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Magnesium in PDB 5iwx: Crystal Structure of 2-C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase From Bacillus Subtitis

Enzymatic activity of Crystal Structure of 2-C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase From Bacillus Subtitis

All present enzymatic activity of Crystal Structure of 2-C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase From Bacillus Subtitis:
4.6.1.12;

Protein crystallography data

The structure of Crystal Structure of 2-C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase From Bacillus Subtitis, PDB code: 5iwx was solved by Z.C.Liu, Y.Jin, G.G.Wang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.05 / 1.99
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 56.964, 89.295, 84.708, 90.00, 100.85, 90.00
R / Rfree (%) 18.1 / 23.1

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of 2-C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase From Bacillus Subtitis (pdb code 5iwx). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Crystal Structure of 2-C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase From Bacillus Subtitis, PDB code: 5iwx:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 5iwx

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Magnesium binding site 1 out of 6 in the Crystal Structure of 2-C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase From Bacillus Subtitis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of 2-C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase From Bacillus Subtitis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg201

b:27.8
occ:1.00
 O A:HOH306 2.0 35.7 1.0
OD2 A:ASP9 2.1 33.3 1.0
ND1 A:HIS43 2.4 28.5 1.0
NE2 A:HIS11 2.5 37.0 1.0
CG A:ASP9 3.1 34.6 1.0
CE1 A:HIS11 3.3 46.8 1.0
CE1 A:HIS43 3.3 30.4 1.0
OD1 A:ASP9 3.4 33.8 1.0
CG A:HIS43 3.4 26.1 1.0
CD2 A:HIS11 3.6 38.4 1.0
CB A:HIS43 3.6 22.5 1.0
NE2 A:HIS43 4.5 30.3 1.0
ND1 A:HIS11 4.5 46.9 1.0
CD1 A:ILE58 4.5 42.4 1.0
CD2 A:HIS43 4.5 28.6 1.0
CB A:ASP9 4.5 31.4 1.0
CG A:HIS11 4.7 40.9 1.0
O A:HOH342 4.8 34.6 1.0

Magnesium binding site 2 out of 6 in 5iwx

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Magnesium binding site 2 out of 6 in the Crystal Structure of 2-C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase From Bacillus Subtitis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of 2-C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase From Bacillus Subtitis within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg201

b:40.0
occ:1.00
 O B:HOH306 1.8 39.9 1.0
OD2 B:ASP9 2.0 39.4 1.0
O B:HOH326 2.2 43.2 1.0
NE2 B:HIS11 2.2 45.2 1.0
ND1 B:HIS43 2.4 33.2 1.0
CE1 B:HIS11 2.8 47.4 1.0
CG B:ASP9 3.1 37.5 1.0
CD2 B:HIS11 3.3 46.7 1.0
CG B:HIS43 3.4 30.5 1.0
CE1 B:HIS43 3.4 32.0 1.0
CB B:HIS43 3.6 27.3 1.0
OD1 B:ASP9 3.6 39.6 1.0
ND1 B:HIS11 4.0 51.0 1.0
CG B:HIS11 4.3 49.3 1.0
CB B:ASP9 4.4 36.4 1.0
NE2 B:HIS43 4.5 36.5 1.0
CD2 B:HIS43 4.5 32.3 1.0
CD1 B:ILE58 4.5 54.9 1.0

Magnesium binding site 3 out of 6 in 5iwx

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Magnesium binding site 3 out of 6 in the Crystal Structure of 2-C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase From Bacillus Subtitis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of 2-C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase From Bacillus Subtitis within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg201

b:39.9
occ:1.00
 OD2 C:ASP9 2.1 37.2 1.0
O C:HOH337 2.2 46.8 1.0
O C:HOH304 2.3 42.1 1.0
ND1 C:HIS43 2.3 38.7 1.0
NE2 C:HIS11 2.4 50.6 1.0
CG C:ASP9 3.2 36.7 1.0
CE1 C:HIS43 3.2 39.2 1.0
CE1 C:HIS11 3.2 52.6 1.0
CG C:HIS43 3.4 33.4 1.0
CD2 C:HIS11 3.4 45.8 1.0
OD1 C:ASP9 3.5 36.7 1.0
CB C:HIS43 3.8 29.5 1.0
ND1 C:HIS11 4.3 51.1 1.0
NE2 C:HIS43 4.4 37.4 1.0
CG C:HIS11 4.5 48.0 1.0
CD1 C:ILE58 4.5 51.7 1.0
CD2 C:HIS43 4.5 34.6 1.0
CB C:ASP9 4.5 35.3 1.0

Magnesium binding site 4 out of 6 in 5iwx

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Magnesium binding site 4 out of 6 in the Crystal Structure of 2-C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase From Bacillus Subtitis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of 2-C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase From Bacillus Subtitis within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg201

b:27.6
occ:1.00
 OD2 D:ASP9 2.0 35.0 1.0
O D:HOH336 2.0 52.3 1.0
O D:HOH332 2.1 38.0 1.0
ND1 D:HIS43 2.3 37.8 1.0
NE2 D:HIS11 2.3 47.4 1.0
CG D:ASP9 3.1 34.9 1.0
CE1 D:HIS11 3.1 54.0 1.0
CE1 D:HIS43 3.1 41.3 1.0
CG D:HIS43 3.3 34.9 1.0
CD2 D:HIS11 3.3 47.0 1.0
OD1 D:ASP9 3.5 39.5 1.0
CB D:HIS43 3.6 29.0 1.0
O D:HOH304 3.8 48.7 1.0
ND1 D:HIS11 4.2 52.2 1.0
NE2 D:HIS43 4.3 42.1 1.0
CG D:HIS11 4.3 44.3 1.0
CD2 D:HIS43 4.4 38.9 1.0
CB D:ASP9 4.4 29.4 1.0

Magnesium binding site 5 out of 6 in 5iwx

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Magnesium binding site 5 out of 6 in the Crystal Structure of 2-C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase From Bacillus Subtitis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structure of 2-C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase From Bacillus Subtitis within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg201

b:27.0
occ:1.00
 O E:HOH332 1.8 39.6 1.0
OD2 E:ASP9 2.1 32.6 1.0
NE2 E:HIS11 2.2 45.3 1.0
O E:HOH302 2.2 41.2 1.0
O E:HOH340 2.4 51.7 1.0
ND1 E:HIS43 2.5 36.4 1.0
CE1 E:HIS11 2.8 48.3 1.0
CG E:ASP9 3.1 32.4 1.0
OD1 E:ASP9 3.3 30.9 1.0
CD2 E:HIS11 3.3 47.7 1.0
CG E:HIS43 3.4 34.2 1.0
CE1 E:HIS43 3.4 38.0 1.0
CB E:HIS43 3.6 25.9 1.0
ND1 E:HIS11 4.0 48.2 1.0
CG E:HIS11 4.3 41.6 1.0
CB E:ASP9 4.4 30.6 1.0
NE2 E:HIS43 4.6 40.0 1.0
CD2 E:HIS43 4.6 35.9 1.0
CA E:VAL40 4.9 22.6 1.0

Magnesium binding site 6 out of 6 in 5iwx

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Magnesium binding site 6 out of 6 in the Crystal Structure of 2-C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase From Bacillus Subtitis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Crystal Structure of 2-C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase From Bacillus Subtitis within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg201

b:32.2
occ:1.00
 OD2 F:ASP9 2.2 33.2 1.0
O F:HOH332 2.2 42.6 1.0
O F:HOH334 2.2 43.9 1.0
NE2 F:HIS11 2.3 44.3 1.0
ND1 F:HIS43 2.3 46.8 1.0
O F:HOH303 2.6 39.4 1.0
CE1 F:HIS11 3.1 45.2 1.0
CG F:ASP9 3.1 31.6 1.0
CE1 F:HIS43 3.2 43.5 1.0
CG F:HIS43 3.3 40.9 1.0
OD1 F:ASP9 3.4 35.1 1.0
CD2 F:HIS11 3.4 43.4 1.0
CB F:HIS43 3.6 30.7 1.0
NE2 F:HIS43 4.3 45.9 1.0
ND1 F:HIS11 4.3 44.6 1.0
CD2 F:HIS43 4.3 43.8 1.0
CG F:HIS11 4.5 40.8 1.0
CB F:ASP9 4.5 28.0 1.0
CB F:HIS35 4.8 70.3 1.0
N F:HIS35 4.8 59.8 1.0

Reference:

Z.C.Liu, Y.Jin, W.F.Liu, Y.Tao, G.G.Wang. Crystal Structure of Ispf From Bacillus Subtilis and Absence of Protein Complex Assembly Among Ispd/Ispe/Ispf Enzymes in the Mep Pathway. Biosci. Rep. 2018.
ISSN: ISSN 1573-4935
PubMed: 29335298
DOI: 10.1042/BSR20171370
Page generated: Tue Aug 12 11:54:44 2025

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