Atomistry » Magnesium » PDB 9kqq-9mgz » 9m5o
Atomistry »
  Magnesium »
    PDB 9kqq-9mgz »
      9m5o »

Magnesium in PDB 9m5o: Plasmodium Vivax Aspartyl-Trna Synthetase in Complex with Aspartyl Sulfamoyl Adenosine (Asp-Ams) Complex

Enzymatic activity of Plasmodium Vivax Aspartyl-Trna Synthetase in Complex with Aspartyl Sulfamoyl Adenosine (Asp-Ams) Complex

All present enzymatic activity of Plasmodium Vivax Aspartyl-Trna Synthetase in Complex with Aspartyl Sulfamoyl Adenosine (Asp-Ams) Complex:
6.1.1.12;

Protein crystallography data

The structure of Plasmodium Vivax Aspartyl-Trna Synthetase in Complex with Aspartyl Sulfamoyl Adenosine (Asp-Ams) Complex, PDB code: 9m5o was solved by V.K.Sharma, Y.Manickam, A.Sharma, S.Bagale, P.I.Pradeepkumar, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.20 / 1.84
Space group P 61 2 2
Cell size a, b, c (Å), α, β, γ (°) 140.253, 140.253, 267.611, 90, 90, 120
R / Rfree (%) 16.8 / 19.6

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Plasmodium Vivax Aspartyl-Trna Synthetase in Complex with Aspartyl Sulfamoyl Adenosine (Asp-Ams) Complex (pdb code 9m5o). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Plasmodium Vivax Aspartyl-Trna Synthetase in Complex with Aspartyl Sulfamoyl Adenosine (Asp-Ams) Complex, PDB code: 9m5o:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 9m5o

Go back to Magnesium Binding Sites List in 9m5o
Magnesium binding site 1 out of 4 in the Plasmodium Vivax Aspartyl-Trna Synthetase in Complex with Aspartyl Sulfamoyl Adenosine (Asp-Ams) Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Plasmodium Vivax Aspartyl-Trna Synthetase in Complex with Aspartyl Sulfamoyl Adenosine (Asp-Ams) Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg702

b:37.3
occ:0.58
 O A:HOH963 2.0 38.4 0.9
OE1 A:GLU554 2.1 28.5 1.0
O A:HOH1025 2.1 35.3 0.9
O A:HOH1189 2.1 30.9 0.9
O A:HOH801 2.2 44.7 1.0
O A:HOH811 2.5 37.7 1.0
O A:HOH1089 3.1 53.3 1.0
CD A:GLU554 3.2 26.3 1.0
MG A:MG703 3.3 30.4 0.8
OD2 A:ASP547 3.6 30.0 1.0
OE2 A:GLU554 3.9 28.9 1.0
OE1 A:GLU503 4.1 33.7 1.0
CG A:GLU554 4.2 23.8 1.0
O A:HOH916 4.3 42.7 1.0
CB A:GLU554 4.3 21.4 1.0
OE2 A:GLU503 4.4 32.1 1.0
O A:HOH1087 4.5 35.5 0.7
O A:HOH1081 4.5 32.5 0.8
O A:HOH1069 4.6 43.7 1.0
CD A:GLU503 4.7 33.5 1.0
O A:HOH1130 4.7 44.5 1.0
CG A:ASP547 4.7 29.6 1.0
O A:HOH955 4.8 65.8 1.0

Magnesium binding site 2 out of 4 in 9m5o

Go back to Magnesium Binding Sites List in 9m5o
Magnesium binding site 2 out of 4 in the Plasmodium Vivax Aspartyl-Trna Synthetase in Complex with Aspartyl Sulfamoyl Adenosine (Asp-Ams) Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Plasmodium Vivax Aspartyl-Trna Synthetase in Complex with Aspartyl Sulfamoyl Adenosine (Asp-Ams) Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg703

b:30.4
occ:0.77
 O A:HOH1087 2.1 35.5 0.7
OE2 A:GLU554 2.4 28.9 1.0
O A:HOH1081 2.4 32.5 0.8
OAY A:DSZ701 2.5 23.4 0.9
O A:HOH1025 2.7 35.3 0.9
O A:HOH811 2.7 37.7 1.0
OE1 A:GLU554 2.8 28.5 1.0
CD A:GLU554 2.9 26.3 1.0
MG A:MG702 3.3 37.3 0.6
O A:HOH1147 3.5 59.3 1.0
SBE A:DSZ701 3.7 24.4 0.9
OG A:SER557 4.1 34.8 1.0
CB A:SER557 4.1 27.4 1.0
OAX A:DSZ701 4.2 24.2 0.9
O A:HOH1089 4.3 53.3 1.0
CG A:GLU554 4.4 23.8 1.0
O3' A:DSZ701 4.5 22.3 0.9
O A:HOH1071 4.5 37.3 1.0
O A:HOH1052 4.5 38.7 1.0
C3' A:DSZ701 4.6 23.3 0.9
O A:HOH1189 4.6 30.9 0.9
OD2 A:ASP547 4.7 30.0 1.0
NAT A:DSZ701 4.7 22.4 0.9
O5' A:DSZ701 4.8 19.7 0.9

Magnesium binding site 3 out of 4 in 9m5o

Go back to Magnesium Binding Sites List in 9m5o
Magnesium binding site 3 out of 4 in the Plasmodium Vivax Aspartyl-Trna Synthetase in Complex with Aspartyl Sulfamoyl Adenosine (Asp-Ams) Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Plasmodium Vivax Aspartyl-Trna Synthetase in Complex with Aspartyl Sulfamoyl Adenosine (Asp-Ams) Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg702

b:28.7
occ:0.74
 O B:HOH921 2.1 28.0 0.9
O B:HOH1206 2.1 31.3 1.0
O B:HOH823 2.1 22.6 0.8
OE2 B:GLU554 2.1 28.3 1.0
O B:HOH1062 2.1 29.5 1.0
O B:HOH816 2.1 28.1 0.8
CD B:GLU554 3.2 24.2 1.0
MG B:MG703 3.3 32.2 0.8
OD2 B:ASP547 3.5 29.5 1.0
OE1 B:GLU554 3.9 26.7 1.0
OE2 B:GLU503 4.0 35.7 1.0
O B:HOH1145 4.0 60.0 1.0
O B:HOH1159 4.1 40.8 1.0
O B:HOH1077 4.2 47.1 1.0
O B:HOH968 4.2 31.0 1.0
CG B:GLU554 4.2 24.3 1.0
OE1 B:GLU503 4.3 30.2 1.0
O B:HOH1005 4.3 29.6 0.8
O B:HOH1117 4.3 34.8 0.7
CB B:GLU554 4.4 23.9 1.0
CD B:GLU503 4.6 31.8 1.0
O B:HOH1022 4.6 43.6 1.0
CG B:ASP547 4.7 28.6 1.0

Magnesium binding site 4 out of 4 in 9m5o

Go back to Magnesium Binding Sites List in 9m5o
Magnesium binding site 4 out of 4 in the Plasmodium Vivax Aspartyl-Trna Synthetase in Complex with Aspartyl Sulfamoyl Adenosine (Asp-Ams) Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Plasmodium Vivax Aspartyl-Trna Synthetase in Complex with Aspartyl Sulfamoyl Adenosine (Asp-Ams) Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg703

b:32.2
occ:0.85
 O B:HOH1117 2.1 34.8 0.7
O B:HOH1005 2.2 29.6 0.8
OE1 B:GLU554 2.3 26.7 1.0
OAY B:DSZ701 2.5 25.5 1.0
O B:HOH1062 2.6 29.5 1.0
O B:HOH823 2.7 22.6 0.8
OE2 B:GLU554 2.9 28.3 1.0
O B:HOH1195 2.9 57.3 1.0
CD B:GLU554 2.9 24.2 1.0
MG B:MG702 3.3 28.7 0.7
O B:HOH1165 3.5 41.0 0.8
SBE B:DSZ701 3.8 24.8 1.0
CB B:SER557 4.1 25.7 1.0
OG B:SER557 4.1 30.4 1.0
OAX B:DSZ701 4.2 23.4 1.0
O B:HOH1114 4.4 37.2 1.0
CG B:GLU554 4.4 24.3 1.0
O3' B:DSZ701 4.5 24.8 1.0
O B:HOH1172 4.6 57.9 1.0
O B:HOH1066 4.6 35.0 1.0
C3' B:DSZ701 4.6 20.8 1.0
OD2 B:ASP547 4.6 29.5 1.0
O B:HOH1206 4.7 31.3 1.0
NAT B:DSZ701 4.7 20.6 1.0
O5' B:DSZ701 4.8 22.6 1.0
O B:HOH921 4.9 28.0 0.9

Reference:

N.Ketprasit, C.W.Tai, V.K.Sharma, Y.Manickam, Y.Khandokar, W.Ye, C.Dogovski, D.H.Hilko, C.Morton, A.S.C.Braun, M.Leeming, S.Bagale, P.I.Pradeepkumar, S.Panjikar, S.A.Poulsen, M.D.W.Griffin, A.Sharma, L.Tilley, S.C.Xie. Natural Product-Mediated Reaction Hijacking Mechanism Validates Plasmodium Aspartyl-Trna Synthetase As An Antimalarial Drug Target To Be Published.
Page generated: Sat Aug 16 05:34:23 2025

Last articles

Mn in 1IGV
Mn in 1IG1
Mn in 1I74
Mn in 1I9A
Mn in 1I5B
Mn in 1I5A
Mn in 1I50
Mn in 1I19
Mn in 1I3H
Mn in 1I0H
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy