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Magnesium in PDB 6nxg: Crystal Structure of Glycylpeptide N-Tetradecanoyltransferase From Plasmodium Vivax in Complex with Inhibitor 303A

Enzymatic activity of Crystal Structure of Glycylpeptide N-Tetradecanoyltransferase From Plasmodium Vivax in Complex with Inhibitor 303A

All present enzymatic activity of Crystal Structure of Glycylpeptide N-Tetradecanoyltransferase From Plasmodium Vivax in Complex with Inhibitor 303A:
2.3.1.97;

Protein crystallography data

The structure of Crystal Structure of Glycylpeptide N-Tetradecanoyltransferase From Plasmodium Vivax in Complex with Inhibitor 303A, PDB code: 6nxg was solved by B.L.Staker, S.Mayclin, Seattle Structural Genomics Center Forinfectious Disease (Ssgcid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.29 / 1.60
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 57.420, 119.030, 175.350, 90.00, 90.00, 90.00
R / Rfree (%) 14.9 / 17.4

Other elements in 6nxg:

The structure of Crystal Structure of Glycylpeptide N-Tetradecanoyltransferase From Plasmodium Vivax in Complex with Inhibitor 303A also contains other interesting chemical elements:

Chlorine (Cl) 5 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Glycylpeptide N-Tetradecanoyltransferase From Plasmodium Vivax in Complex with Inhibitor 303A (pdb code 6nxg). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Crystal Structure of Glycylpeptide N-Tetradecanoyltransferase From Plasmodium Vivax in Complex with Inhibitor 303A, PDB code: 6nxg:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 6nxg

Go back to Magnesium Binding Sites List in 6nxg
Magnesium binding site 1 out of 3 in the Crystal Structure of Glycylpeptide N-Tetradecanoyltransferase From Plasmodium Vivax in Complex with Inhibitor 303A


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Glycylpeptide N-Tetradecanoyltransferase From Plasmodium Vivax in Complex with Inhibitor 303A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg501

b:18.8
occ:1.00
 O A:LEU169 2.7 11.8 1.0
N A:LYS172 2.9 12.9 1.0
O2A A:MYA505 3.0 9.5 1.0
O5A A:MYA505 3.0 9.5 1.0
N A:LEU174 3.2 10.3 1.0
N A:ARG173 3.4 11.4 1.0
CA A:LYS172 3.5 13.0 1.0
N A:SER171 3.5 12.5 1.0
CB A:LEU174 3.5 10.2 0.5
CB A:LEU174 3.5 9.9 0.5
C A:LYS172 3.6 12.2 1.0
CB A:LYS172 3.6 13.7 1.0
C A:ARG170 3.8 12.3 1.0
P1A A:MYA505 3.8 10.2 1.0
CG A:LEU174 3.8 10.2 0.5
C A:LEU169 3.9 11.8 1.0
CG1 A:VAL165 3.9 9.5 1.0
O1A A:MYA505 3.9 10.5 1.0
C A:SER171 3.9 13.1 1.0
CA A:LEU174 3.9 10.0 0.5
CA A:LEU174 4.0 9.8 0.5
CA A:ARG170 4.0 11.7 1.0
CD1 A:LEU174 4.1 10.3 0.5
CA A:SER171 4.2 13.0 1.0
C A:ARG173 4.2 10.7 1.0
P2A A:MYA505 4.2 9.5 1.0
CA A:ARG173 4.3 11.1 1.0
N A:ARG170 4.4 11.8 1.0
O3A A:MYA505 4.4 9.7 1.0
CG A:LYS172 4.4 14.5 1.0
O A:LYS172 4.4 12.2 1.0
N A:ALA175 4.4 8.9 1.0
O A:ARG170 4.5 12.6 1.0
CG2 A:VAL165 4.7 9.1 1.0
O6A A:MYA505 4.7 9.3 1.0
C A:LEU174 4.7 9.4 1.0
CB A:VAL165 4.7 9.1 1.0
CG A:LEU174 4.9 10.4 0.5

Magnesium binding site 2 out of 3 in 6nxg

Go back to Magnesium Binding Sites List in 6nxg
Magnesium binding site 2 out of 3 in the Crystal Structure of Glycylpeptide N-Tetradecanoyltransferase From Plasmodium Vivax in Complex with Inhibitor 303A


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Glycylpeptide N-Tetradecanoyltransferase From Plasmodium Vivax in Complex with Inhibitor 303A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg501

b:18.6
occ:1.00
 O B:LEU169 2.8 12.2 1.0
N B:LYS172 2.9 13.3 1.0
O2A B:MYA504 2.9 9.5 1.0
O5A B:MYA504 3.0 9.8 1.0
N B:LEU174 3.3 10.9 1.0
N B:ARG173 3.4 12.0 1.0
CA B:LYS172 3.5 13.8 1.0
N B:SER171 3.5 12.5 1.0
CB B:LYS172 3.5 15.1 1.0
CB B:LEU174 3.6 11.6 1.0
C B:LYS172 3.6 12.8 1.0
P1A B:MYA504 3.8 10.0 1.0
C B:ARG170 3.8 12.5 1.0
CG1 B:VAL165 3.9 9.9 1.0
CG B:LEU174 3.9 12.6 1.0
C B:LEU169 3.9 12.7 1.0
O1A B:MYA504 4.0 9.8 1.0
C B:SER171 4.0 13.3 1.0
CA B:LEU174 4.0 10.9 1.0
CA B:ARG170 4.0 12.0 1.0
CD1 B:LEU174 4.0 13.1 1.0
P2A B:MYA504 4.2 10.1 1.0
CA B:SER171 4.2 12.9 1.0
C B:ARG173 4.2 11.4 1.0
CA B:ARG173 4.3 11.6 1.0
CG B:LYS172 4.4 16.6 1.0
O3A B:MYA504 4.4 9.7 1.0
N B:ARG170 4.4 12.5 1.0
O B:LYS172 4.5 12.7 1.0
N B:ALA175 4.5 9.3 1.0
O B:ARG170 4.5 12.6 1.0
O6A B:MYA504 4.7 9.8 1.0
CG2 B:VAL165 4.7 9.4 1.0
CB B:VAL165 4.7 9.5 1.0
C B:LEU174 4.7 9.9 1.0

Magnesium binding site 3 out of 3 in 6nxg

Go back to Magnesium Binding Sites List in 6nxg
Magnesium binding site 3 out of 3 in the Crystal Structure of Glycylpeptide N-Tetradecanoyltransferase From Plasmodium Vivax in Complex with Inhibitor 303A


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of Glycylpeptide N-Tetradecanoyltransferase From Plasmodium Vivax in Complex with Inhibitor 303A within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg504

b:18.8
occ:1.00
 O C:LEU169 2.7 11.8 1.0
O2A C:MYA501 2.9 9.9 1.0
N C:LYS172 2.9 13.6 1.0
O5A C:MYA501 3.0 10.3 1.0
N C:LEU174 3.2 10.8 1.0
N C:ARG173 3.4 11.8 1.0
N C:SER171 3.5 12.9 1.0
CA C:LYS172 3.5 13.7 1.0
CB C:LEU174 3.6 11.4 1.0
CB C:LYS172 3.6 14.5 1.0
C C:LYS172 3.6 12.6 1.0
P1A C:MYA501 3.8 9.7 1.0
C C:ARG170 3.8 12.6 1.0
C C:LEU169 3.9 11.9 1.0
O1A C:MYA501 3.9 10.1 1.0
CG C:LEU174 3.9 12.5 1.0
CA C:ARG170 4.0 12.1 1.0
CA C:LEU174 4.0 10.7 1.0
C C:SER171 4.0 13.9 1.0
CD1 C:LEU174 4.1 13.2 1.0
CG1 C:VAL165 4.1 10.0 1.0
CA C:SER171 4.2 13.7 1.0
P2A C:MYA501 4.2 10.4 1.0
C C:ARG173 4.2 11.1 1.0
CA C:ARG173 4.3 11.3 1.0
O3A C:MYA501 4.3 10.3 1.0
N C:ARG170 4.4 12.2 1.0
CG C:LYS172 4.5 15.8 1.0
N C:ALA175 4.5 9.2 1.0
O C:LYS172 4.5 12.4 1.0
O C:ARG170 4.6 12.7 1.0
O6A C:MYA501 4.7 10.2 1.0
C C:LEU174 4.7 9.8 1.0
CG2 C:VAL165 4.8 9.5 1.0
CB C:VAL165 4.8 9.5 1.0

Reference:

A.Harupa, L.De Las Heras, G.Colmenarejo, S.Lyons-Abbott, A.Reers, I.Caballero Hernandez, C.W.Chung, D.Charter, P.J.Myler, R.M.Fernandez-Menendez, F.Calderon, S.Palomo, B.Rodriguez, M.Berlanga, E.Herreros-Aviles, B.L.Staker, E.Fernandez Alvaro, A.Kaushansky. Identification of Selective Inhibitors of Plasmodium N-Myristoyltransferase By High-Throughput Screening. J.Med.Chem. 2019.
ISSN: ISSN 0022-2623
PubMed: 31850752
DOI: 10.1021/ACS.JMEDCHEM.9B01343
Page generated: Tue Oct 1 12:54:35 2024

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