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Magnesium in PDB 5iwy: Crystal Structure of 2-C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase From Bacillus Subtitis Complexed with Cmp and MG2+

Enzymatic activity of Crystal Structure of 2-C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase From Bacillus Subtitis Complexed with Cmp and MG2+

All present enzymatic activity of Crystal Structure of 2-C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase From Bacillus Subtitis Complexed with Cmp and MG2+:
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 Complexed with Cmp and MG2+, PDB code: 5iwy 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) 29.21 / 1.99
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 57.057, 89.460, 87.986, 90.00, 103.80, 90.00
R / Rfree (%) 17.4 / 21.9

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 Complexed with Cmp and MG2+ (pdb code 5iwy). 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 Complexed with Cmp and MG2+, PDB code: 5iwy:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 5iwy

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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 Complexed with Cmp and MG2+


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 Complexed with Cmp and MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg201

b:14.5
occ:1.00
 O A:HOH331 1.9 32.8 1.0
OD2 A:ASP9 1.9 28.7 1.0
ND1 A:HIS43 2.0 23.4 1.0
NE2 A:HIS11 2.0 27.3 1.0
O A:HOH319 2.1 43.3 1.0
O A:HOH357 2.4 44.0 1.0
CE1 A:HIS43 2.9 27.3 1.0
CG A:ASP9 3.0 25.2 1.0
CD2 A:HIS11 3.0 25.1 1.0
CE1 A:HIS11 3.0 29.4 1.0
CG A:HIS43 3.1 22.6 1.0
OD1 A:ASP9 3.3 26.4 1.0
CB A:HIS43 3.5 21.9 1.0
NE2 A:HIS43 4.1 25.5 1.0
ND1 A:HIS11 4.1 30.6 1.0
CG A:HIS11 4.2 24.5 1.0
CD2 A:HIS43 4.2 25.1 1.0
O A:HOH301 4.2 33.6 1.0
CB A:ASP9 4.3 22.7 1.0
O A:HOH312 4.7 43.9 1.0
O A:HOH306 4.8 37.5 1.0
CA A:VAL40 5.0 22.1 1.0
O A:VAL10 5.0 25.7 1.0
CA A:HIS43 5.0 21.6 1.0

Magnesium binding site 2 out of 6 in 5iwy

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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 Complexed with Cmp and MG2+


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 Complexed with Cmp and MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg202

b:22.1
occ:1.00
 OD2 B:ASP9 1.9 29.3 1.0
NE2 B:HIS11 2.2 35.4 1.0
ND1 B:HIS43 2.2 29.6 1.0
O B:HOH328 2.2 44.5 1.0
O B:HOH341 2.4 44.6 1.0
O B:HOH307 2.6 36.4 1.0
CG B:ASP9 3.0 27.5 1.0
CE1 B:HIS11 3.1 37.6 1.0
CE1 B:HIS43 3.2 30.5 1.0
CG B:HIS43 3.2 26.9 1.0
CD2 B:HIS11 3.2 34.8 1.0
CB B:HIS43 3.5 24.9 1.0
OD1 B:ASP9 3.5 29.0 1.0
ND1 B:HIS11 4.2 35.8 1.0
NE2 B:HIS43 4.3 27.8 1.0
CB B:ASP9 4.3 25.3 1.0
CG B:HIS11 4.3 31.7 1.0
CD2 B:HIS43 4.3 27.9 1.0
O C:HOH301 4.4 31.7 1.0
O B:HOH334 4.5 51.8 1.0
O B:HOH330 4.6 41.3 1.0
CD1 B:ILE58 4.6 59.4 1.0
O B:VAL10 4.9 25.4 1.0
O1P C:C5P201 4.9 45.2 0.8
CA B:VAL40 5.0 27.6 1.0
CA B:HIS43 5.0 26.1 1.0

Magnesium binding site 3 out of 6 in 5iwy

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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 Complexed with Cmp and MG2+


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 Complexed with Cmp and MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg202

b:12.7
occ:1.00
 O C:HOH324 1.9 40.4 1.0
OD2 C:ASP9 1.9 28.5 1.0
O C:HOH331 2.0 29.9 1.0
ND1 C:HIS43 2.1 30.6 1.0
NE2 C:HIS11 2.1 33.1 1.0
CG C:ASP9 2.9 26.1 1.0
CE1 C:HIS43 3.0 30.8 1.0
CD2 C:HIS11 3.1 31.5 1.0
CE1 C:HIS11 3.1 33.5 1.0
OD1 C:ASP9 3.1 28.4 1.0
CG C:HIS43 3.1 28.7 1.0
CB C:HIS43 3.4 25.0 1.0
O A:HOH318 3.9 45.3 1.0
O C:HOH302 4.0 23.8 1.0
O A:HOH304 4.0 43.0 1.0
NE2 C:HIS43 4.2 28.8 1.0
ND1 C:HIS11 4.2 35.7 1.0
CG C:HIS11 4.2 32.2 1.0
CD2 C:HIS43 4.2 30.4 1.0
CB C:ASP9 4.2 22.1 1.0
O A:HOH352 4.5 45.7 1.0
CD1 C:ILE58 4.7 50.5 1.0
O C:HOH344 4.8 43.4 1.0
O A:HOH342 4.8 50.8 1.0
O C:VAL10 4.9 24.8 1.0
CA C:VAL40 4.9 24.6 1.0
CA C:HIS43 5.0 23.1 1.0

Magnesium binding site 4 out of 6 in 5iwy

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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 Complexed with Cmp and MG2+


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 Complexed with Cmp and MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg201

b:22.6
occ:1.00
 O D:HOH332 2.0 36.5 1.0
OD2 D:ASP9 2.0 30.4 1.0
O D:HOH308 2.2 52.1 1.0
NE2 D:HIS11 2.2 40.7 1.0
ND1 D:HIS43 2.3 32.1 1.0
O D:HOH339 2.4 43.2 1.0
CE1 D:HIS11 2.9 45.0 1.0
CG D:ASP9 3.1 30.8 1.0
CG D:HIS43 3.3 29.9 1.0
CE1 D:HIS43 3.3 32.0 1.0
CD2 D:HIS11 3.3 45.9 1.0
OD1 D:ASP9 3.4 29.3 1.0
CB D:HIS43 3.5 24.8 1.0
O D:HOH318 3.8 35.5 1.0
ND1 D:HIS11 4.1 44.5 1.0
CG D:HIS11 4.3 37.1 1.0
CB D:ASP9 4.4 26.4 1.0
NE2 D:HIS43 4.4 32.2 1.0
CD2 D:HIS43 4.4 34.5 1.0
O D:HOH317 4.7 44.7 1.0
O D:HOH301 4.7 42.9 1.0

Magnesium binding site 5 out of 6 in 5iwy

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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 Complexed with Cmp and MG2+


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 Complexed with Cmp and MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg201

b:34.5
occ:1.00
 O E:HOH323 2.1 46.2 1.0
OD2 E:ASP9 2.2 32.1 1.0
O E:HOH324 2.3 52.4 1.0
O E:HOH302 2.4 56.5 1.0
NE2 E:HIS11 2.4 42.8 1.0
ND1 E:HIS43 2.5 45.6 1.0
CG E:ASP9 3.0 32.9 1.0
OD1 E:ASP9 3.1 34.2 1.0
CE1 E:HIS11 3.2 47.1 1.0
CE1 E:HIS43 3.4 48.8 1.0
CG E:HIS43 3.4 41.6 1.0
CD2 E:HIS11 3.5 47.6 1.0
CB E:HIS43 3.7 33.7 1.0
O E:HOH322 4.0 52.5 1.0
ND1 E:HIS11 4.4 49.1 1.0
CB E:ASP9 4.4 28.3 1.0
NE2 E:HIS43 4.5 47.5 1.0
CD2 E:HIS43 4.5 45.9 1.0
CG E:HIS11 4.6 45.4 1.0
O F:HOH303 4.8 52.3 1.0

Magnesium binding site 6 out of 6 in 5iwy

Go back to Magnesium Binding Sites List in 5iwy
Magnesium binding site 6 out of 6 in the Crystal Structure of 2-C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase From Bacillus Subtitis Complexed with Cmp and MG2+


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 Complexed with Cmp and MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg202

b:24.8
occ:1.00
 O F:HOH310 2.1 30.9 1.0
OD2 F:ASP9 2.1 31.6 1.0
O F:HOH331 2.2 36.8 1.0
ND1 F:HIS43 2.2 38.5 1.0
O F:HOH332 2.2 35.6 1.0
NE2 F:HIS11 2.3 51.8 1.0
CE1 F:HIS11 2.9 48.5 1.0
CG F:ASP9 3.2 28.1 1.0
CE1 F:HIS43 3.2 38.5 1.0
CG F:HIS43 3.2 36.7 1.0
OD1 F:ASP9 3.5 30.0 1.0
CD2 F:HIS11 3.5 51.9 1.0
CB F:HIS43 3.5 27.4 1.0
O F:HOH301 3.8 35.1 1.0
ND1 F:HIS11 4.1 49.5 1.0
NE2 F:HIS43 4.3 36.8 1.0
CD2 F:HIS43 4.3 34.4 1.0
CG F:HIS11 4.4 47.3 1.0
O F:HOH305 4.5 47.5 1.0
CB F:ASP9 4.5 24.2 1.0
N F:HIS35 4.8 69.3 1.0
CB F:HIS35 4.8 76.0 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: Sun Sep 29 17:07:21 2024

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