Atomistry » Magnesium » PDB 8bux-8c0k » 8bzx
Atomistry »
  Magnesium »
    PDB 8bux-8c0k »
      8bzx »

Magnesium in PDB 8bzx: 1-Deoxy-D-Xylulose 5-Phosphate Synthase From Klebsiella Pneumoniae (Kpdxps),Co-Crystal with Thiamine Monophosphate Analog

Enzymatic activity of 1-Deoxy-D-Xylulose 5-Phosphate Synthase From Klebsiella Pneumoniae (Kpdxps),Co-Crystal with Thiamine Monophosphate Analog

All present enzymatic activity of 1-Deoxy-D-Xylulose 5-Phosphate Synthase From Klebsiella Pneumoniae (Kpdxps),Co-Crystal with Thiamine Monophosphate Analog:
2.2.1.7;

Protein crystallography data

The structure of 1-Deoxy-D-Xylulose 5-Phosphate Synthase From Klebsiella Pneumoniae (Kpdxps),Co-Crystal with Thiamine Monophosphate Analog, PDB code: 8bzx was solved by R.Hamid, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.79 / 2.05
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 119.249, 150.969, 142.145, 90, 90, 90
R / Rfree (%) 21.7 / 26.4

Magnesium Binding Sites:

The binding sites of Magnesium atom in the 1-Deoxy-D-Xylulose 5-Phosphate Synthase From Klebsiella Pneumoniae (Kpdxps),Co-Crystal with Thiamine Monophosphate Analog (pdb code 8bzx). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the 1-Deoxy-D-Xylulose 5-Phosphate Synthase From Klebsiella Pneumoniae (Kpdxps),Co-Crystal with Thiamine Monophosphate Analog, PDB code: 8bzx:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 8bzx

Go back to Magnesium Binding Sites List in 8bzx
Magnesium binding site 1 out of 3 in the 1-Deoxy-D-Xylulose 5-Phosphate Synthase From Klebsiella Pneumoniae (Kpdxps),Co-Crystal with Thiamine Monophosphate Analog


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of 1-Deoxy-D-Xylulose 5-Phosphate Synthase From Klebsiella Pneumoniae (Kpdxps),Co-Crystal with Thiamine Monophosphate Analog within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg602

b:59.2
occ:1.00
 O23 A:SW6601 2.0 50.8 1.0
OD1 A:ASN181 2.2 63.2 1.0
OD1 A:ASP152 2.5 55.8 1.0
O A:MET183 2.6 91.8 1.0
O24 A:SW6601 3.0 47.4 1.0
CG A:ASN181 3.0 63.0 1.0
P21 A:SW6601 3.0 48.4 1.0
ND2 A:ASN181 3.1 61.3 1.0
CG A:ASP152 3.5 57.9 1.0
C A:MET183 3.5 95.6 1.0
CA A:SER184 3.7 77.7 1.0
O20 A:SW6601 3.8 55.8 1.0
OD2 A:ASP152 3.9 64.0 1.0
N A:SER184 4.0 88.3 1.0
O A:HOH746 4.0 47.1 1.0
O A:SER184 4.0 77.2 1.0
N A:ASP152 4.2 44.4 1.0
N A:GLY153 4.2 50.4 1.0
O22 A:SW6601 4.3 43.3 1.0
C A:SER184 4.4 79.1 1.0
CB A:ASN181 4.4 61.7 1.0
O A:ASN179 4.5 47.2 1.0
N A:ASN181 4.5 56.6 1.0
N A:MET183 4.6 93.4 1.0
NZ A:LYS250 4.6 62.3 1.0
CA A:MET183 4.7 94.8 1.0
CB A:ASP152 4.7 51.9 1.0
CA A:GLY151 4.8 43.6 1.0
CA A:ASN181 4.9 60.1 1.0
C A:GLY151 4.9 43.2 1.0
CA A:ASP152 4.9 47.8 1.0
CB A:SER184 4.9 71.8 1.0

Magnesium binding site 2 out of 3 in 8bzx

Go back to Magnesium Binding Sites List in 8bzx
Magnesium binding site 2 out of 3 in the 1-Deoxy-D-Xylulose 5-Phosphate Synthase From Klebsiella Pneumoniae (Kpdxps),Co-Crystal with Thiamine Monophosphate Analog


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of 1-Deoxy-D-Xylulose 5-Phosphate Synthase From Klebsiella Pneumoniae (Kpdxps),Co-Crystal with Thiamine Monophosphate Analog within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg602

b:46.9
occ:1.00
 O24 B:SW6601 2.0 42.2 1.0
O B:MET183 2.2 48.6 1.0
OD1 B:ASN181 2.3 47.2 1.0
OD1 B:ASP152 2.8 44.3 1.0
CG B:ASN181 2.9 48.9 1.0
ND2 B:ASN181 2.9 48.8 1.0
P21 B:SW6601 3.0 43.9 1.0
O23 B:SW6601 3.0 40.4 1.0
C B:MET183 3.2 52.9 1.0
O B:SER184 3.7 49.7 1.0
O20 B:SW6601 3.8 47.3 1.0
CG B:ASP152 3.8 46.2 1.0
O B:HOH794 4.0 41.2 1.0
CA B:MET183 4.0 54.6 1.0
N B:SER184 4.1 54.8 1.0
CB B:MET183 4.1 53.4 1.0
N B:MET183 4.2 51.7 1.0
CA B:SER184 4.2 51.9 1.0
O22 B:SW6601 4.3 37.6 1.0
OD2 B:ASP152 4.3 46.4 1.0
CB B:ASN181 4.4 49.4 1.0
C B:SER184 4.4 50.7 1.0
N B:ASP152 4.6 41.8 1.0
N B:GLY153 4.6 41.2 1.0
N B:ASN181 4.8 46.2 1.0
NZ B:LYS250 4.8 57.1 1.0
O B:ASN179 4.8 42.7 1.0
CA B:ASN181 5.0 47.8 1.0

Magnesium binding site 3 out of 3 in 8bzx

Go back to Magnesium Binding Sites List in 8bzx
Magnesium binding site 3 out of 3 in the 1-Deoxy-D-Xylulose 5-Phosphate Synthase From Klebsiella Pneumoniae (Kpdxps),Co-Crystal with Thiamine Monophosphate Analog


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of 1-Deoxy-D-Xylulose 5-Phosphate Synthase From Klebsiella Pneumoniae (Kpdxps),Co-Crystal with Thiamine Monophosphate Analog within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg603

b:59.6
occ:1.00
 ND2 B:ASN215 2.5 50.5 1.0
CG B:ASN215 3.3 47.3 1.0
OD1 B:ASN215 3.5 44.8 1.0
O B:TYR216 4.1 46.8 1.0
OE1 B:GLU210 4.4 64.2 1.0
N B:TYR216 4.5 45.2 1.0
CB B:ASN215 4.5 43.5 1.0
CA B:ASN215 4.6 47.0 1.0
OE2 B:GLU210 4.6 62.4 1.0
C B:ASN215 4.9 46.4 1.0
CD B:GLU210 5.0 59.7 1.0

Reference:

A.H.Y.Chan, T.C.S.Ho, R.Irfan, R.A.A.Hamid, E.S.Rudge, A.Iqbal, A.Turner, A.K.H.Hirsch, F.J.Leeper. Design of Thiamine Analogues For Inhibition of Thiamine Diphosphate (Thdp)-Dependent Enzymes: Systematic Investigation Through Scaffold-Hopping and C2-Functionalisation. Bioorg.Chem. V. 138 06602 2023.
ISSN: ISSN 0045-2068
PubMed: 37201323
DOI: 10.1016/J.BIOORG.2023.106602
Page generated: Thu Oct 3 19:59:29 2024

Last articles

Fe in 2YXO
Fe in 2YRS
Fe in 2YXC
Fe in 2YNM
Fe in 2YVJ
Fe in 2YP1
Fe in 2YU2
Fe in 2YU1
Fe in 2YQB
Fe in 2YOO
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy