Atomistry » Magnesium » PDB 4u9h-4ukd » 4ufw
Atomistry »
  Magnesium »
    PDB 4u9h-4ukd »
      4ufw »

Magnesium in PDB 4ufw: Plasmodium Vivax N-Myristoyltransferase in Complex with A Pyridyl Inhibitor (Compound 22)

Enzymatic activity of Plasmodium Vivax N-Myristoyltransferase in Complex with A Pyridyl Inhibitor (Compound 22)

All present enzymatic activity of Plasmodium Vivax N-Myristoyltransferase in Complex with A Pyridyl Inhibitor (Compound 22):
2.3.1.97;

Protein crystallography data

The structure of Plasmodium Vivax N-Myristoyltransferase in Complex with A Pyridyl Inhibitor (Compound 22), PDB code: 4ufw was solved by Z.Yu, J.A.Brannigan, K.Rangachari, W.P.Heal, A.J.Wilkinson, A.A.Holder, E.W.Tate, R.J.Leatherbarrow, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 100.73 / 1.50
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 57.520, 121.910, 178.800, 90.00, 90.00, 90.00
R / Rfree (%) 21.444 / 26.101

Other elements in 4ufw:

The structure of Plasmodium Vivax N-Myristoyltransferase in Complex with A Pyridyl Inhibitor (Compound 22) also contains other interesting chemical elements:

Chlorine (Cl) 6 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Plasmodium Vivax N-Myristoyltransferase in Complex with A Pyridyl Inhibitor (Compound 22) (pdb code 4ufw). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Plasmodium Vivax N-Myristoyltransferase in Complex with A Pyridyl Inhibitor (Compound 22), PDB code: 4ufw:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 4ufw

Go back to Magnesium Binding Sites List in 4ufw
Magnesium binding site 1 out of 3 in the Plasmodium Vivax N-Myristoyltransferase in Complex with A Pyridyl Inhibitor (Compound 22)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Plasmodium Vivax N-Myristoyltransferase in Complex with A Pyridyl Inhibitor (Compound 22) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1413

b:22.1
occ:1.00
 O2A A:NHW1000 2.7 11.2 1.0
O4A A:NHW1000 2.8 11.4 1.0
O A:LEU169 2.9 15.4 1.0
N A:LYS172 3.0 15.3 1.0
N A:LEU174 3.2 12.6 1.0
N A:SER171 3.3 14.0 1.0
N A:ARG173 3.4 12.5 1.0
CA A:LYS172 3.6 14.7 1.0
C A:LYS172 3.6 13.7 1.0
P1A A:NHW1000 3.6 13.1 1.0
CB A:LEU174 3.7 15.0 1.0
CB A:LYS172 3.7 15.6 1.0
C A:ARG170 3.8 15.6 1.0
O1A A:NHW1000 3.8 13.7 1.0
CA A:ARG170 3.9 12.8 1.0
CA A:LEU174 3.9 12.7 1.0
C A:LEU169 4.0 14.9 1.0
C A:SER171 4.0 16.8 1.0
P2A A:NHW1000 4.0 13.4 1.0
CA A:SER171 4.1 13.9 1.0
CG A:LEU174 4.1 18.0 1.0
CG1 A:VAL165 4.1 9.0 1.0
C A:ARG173 4.2 14.0 1.0
O3A A:NHW1000 4.2 11.7 1.0
CD1 A:LEU174 4.3 20.0 1.0
CA A:ARG173 4.3 13.3 1.0
N A:ALA175 4.4 11.0 1.0
N A:ARG170 4.4 13.1 1.0
O A:LYS172 4.5 15.2 1.0
O6A A:NHW1000 4.5 13.0 1.0
CG A:LYS172 4.6 17.9 1.0
O A:ARG170 4.7 15.0 1.0
C A:LEU174 4.7 11.6 1.0
CG2 A:VAL165 4.7 10.5 1.0
CB A:VAL165 4.8 9.5 1.0

Magnesium binding site 2 out of 3 in 4ufw

Go back to Magnesium Binding Sites List in 4ufw
Magnesium binding site 2 out of 3 in the Plasmodium Vivax N-Myristoyltransferase in Complex with A Pyridyl Inhibitor (Compound 22)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Plasmodium Vivax N-Myristoyltransferase in Complex with A Pyridyl Inhibitor (Compound 22) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1412

b:27.4
occ:1.00
 O B:LEU169 2.7 14.9 1.0
O2A B:NHW1000 2.8 12.4 1.0
N B:LYS172 2.9 16.2 1.0
O5A B:NHW1000 3.1 13.8 1.0
N B:LEU174 3.2 12.9 1.0
N B:ARG173 3.5 16.9 1.0
CB B:LEU174 3.5 14.1 1.0
CA B:LYS172 3.5 15.0 1.0
CB B:LYS172 3.6 15.1 1.0
N B:SER171 3.6 13.8 1.0
C B:LYS172 3.6 16.4 1.0
P1A B:NHW1000 3.8 11.8 1.0
CG B:LEU174 3.8 15.5 1.0
CD1 B:LEU174 3.9 17.3 1.0
C B:LEU169 3.9 14.2 1.0
CG1 B:VAL165 3.9 14.7 1.0
CA B:LEU174 3.9 14.0 1.0
C B:ARG170 3.9 16.4 1.0
CA B:ARG170 4.0 14.1 1.0
C B:SER171 4.0 16.3 1.0
O1A B:NHW1000 4.1 14.6 1.0
CA B:SER171 4.2 17.0 1.0
P2A B:NHW1000 4.2 12.5 1.0
C B:ARG173 4.3 14.7 1.0
O B:LYS172 4.4 18.1 1.0
N B:ARG170 4.4 13.4 1.0
N B:ALA175 4.4 13.0 1.0
CA B:ARG173 4.4 12.5 1.0
O3A B:NHW1000 4.4 13.1 1.0
CG B:LYS172 4.5 15.6 1.0
O6A B:NHW1000 4.7 11.8 1.0
O B:ARG170 4.7 17.0 1.0
CG2 B:VAL165 4.7 13.3 1.0
C B:LEU174 4.7 14.2 1.0
CB B:VAL165 4.8 12.8 1.0

Magnesium binding site 3 out of 3 in 4ufw

Go back to Magnesium Binding Sites List in 4ufw
Magnesium binding site 3 out of 3 in the Plasmodium Vivax N-Myristoyltransferase in Complex with A Pyridyl Inhibitor (Compound 22)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Plasmodium Vivax N-Myristoyltransferase in Complex with A Pyridyl Inhibitor (Compound 22) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg1412

b:22.4
occ:1.00
 O C:LEU169 2.9 12.8 1.0
N C:LYS172 2.9 16.7 1.0
O2A C:NHW1000 3.0 12.9 1.0
O4A C:NHW1000 3.0 12.2 1.0
N C:LEU174 3.1 12.1 1.0
N C:ARG173 3.3 14.0 1.0
CA C:LYS172 3.5 15.9 1.0
C C:LYS172 3.5 14.6 1.0
N C:SER171 3.5 18.5 1.0
CB C:LEU174 3.6 13.4 1.0
CB C:LYS172 3.7 17.8 1.0
P1A C:NHW1000 3.7 12.5 1.0
O1A C:NHW1000 3.7 14.6 1.0
C C:ARG170 3.8 14.8 1.0
CA C:LEU174 3.8 12.2 1.0
CG C:LEU174 3.9 14.4 1.0
C C:SER171 4.0 17.7 1.0
CA C:ARG170 4.0 14.5 1.0
C C:LEU169 4.0 14.0 1.0
C C:ARG173 4.1 12.4 1.0
CG1 C:VAL165 4.1 13.0 1.0
CA C:SER171 4.1 16.8 1.0
P2A C:NHW1000 4.1 13.8 1.0
CA C:ARG173 4.2 12.9 1.0
CD1 C:LEU174 4.2 13.7 1.0
O3A C:NHW1000 4.3 12.7 1.0
N C:ALA175 4.3 11.7 1.0
O C:LYS172 4.4 14.8 1.0
O C:ARG170 4.5 15.1 1.0
N C:ARG170 4.5 13.7 1.0
O6A C:NHW1000 4.5 12.6 1.0
C C:LEU174 4.6 13.2 1.0
CG C:LYS172 4.7 20.4 1.0
CB C:VAL165 4.9 13.5 1.0
CG2 C:VAL165 4.9 14.3 1.0

Reference:

Z.Yu, J.A.Brannigan, K.Rangachari, W.P.Heal, A.J.Wilkinson, A.A.Holder, R.J.Leatherbarrow, E.W.Tate. Discovery of Pyridyl-Based Inhibitors of Plasmodium Falciparum N-Myristoyltransferase Medchemcomm V. 6 1767 2015.
ISSN: ISSN 2040-2503
PubMed: 26962430
DOI: 10.1039/C5MD00242G
Page generated: Tue Aug 20 04:42:20 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