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

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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

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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 Jul 27 22:35:34 2023

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