4.4 46.0 1.0
C22 A:4W0611 4.9 53.6 1.0
CA A:ASN478 5.0 38.5 1.0
C17 A:4W0611 5.0 53.2 1.0

Reference:

Y.Yang, Y.Yu, X.Li, J.Li, Y.Wu, J.Yu, J.Ge, Z.Huang, L.Jiang, Y.Rao, M.Yang. Target Elucidation By Cocrystal Structures of Nadh-Ubiquinone Oxidoreductase of Plasmodium Falciparum (PFNDH2) with Small Molecule to Eliminate Drug-Resistant Malaria J. Med. Chem. V. 60 1994 2017.
ISSN: ISSN 1520-4804
PubMed: 28195463
DOI: 10.1021/ACS.JMEDCHEM.6B01733
Page generated: Tue Jul 15 04:34:24 2025

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