Magnesium in PDB 8s65: 1-Deoxy-D-Xylulose 5-Phosphate Reductoisomerase (Dxr) As Target For Anti Toxoplasma Gondii Compounds: Crystal Structure, Biochemical Characterization and Biological Evaluation of Inhibitors

Enzymatic activity of 1-Deoxy-D-Xylulose 5-Phosphate Reductoisomerase (Dxr) As Target For Anti Toxoplasma Gondii Compounds: Crystal Structure, Biochemical Characterization and Biological Evaluation of Inhibitors

All present enzymatic activity of 1-Deoxy-D-Xylulose 5-Phosphate Reductoisomerase (Dxr) As Target For Anti Toxoplasma Gondii Compounds: Crystal Structure, Biochemical Characterization and Biological Evaluation of Inhibitors:
1.1.1.267;

Protein crystallography data

The structure of 1-Deoxy-D-Xylulose 5-Phosphate Reductoisomerase (Dxr) As Target For Anti Toxoplasma Gondii Compounds: Crystal Structure, Biochemical Characterization and Biological Evaluation of Inhibitors, PDB code: 8s65 was solved by F.Mazzone, A.Hoeppner, J.Reiners, V.Applegate, M.Abdullaziz, J.Gottstein, M.Wesemann, T.Kurz, S.H.Smits, K.Pfeffer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 66.50 / 2.56
Space group P 65
Cell size a, b, c (Å), α, β, γ (°) 159.524, 159.524, 75.873, 90, 90, 120
R / Rfree (%) 19.4 / 22.5

Other elements in 8s65:

The structure of 1-Deoxy-D-Xylulose 5-Phosphate Reductoisomerase (Dxr) As Target For Anti Toxoplasma Gondii Compounds: Crystal Structure, Biochemical Characterization and Biological Evaluation of Inhibitors also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the 1-Deoxy-D-Xylulose 5-Phosphate Reductoisomerase (Dxr) As Target For Anti Toxoplasma Gondii Compounds: Crystal Structure, Biochemical Characterization and Biological Evaluation of Inhibitors (pdb code 8s65). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the 1-Deoxy-D-Xylulose 5-Phosphate Reductoisomerase (Dxr) As Target For Anti Toxoplasma Gondii Compounds: Crystal Structure, Biochemical Characterization and Biological Evaluation of Inhibitors, PDB code: 8s65:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 8s65

Go back to Magnesium Binding Sites List in 8s65
Magnesium binding site 1 out of 4 in the 1-Deoxy-D-Xylulose 5-Phosphate Reductoisomerase (Dxr) As Target For Anti Toxoplasma Gondii Compounds: Crystal Structure, Biochemical Characterization and Biological Evaluation of Inhibitors


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 Reductoisomerase (Dxr) As Target For Anti Toxoplasma Gondii Compounds: Crystal Structure, Biochemical Characterization and Biological Evaluation of Inhibitors within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg504

b:54.8
occ:1.00
 O A:ILE55 2.5 75.2 1.0
O A:PHE75 2.7 55.4 1.0
O A:ARG76 2.8 56.7 1.0
HB2 A:ARG76 3.3 80.7 1.0
H A:ILE55 3.4 67.2 1.0
C A:ARG76 3.5 60.9 1.0
OE1 A:GLN78 3.5 101.6 1.0
HG3 A:GLN54 3.5 121.8 1.0
C A:ILE55 3.6 59.8 1.0
HG2 A:GLN54 3.7 121.8 1.0
HA A:PRO77 3.7 76.2 1.0
HB A:ILE55 3.9 58.0 1.0
C A:PHE75 3.9 55.4 1.0
HA A:VAL56 4.0 67.2 1.0
N A:ILE55 4.0 56.1 1.0
CG A:GLN54 4.1 101.6 1.0
HE22 A:GLN78 4.1 103.5 1.0
CB A:ARG76 4.1 67.4 1.0
N A:PRO77 4.2 56.6 1.0
CA A:ARG76 4.2 63.4 1.0
CA A:ILE55 4.3 56.4 1.0
CA A:PRO77 4.4 63.6 1.0
CD A:GLN78 4.5 90.2 1.0
N A:ARG76 4.5 62.6 1.0
CB A:ILE55 4.6 48.5 1.0
N A:VAL56 4.6 55.0 1.0
NE2 A:GLN78 4.6 86.4 1.0
HB3 A:PHE75 4.7 69.4 1.0
HB3 A:ARG76 4.8 80.7 1.0
CA A:VAL56 4.8 56.1 1.0
OE1 A:GLN54 4.8 86.6 1.0
HG2 A:ARG76 4.9 97.4 1.0
HG3 A:ARG76 4.9 97.4 1.0
HA A:GLN54 4.9 71.4 1.0
CD A:GLN54 4.9 104.5 1.0
CG A:ARG76 4.9 81.3 1.0
HA A:PHE75 4.9 73.8 1.0
HG12 A:VAL56 4.9 72.6 1.0
C A:GLN54 4.9 60.4 1.0
H A:GLN78 4.9 78.8 1.0

Magnesium binding site 2 out of 4 in 8s65

Go back to Magnesium Binding Sites List in 8s65
Magnesium binding site 2 out of 4 in the 1-Deoxy-D-Xylulose 5-Phosphate Reductoisomerase (Dxr) As Target For Anti Toxoplasma Gondii Compounds: Crystal Structure, Biochemical Characterization and Biological Evaluation of Inhibitors


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 Reductoisomerase (Dxr) As Target For Anti Toxoplasma Gondii Compounds: Crystal Structure, Biochemical Characterization and Biological Evaluation of Inhibitors within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg505

b:91.6
occ:1.00
 O A:GLU398 3.0 65.7 1.0
C A:GLU398 4.2 66.9 1.0
O A:ARG399 4.3 74.9 1.0
HA A:GLU398 4.7 78.5 1.0
C A:ARG399 4.8 61.9 1.0
OE2 A:GLU398 4.8 79.0 1.0
HA A:ARG399 4.8 76.2 1.0
HA3 A:GLY400 4.8 79.9 1.0

Magnesium binding site 3 out of 4 in 8s65

Go back to Magnesium Binding Sites List in 8s65
Magnesium binding site 3 out of 4 in the 1-Deoxy-D-Xylulose 5-Phosphate Reductoisomerase (Dxr) As Target For Anti Toxoplasma Gondii Compounds: Crystal Structure, Biochemical Characterization and Biological Evaluation of Inhibitors


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 Reductoisomerase (Dxr) As Target For Anti Toxoplasma Gondii Compounds: Crystal Structure, Biochemical Characterization and Biological Evaluation of Inhibitors within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg506

b:77.8
occ:1.00
 H A:GLY39 2.2 60.3 1.0
O2N A:NAP501 2.4 71.5 1.0
HB A:ILE38 2.5 68.8 1.0
H A:ILE38 2.5 74.4 1.0
HA3 A:GLY36 2.8 64.1 1.0
HB1 A:ALA131 2.8 71.0 1.0
N A:GLY39 3.0 50.4 1.0
N A:ILE38 3.1 62.1 1.0
O A:GLY33 3.3 56.6 1.0
CB A:ILE38 3.3 57.5 1.0
C A:GLY36 3.5 54.0 1.0
O A:ALA131 3.5 54.7 1.0
CA A:GLY36 3.5 53.5 1.0
CA A:ILE38 3.5 59.7 1.0
H4B A:NAP501 3.5 78.1 1.0
HB3 A:ALA131 3.6 71.0 1.0
H51N A:NAP501 3.6 95.7 1.0
N A:SER37 3.6 62.4 1.0
CB A:ALA131 3.6 59.3 1.0
H A:GLY36 3.6 63.7 1.0
O5B A:NAP501 3.7 67.5 1.0
H A:SER37 3.7 74.7 1.0
C A:ILE38 3.7 58.1 1.0
HG12 A:ILE38 3.7 77.7 1.0
PN A:NAP501 3.8 78.8 1.0
O A:GLY36 3.8 50.8 1.0
HA3 A:GLY39 3.9 66.9 1.0
C A:SER37 4.0 55.8 1.0
N A:GLY36 4.0 53.2 1.0
CG1 A:ILE38 4.0 64.9 1.0
CA A:GLY39 4.1 55.9 1.0
H52N A:NAP501 4.1 95.7 1.0
O3 A:NAP501 4.2 84.5 1.0
HB2 A:ALA131 4.2 71.0 1.0
C5D A:NAP501 4.2 79.8 1.0
HG13 A:ILE38 4.2 77.7 1.0
HA3 A:GLY33 4.3 67.3 1.0
HA2 A:GLY36 4.3 64.1 1.0
CA A:SER37 4.3 57.4 1.0
O1A A:NAP501 4.4 75.2 1.0
C4B A:NAP501 4.4 65.2 1.0
C A:ALA131 4.4 51.8 1.0
C A:GLY33 4.4 58.7 1.0
PA A:NAP501 4.4 69.6 1.0
HA A:ILE38 4.5 71.4 1.0
HB3 A:SER37 4.5 76.5 1.0
HG22 A:ILE38 4.5 65.8 1.0
CG2 A:ILE38 4.5 54.9 1.0
HA2 A:GLY39 4.5 66.9 1.0
C5B A:NAP501 4.5 68.1 1.0
O5D A:NAP501 4.6 90.0 1.0
CA A:ALA131 4.6 53.9 1.0
H51A A:NAP501 4.7 81.6 1.0
HG21 A:ILE38 4.8 65.8 1.0
H A:LYS40 4.8 61.1 1.0
O1N A:NAP501 4.8 74.8 1.0
CA A:GLY33 4.9 56.2 1.0
CB A:SER37 4.9 63.9 1.0
HA A:ALA131 4.9 64.5 1.0
O A:ILE38 4.9 54.9 1.0
O A:SER37 4.9 51.4 1.0

Magnesium binding site 4 out of 4 in 8s65

Go back to Magnesium Binding Sites List in 8s65
Magnesium binding site 4 out of 4 in the 1-Deoxy-D-Xylulose 5-Phosphate Reductoisomerase (Dxr) As Target For Anti Toxoplasma Gondii Compounds: Crystal Structure, Biochemical Characterization and Biological Evaluation of Inhibitors


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of 1-Deoxy-D-Xylulose 5-Phosphate Reductoisomerase (Dxr) As Target For Anti Toxoplasma Gondii Compounds: Crystal Structure, Biochemical Characterization and Biological Evaluation of Inhibitors within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg504

b:69.3
occ:1.00
 O B:PHE75 2.7 62.0 1.0
O B:ARG76 2.9 56.0 1.0
O B:ILE55 3.0 71.1 1.0
HB2 B:ARG76 3.3 75.2 1.0
OE1 B:GLN54 3.4 119.4 1.0
C B:ARG76 3.5 53.5 1.0
H B:ILE55 3.6 75.3 1.0
HB3 B:ARG76 3.8 75.2 1.0
CB B:ARG76 3.9 62.8 1.0
C B:PHE75 3.9 59.9 1.0
C B:ILE55 4.0 65.6 1.0
HA B:PRO77 4.1 74.4 1.0
OE1 B:GLN78 4.1 120.9 1.0
HB B:ILE55 4.1 63.8 1.0
N B:ILE55 4.2 62.9 1.0
CA B:ARG76 4.2 67.3 1.0
N B:PRO77 4.3 47.2 1.0
HG3 B:GLN78 4.3 111.7 1.0
HA B:VAL56 4.4 79.1 1.0
HB3 B:GLN54 4.5 81.8 1.0
CD B:GLN54 4.5 103.5 1.0
N B:ARG76 4.6 68.3 1.0
NE2 B:GLN78 4.6 108.9 1.0
CA B:ILE55 4.6 62.9 1.0
CA B:PRO77 4.6 62.2 1.0
CD B:GLN78 4.6 115.6 1.0
HE21 B:GLN78 4.6 130.5 1.0
HE22 B:GLN78 4.8 130.5 1.0
H B:GLN78 4.8 74.4 1.0
CB B:ILE55 4.8 53.3 1.0
HB3 B:PHE75 4.9 79.4 1.0
HA B:GLN54 4.9 79.3 1.0
HA B:PHE75 4.9 74.3 1.0

Reference:

F.Mazzone, A.Hoeppner, J.Reiners, C.G.W.Gertzen, V.Applegate, M.A.Abdullaziz, J.Gottstein, D.Degrandi, M.Wesemann, T.Kurz, S.H.Smits, K.Pfeffer. 1-Deoxy-D-Xylulose 5-Phosphate Reductoisomerase (Dxr) As Target For Anti Toxoplasma Gondii Agents: Crystal Structure, Biochemical Characterisation and Biological Evaluation of Inhibitors. Biochem.J. 2024.
ISSN: ESSN 1470-8728
PubMed: 39105673
DOI: 10.1042/BCJ20240110
Page generated: Fri Oct 4 18:04:04 2024

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