Atomistry » Magnesium » PDB 5iwa-5j2m » 5iwy
Atomistry »
  Magnesium »
    PDB 5iwa-5j2m »
      5iwy »

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

Go back to Magnesium Binding Sites List in 5iwy
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

Go back to Magnesium Binding Sites List in 5iwy
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

Go back to Magnesium Binding Sites List in 5iwy
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

Go back to Magnesium Binding Sites List in 5iwy
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

Go back to Magnesium Binding Sites List in 5iwy
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

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy