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Sodium in PDB 8ez4: Plasmodium Falciparum M17 in Complex with Inhibitor 9AA

Enzymatic activity of Plasmodium Falciparum M17 in Complex with Inhibitor 9AA

All present enzymatic activity of Plasmodium Falciparum M17 in Complex with Inhibitor 9AA:
3.4.11.1;

Protein crystallography data

The structure of Plasmodium Falciparum M17 in Complex with Inhibitor 9AA, PDB code: 8ez4 was solved by P.P.S.Calic, S.Mcgowan, C.T.Webb, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.47 / 1.89
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 173.94, 176.6, 230.901, 90, 90, 90
R / Rfree (%) 17.7 / 21.6

Other elements in 8ez4:

The structure of Plasmodium Falciparum M17 in Complex with Inhibitor 9AA also contains other interesting chemical elements:

Fluorine (F) 36 atoms
Zinc (Zn) 24 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Plasmodium Falciparum M17 in Complex with Inhibitor 9AA (pdb code 8ez4). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 9 binding sites of Sodium where determined in the Plasmodium Falciparum M17 in Complex with Inhibitor 9AA, PDB code: 8ez4:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Sodium binding site 1 out of 9 in 8ez4

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Sodium binding site 1 out of 9 in the Plasmodium Falciparum M17 in Complex with Inhibitor 9AA


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Plasmodium Falciparum M17 in Complex with Inhibitor 9AA within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na711

b:25.6
occ:1.00
 O A:ALA300 2.3 19.0 1.0
O A:HOH1041 2.3 19.0 1.0
O A:LEU297 2.5 19.2 1.0
O A:ILE298 2.6 19.7 1.0
C A:ILE298 3.2 21.6 1.0
SD A:MET400 3.3 20.1 1.0
O A:LYS397 3.4 21.2 1.0
C A:ALA300 3.5 19.0 1.0
CA A:ILE298 3.5 20.4 1.0
C A:LEU297 3.6 19.3 1.0
SG A:CYS305 3.8 23.4 1.0
CB A:CYS305 3.8 19.2 1.0
N A:ALA300 3.9 19.6 1.0
N A:ILE298 4.0 19.8 1.0
CA A:ALA300 4.1 21.4 1.0
CB A:LYS397 4.1 20.9 1.0
CE A:MET400 4.2 19.3 1.0
C A:LYS397 4.2 21.4 1.0
N A:ALA299 4.3 19.6 1.0
CB A:ALA300 4.3 19.4 1.0
CG A:MET400 4.3 20.2 1.0
C A:ALA299 4.4 19.5 1.0
CG A:LYS397 4.4 22.7 1.0
N A:PRO301 4.6 19.3 1.0
CA A:LYS397 4.6 20.4 1.0
CD A:LYS397 4.7 24.9 1.0
C A:PRO301 4.8 18.9 1.0
CA A:PRO301 4.8 21.1 1.0
CA A:ALA299 4.8 21.4 1.0
CA A:LEU297 4.9 19.4 1.0
O A:PRO301 4.9 18.9 1.0
CB A:ILE298 4.9 19.2 1.0
O A:ALA299 4.9 18.9 1.0

Sodium binding site 2 out of 9 in 8ez4

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Sodium binding site 2 out of 9 in the Plasmodium Falciparum M17 in Complex with Inhibitor 9AA


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Plasmodium Falciparum M17 in Complex with Inhibitor 9AA within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na1405

b:23.4
occ:1.00
 O B:ALA300 2.4 19.5 1.0
O B:HOH1658 2.4 24.5 1.0
O B:ILE298 2.5 20.6 1.0
O B:LEU297 2.6 19.5 1.0
C B:ILE298 3.2 21.3 1.0
O B:LYS397 3.3 23.7 1.0
SD B:MET400 3.4 20.3 1.0
CA B:ILE298 3.5 19.4 1.0
C B:ALA300 3.5 19.6 1.0
C B:LEU297 3.6 19.6 1.0
SG B:CYS305 3.9 24.4 1.0
CB B:CYS305 3.9 24.0 1.0
N B:ALA300 4.0 19.7 1.0
N B:ILE298 4.1 19.6 1.0
CB B:LYS397 4.1 19.1 1.0
C B:LYS397 4.1 25.4 1.0
CE B:MET400 4.1 19.3 1.0
CA B:ALA300 4.2 19.7 1.0
CG B:MET400 4.2 19.1 1.0
N B:ALA299 4.3 19.6 1.0
CG B:LYS397 4.4 25.2 1.0
C B:ALA299 4.4 20.9 1.0
CB B:ALA300 4.4 19.7 1.0
CA B:LYS397 4.5 21.8 1.0
N B:PRO301 4.6 20.2 1.0
CD B:LYS397 4.6 23.0 1.0
C B:PRO301 4.8 19.4 1.0
CA B:PRO301 4.8 19.4 1.0
CA B:ALA299 4.8 20.5 1.0
CB B:ILE298 4.9 20.0 1.0
O B:PRO301 4.9 23.3 1.0
O B:ALA299 4.9 19.6 1.0
CA B:LEU297 5.0 19.7 1.0

Sodium binding site 3 out of 9 in 8ez4

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Sodium binding site 3 out of 9 in the Plasmodium Falciparum M17 in Complex with Inhibitor 9AA


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Plasmodium Falciparum M17 in Complex with Inhibitor 9AA within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na709

b:22.9
occ:1.00
 O D:ALA300 2.4 18.5 1.0
O D:HOH1056 2.4 23.8 1.0
O D:ILE298 2.5 19.8 1.0
O D:LEU297 2.5 18.5 1.0
C D:ILE298 3.1 18.8 1.0
SD D:MET400 3.4 19.7 1.0
O D:LYS397 3.4 21.8 1.0
CA D:ILE298 3.5 19.1 1.0
C D:ALA300 3.5 20.1 1.0
C D:LEU297 3.6 21.9 1.0
SG D:CYS305 3.8 22.4 1.0
N D:ALA300 3.9 18.5 1.0
CB D:CYS305 3.9 18.5 1.0
N D:ILE298 4.0 18.4 1.0
CB D:LYS397 4.1 24.3 1.0
CA D:ALA300 4.1 20.6 1.0
CE D:MET400 4.1 23.0 1.0
N D:ALA299 4.2 19.4 1.0
C D:LYS397 4.2 21.6 1.0
CG D:LYS397 4.3 21.2 1.0
CG D:MET400 4.3 18.2 1.0
CB D:ALA300 4.3 18.6 1.0
C D:ALA299 4.3 20.6 1.0
N D:PRO301 4.6 19.4 1.0
CA D:LYS397 4.6 21.0 1.0
CD D:LYS397 4.7 22.2 1.0
CA D:ALA299 4.7 18.4 1.0
C D:PRO301 4.8 21.1 1.0
CA D:PRO301 4.8 20.3 1.0
O D:ALA299 4.8 21.7 1.0
O D:PRO301 4.9 23.4 1.0
CB D:ILE298 4.9 18.3 1.0
CA D:LEU297 4.9 18.5 1.0

Sodium binding site 4 out of 9 in 8ez4

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Sodium binding site 4 out of 9 in the Plasmodium Falciparum M17 in Complex with Inhibitor 9AA


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Plasmodium Falciparum M17 in Complex with Inhibitor 9AA within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Na710

b:23.8
occ:1.00
 O F:HOH1007 2.2 23.5 1.0
O F:ALA300 2.4 21.1 1.0
O F:LEU297 2.5 19.6 1.0
O F:ILE298 2.7 22.1 1.0
O F:LYS397 3.3 29.7 1.0
SD F:MET400 3.3 20.3 1.0
C F:ILE298 3.3 22.2 1.0
C F:ALA300 3.6 19.6 1.0
CA F:ILE298 3.6 19.6 1.0
C F:LEU297 3.6 19.6 1.0
SG F:CYS305 3.6 24.9 1.0
CB F:CYS305 3.8 20.7 1.0
N F:ALA300 4.0 19.6 1.0
N F:ILE298 4.1 19.6 1.0
CG F:MET400 4.2 21.6 1.0
CE F:MET400 4.2 19.5 1.0
C F:LYS397 4.2 25.1 1.0
CB F:LYS397 4.2 20.1 1.0
CA F:ALA300 4.2 19.6 1.0
CB F:ALA300 4.3 19.6 1.0
N F:ALA299 4.4 19.6 1.0
CG F:LYS397 4.4 23.2 1.0
C F:ALA299 4.5 21.7 1.0
CA F:LYS397 4.6 19.1 1.0
N F:PRO301 4.6 19.4 1.0
C F:PRO301 4.8 22.4 1.0
CD F:LYS397 4.8 20.0 1.0
CA F:PRO301 4.8 21.2 1.0
O F:PRO301 4.9 19.8 1.0
CA F:LEU297 4.9 19.8 1.0
CA F:ALA299 4.9 22.3 1.0
CB F:ILE298 5.0 19.6 1.0

Sodium binding site 5 out of 9 in 8ez4

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Sodium binding site 5 out of 9 in the Plasmodium Falciparum M17 in Complex with Inhibitor 9AA


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Plasmodium Falciparum M17 in Complex with Inhibitor 9AA within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Na709

b:22.9
occ:1.00
 O G:HOH1052 2.3 18.8 1.0
O G:ALA300 2.3 20.2 1.0
O G:LEU297 2.5 19.0 1.0
O G:ILE298 2.5 18.7 1.0
C G:ILE298 3.2 20.2 1.0
O G:LYS397 3.4 23.2 1.0
SD G:MET400 3.4 20.8 1.0
C G:ALA300 3.5 19.0 1.0
CA G:ILE298 3.5 18.6 1.0
C G:LEU297 3.6 19.0 1.0
SG G:CYS305 3.8 23.9 1.0
N G:ALA300 3.9 18.7 1.0
CB G:CYS305 3.9 19.0 1.0
CB G:LYS397 4.0 19.8 1.0
N G:ILE298 4.1 18.6 1.0
CE G:MET400 4.1 18.7 1.0
CA G:ALA300 4.2 18.8 1.0
C G:LYS397 4.2 22.8 1.0
CG G:MET400 4.2 18.7 1.0
N G:ALA299 4.3 18.6 1.0
CG G:LYS397 4.3 20.3 1.0
C G:ALA299 4.3 18.6 1.0
CB G:ALA300 4.4 18.9 1.0
N G:PRO301 4.6 18.8 1.0
CA G:LYS397 4.6 21.5 1.0
CD G:LYS397 4.6 20.5 1.0
C G:PRO301 4.7 19.1 1.0
CA G:PRO301 4.8 18.7 1.0
CA G:ALA299 4.8 18.5 1.0
O G:ALA299 4.9 18.6 1.0
CB G:ILE298 4.9 18.8 1.0
O G:PRO301 4.9 20.0 1.0
CA G:LEU297 4.9 18.9 1.0

Sodium binding site 6 out of 9 in 8ez4

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Sodium binding site 6 out of 9 in the Plasmodium Falciparum M17 in Complex with Inhibitor 9AA


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Plasmodium Falciparum M17 in Complex with Inhibitor 9AA within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Na708

b:23.6
occ:1.00
 O H:ALA300 2.4 19.9 1.0
O H:HOH917 2.4 21.9 1.0
O H:ILE298 2.6 19.3 1.0
O H:LEU297 2.6 21.2 1.0
C H:ILE298 3.2 22.5 1.0
O H:LYS397 3.3 20.4 1.0
SD H:MET400 3.3 23.3 1.0
CA H:ILE298 3.5 21.0 1.0
C H:ALA300 3.5 22.1 1.0
C H:LEU297 3.7 21.8 1.0
SG H:CYS305 3.9 24.2 1.0
CB H:CYS305 3.9 20.3 1.0
CB H:LYS397 4.0 24.9 1.0
N H:ALA300 4.0 19.5 1.0
C H:LYS397 4.1 24.2 1.0
N H:ILE298 4.1 19.5 1.0
CE H:MET400 4.1 19.6 1.0
CG H:MET400 4.2 23.2 1.0
CA H:ALA300 4.2 19.5 1.0
N H:ALA299 4.3 22.0 1.0
CG H:LYS397 4.4 21.9 1.0
CB H:ALA300 4.4 20.1 1.0
C H:ALA299 4.4 19.9 1.0
CA H:LYS397 4.5 23.0 1.0
N H:PRO301 4.6 20.1 1.0
CD H:LYS397 4.6 21.0 1.0
C H:PRO301 4.8 19.3 1.0
CA H:PRO301 4.8 24.4 1.0
CA H:ALA299 4.9 21.3 1.0
O H:PRO301 4.9 20.5 1.0
CB H:ILE298 4.9 19.3 1.0
CA H:LEU297 5.0 24.1 1.0
O H:ALA299 5.0 19.3 1.0
O H:THR377 5.0 20.0 1.0

Sodium binding site 7 out of 9 in 8ez4

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Sodium binding site 7 out of 9 in the Plasmodium Falciparum M17 in Complex with Inhibitor 9AA


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of Plasmodium Falciparum M17 in Complex with Inhibitor 9AA within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Na709

b:20.2
occ:1.00
 O I:HOH1053 2.4 19.9 1.0
O I:ILE298 2.4 19.6 1.0
O I:ALA300 2.4 19.0 1.0
O I:LEU297 2.5 19.1 1.0
C I:ILE298 3.1 22.7 1.0
O I:LYS397 3.3 26.1 1.0
SD I:MET400 3.3 19.9 1.0
CA I:ILE298 3.4 18.9 1.0
C I:ALA300 3.6 19.9 1.0
C I:LEU297 3.6 19.1 1.0
SG I:CYS305 3.9 20.9 1.0
CB I:CYS305 3.9 19.2 1.0
N I:ALA300 3.9 19.1 1.0
N I:ILE298 4.0 19.0 1.0
CE I:MET400 4.1 19.1 1.0
CA I:ALA300 4.1 19.1 1.0
N I:ALA299 4.2 18.9 1.0
C I:LYS397 4.2 23.6 1.0
CG I:MET400 4.2 19.2 1.0
CB I:LYS397 4.2 22.1 1.0
CB I:ALA300 4.3 19.2 1.0
C I:ALA299 4.3 20.3 1.0
CG I:LYS397 4.4 20.6 1.0
CD I:LYS397 4.6 20.1 1.0
N I:PRO301 4.6 19.7 1.0
CA I:LYS397 4.7 19.3 1.0
CA I:ALA299 4.8 18.9 1.0
CB I:ILE298 4.8 18.9 1.0
C I:PRO301 4.9 19.1 1.0
CA I:LEU297 4.9 20.1 1.0
CA I:PRO301 4.9 19.7 1.0
O I:ALA299 4.9 19.0 1.0
O I:PRO301 5.0 19.6 1.0

Sodium binding site 8 out of 9 in 8ez4

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Sodium binding site 8 out of 9 in the Plasmodium Falciparum M17 in Complex with Inhibitor 9AA


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of Plasmodium Falciparum M17 in Complex with Inhibitor 9AA within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Na708

b:21.3
occ:1.00
 O J:HOH1036 2.3 19.0 1.0
O J:ALA300 2.4 18.8 1.0
O J:LEU297 2.6 19.9 1.0
O J:ILE298 2.6 19.8 1.0
C J:ILE298 3.3 21.9 1.0
O J:LYS397 3.3 21.8 1.0
SD J:MET400 3.4 21.4 1.0
CA J:ILE298 3.6 17.3 1.0
C J:ALA300 3.6 19.8 1.0
C J:LEU297 3.7 22.9 1.0
SG J:CYS305 3.8 23.0 1.0
CB J:CYS305 3.9 20.0 1.0
N J:ALA300 4.0 17.6 1.0
CB J:LYS397 4.1 19.1 1.0
CE J:MET400 4.1 17.3 1.0
N J:ILE298 4.1 18.9 1.0
C J:LYS397 4.2 20.1 1.0
CA J:ALA300 4.2 18.2 1.0
CG J:MET400 4.2 17.3 1.0
N J:ALA299 4.3 17.2 1.0
CG J:LYS397 4.3 21.7 1.0
CB J:ALA300 4.4 17.7 1.0
C J:ALA299 4.4 17.1 1.0
CD J:LYS397 4.6 23.4 1.0
CA J:LYS397 4.6 18.1 1.0
N J:PRO301 4.7 20.6 1.0
C J:PRO301 4.8 18.2 1.0
CA J:ALA299 4.9 18.3 1.0
CA J:PRO301 4.9 21.3 1.0
O J:PRO301 4.9 17.9 1.0
CB J:ILE298 4.9 17.3 1.0
CA J:LEU297 5.0 18.0 1.0

Sodium binding site 9 out of 9 in 8ez4

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Sodium binding site 9 out of 9 in the Plasmodium Falciparum M17 in Complex with Inhibitor 9AA


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 9 of Plasmodium Falciparum M17 in Complex with Inhibitor 9AA within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Na708

b:21.8
occ:1.00
 O K:HOH1037 2.3 21.1 1.0
O K:ALA300 2.4 19.7 1.0
O K:LEU297 2.4 17.9 1.0
O K:ILE298 2.5 20.4 1.0
C K:ILE298 3.1 19.5 1.0
SD K:MET400 3.3 20.2 1.0
O K:LYS397 3.4 20.6 1.0
CA K:ILE298 3.4 17.9 1.0
C K:LEU297 3.5 18.0 1.0
C K:ALA300 3.6 18.6 1.0
SG K:CYS305 3.8 20.6 1.0
CB K:CYS305 3.9 17.8 1.0
N K:ALA300 3.9 18.4 1.0
N K:ILE298 4.0 18.0 1.0
CB K:LYS397 4.1 18.6 1.0
CE K:MET400 4.1 17.9 1.0
CA K:ALA300 4.2 17.9 1.0
C K:LYS397 4.2 21.1 1.0
CG K:MET400 4.2 17.8 1.0
N K:ALA299 4.2 17.9 1.0
CB K:ALA300 4.4 17.9 1.0
C K:ALA299 4.4 17.9 1.0
CG K:LYS397 4.4 20.9 1.0
CD K:LYS397 4.5 19.7 1.0
CA K:LYS397 4.6 22.0 1.0
N K:PRO301 4.7 20.2 1.0
CA K:ALA299 4.8 17.9 1.0
CB K:ILE298 4.8 18.0 1.0
CA K:LEU297 4.9 18.0 1.0
C K:PRO301 4.9 17.7 1.0
CA K:PRO301 4.9 19.9 1.0
O K:PRO301 4.9 19.8 1.0
O K:ALA299 5.0 17.9 1.0

Reference:

P.P.S.Calic, N.B.Vinh, C.T.Webb, T.R.Malcolm, A.Ngo, K.Lowes, N.Drinkwater, S.Mcgowan, P.J.Scammells. Structure-Based Development of Potent Plasmodium Falciparum M1 and M17 Aminopeptidase Selective and Dual Inhibitors Via S1'-Region Optimisation Eur.J.Med.Chem. 2023.
ISSN: ISSN 0223-5234
Page generated: Wed Oct 9 11:45:47 2024

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