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Magnesium in PDB 2o1s: 1-Deoxy-D-Xylulose 5-Phosphate Synthase (Dxs) From Escherichia Coli

Enzymatic activity of 1-Deoxy-D-Xylulose 5-Phosphate Synthase (Dxs) From Escherichia Coli

All present enzymatic activity of 1-Deoxy-D-Xylulose 5-Phosphate Synthase (Dxs) From Escherichia Coli:
2.2.1.7;

Protein crystallography data

The structure of 1-Deoxy-D-Xylulose 5-Phosphate Synthase (Dxs) From Escherichia Coli, PDB code: 2o1s was solved by S.Xiang, G.Usunow, G.Lange, M.Busch, L.Tong, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 2.40
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 86.787, 171.154, 94.799, 90.00, 107.25, 90.00
R / Rfree (%) 19.1 / 23.4

Other elements in 2o1s:

The structure of 1-Deoxy-D-Xylulose 5-Phosphate Synthase (Dxs) From Escherichia Coli also contains other interesting chemical elements:

Potassium (K) 4 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the 1-Deoxy-D-Xylulose 5-Phosphate Synthase (Dxs) From Escherichia Coli (pdb code 2o1s). 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 Synthase (Dxs) From Escherichia Coli, PDB code: 2o1s:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 2o1s

Go back to Magnesium Binding Sites List in 2o1s
Magnesium binding site 1 out of 4 in the 1-Deoxy-D-Xylulose 5-Phosphate Synthase (Dxs) From Escherichia Coli


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 (Dxs) From Escherichia Coli within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1001

b:10.0
occ:1.00
 O23 A:TDP3001 2.1 13.6 1.0
O12 A:TDP3001 2.1 15.1 1.0
OD1 A:ASN181 2.2 12.4 1.0
OD2 A:ASP152 2.3 11.4 1.0
O A:HOH3137 2.4 16.3 1.0
O A:HOH3138 2.5 23.6 1.0
CG A:ASN181 3.0 15.6 1.0
P2 A:TDP3001 3.1 11.8 1.0
CG A:ASP152 3.2 9.5 1.0
O11 A:TDP3001 3.3 14.1 1.0
P1 A:TDP3001 3.3 10.6 1.0
ND2 A:ASN181 3.3 13.7 1.0
OD1 A:ASP152 3.5 12.3 1.0
N A:ASP152 4.2 8.9 1.0
O5G A:TDP3001 4.2 14.7 1.0
NZ A:LYS284 4.2 36.9 1.0
O A:HOH3108 4.2 36.4 1.0
O22 A:TDP3001 4.2 14.8 1.0
O21 A:TDP3001 4.3 15.5 1.0
N A:ASN181 4.3 13.6 1.0
O A:ASN179 4.3 9.8 1.0
CE A:LYS284 4.3 35.7 1.0
O13 A:TDP3001 4.3 15.4 1.0
N A:GLY153 4.3 6.8 1.0
O A:HOH3100 4.3 13.7 1.0
CB A:ASN181 4.4 15.6 1.0
CB A:ASP152 4.5 8.0 1.0
CA A:ASN181 4.7 16.6 1.0
C A:ASN181 4.8 19.1 1.0
CA A:ASP152 4.8 8.4 1.0
CA A:GLY151 4.9 8.3 1.0
C A:GLY151 5.0 9.4 1.0

Magnesium binding site 2 out of 4 in 2o1s

Go back to Magnesium Binding Sites List in 2o1s
Magnesium binding site 2 out of 4 in the 1-Deoxy-D-Xylulose 5-Phosphate Synthase (Dxs) From Escherichia Coli


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 (Dxs) From Escherichia Coli within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1002

b:48.6
occ:1.00
 O2 B:DPO4001 2.5 55.5 1.0
OD1 B:ASP152 2.5 29.4 1.0
O B:HOH4130 2.5 39.5 1.0
O7 B:DPO4001 2.7 50.7 1.0
OD1 B:ASN181 2.8 28.4 1.0
O4 B:DPO4001 3.1 53.3 1.0
CG B:ASN181 3.2 29.4 1.0
P1 B:DPO4001 3.2 55.1 1.0
O B:ASN179 3.3 22.1 1.0
P2 B:DPO4001 3.4 50.4 1.0
ND2 B:ASN181 3.4 28.0 1.0
CG B:ASP152 3.6 26.5 1.0
N B:ASP152 3.6 20.9 1.0
O3 B:DPO4001 3.7 56.2 1.0
CA B:GLY151 3.8 18.6 1.0
O6 B:DPO4001 4.0 51.0 1.0
OD2 B:ASP152 4.1 26.9 1.0
C B:GLY151 4.1 19.3 1.0
N B:ASN181 4.3 25.8 1.0
ND2 B:ASN179 4.3 23.6 1.0
CB B:ASN181 4.3 27.5 1.0
C B:ASN179 4.6 20.7 1.0
CA B:ASP152 4.6 22.6 1.0
CB B:ASP152 4.6 24.5 1.0
N B:GLY153 4.6 20.4 1.0
O1 B:DPO4001 4.7 55.8 1.0
O5 B:DPO4001 4.8 50.2 1.0
CA B:ASN181 4.9 27.9 1.0
CG B:ASN179 4.9 23.7 1.0

Magnesium binding site 3 out of 4 in 2o1s

Go back to Magnesium Binding Sites List in 2o1s
Magnesium binding site 3 out of 4 in the 1-Deoxy-D-Xylulose 5-Phosphate Synthase (Dxs) From Escherichia Coli


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 (Dxs) From Escherichia Coli within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg1003

b:26.6
occ:1.00
 O12 C:TDP3002 2.3 10.5 1.0
OD1 C:ASN181 2.3 2.0 1.0
O23 C:TDP3002 2.3 13.0 1.0
OD1 C:ASP152 2.4 12.0 1.0
OD2 C:ASP152 2.7 9.6 1.0
CG C:ASP152 2.9 11.0 1.0
O C:HOH3121 2.9 10.2 1.0
CG C:ASN181 3.4 7.2 1.0
NZ C:LYS284 3.5 30.1 1.0
P2 C:TDP3002 3.6 8.4 1.0
P1 C:TDP3002 3.7 11.3 1.0
CE C:LYS284 3.8 30.3 1.0
ND2 C:ASN181 3.9 1.4 1.0
O11 C:TDP3002 4.1 12.6 1.0
N C:GLY153 4.2 10.7 1.0
O22 C:TDP3002 4.3 14.2 1.0
O5G C:TDP3002 4.3 13.5 1.0
CB C:ASP152 4.3 10.4 1.0
C C:GLU182 4.5 32.1 1.0
N C:ASN181 4.5 13.4 1.0
N C:ASP152 4.6 8.8 1.0
C C:ASN181 4.6 19.1 1.0
N C:GLU182 4.7 24.2 1.0
CB C:ASN181 4.7 11.2 1.0
O13 C:TDP3002 4.8 13.1 1.0
CA C:ASP152 4.9 10.9 1.0
CA C:ASN181 4.9 16.0 1.0
CA C:GLY153 4.9 10.3 1.0
O21 C:TDP3002 4.9 15.2 1.0
C C:ASP152 4.9 11.2 1.0
O C:ASN181 4.9 19.7 1.0

Magnesium binding site 4 out of 4 in 2o1s

Go back to Magnesium Binding Sites List in 2o1s
Magnesium binding site 4 out of 4 in the 1-Deoxy-D-Xylulose 5-Phosphate Synthase (Dxs) From Escherichia Coli


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 Synthase (Dxs) From Escherichia Coli within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg1004

b:61.3
occ:1.00
 O2 D:DPO4002 2.3 53.8 1.0
OD2 D:ASP152 2.4 31.1 1.0
OD1 D:ASP152 2.5 30.4 1.0
O D:HOH4113 2.6 31.2 1.0
CG D:ASP152 2.7 28.9 1.0
O7 D:DPO4002 2.8 51.1 1.0
CB D:ASN181 2.9 31.4 1.0
OD1 D:ASN181 3.1 29.0 1.0
CG D:ASN181 3.2 30.7 1.0
N D:ASN181 3.7 29.0 1.0
P1 D:DPO4002 3.7 53.8 1.0
N D:ASP152 3.9 24.1 1.0
CA D:ASN181 3.9 31.1 1.0
P2 D:DPO4002 3.9 51.6 1.0
O4 D:DPO4002 4.0 53.5 1.0
CB D:ASP152 4.1 27.5 1.0
O D:ASN179 4.1 20.6 1.0
ND2 D:ASN181 4.4 30.4 1.0
O3 D:DPO4002 4.4 54.3 1.0
O D:ASN181 4.5 31.3 1.0
CA D:ASP152 4.5 25.6 1.0
N D:GLY153 4.6 23.6 1.0
C D:ASP180 4.7 26.6 1.0
C D:ASN181 4.7 30.9 1.0
C D:GLY151 4.8 23.4 1.0
O1 D:DPO4002 4.8 54.5 1.0
CA D:GLY151 4.8 22.0 1.0
O5 D:DPO4002 5.0 50.9 1.0

Reference:

S.Xiang, G.Usunow, G.Lange, M.Busch, L.Tong. Crystal Structure of 1-Deoxy-D-Xylulose 5-Phosphate Synthase, A Crucial Enzyme For Isoprenoids Biosynthesis. J.Biol.Chem. V. 282 2676 2007.
ISSN: ISSN 0021-9258
PubMed: 17135236
DOI: 10.1074/JBC.M610235200
Page generated: Wed Aug 14 01:00:06 2024

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