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Magnesium in PDB 5b8f: X-Ray Crystal Structure of A 2-C-Methyl-D-Erythritol 2,4- Cyclodiphosphate Synthase From Pseudomonas Aeruginosa

Enzymatic activity of X-Ray Crystal Structure of A 2-C-Methyl-D-Erythritol 2,4- Cyclodiphosphate Synthase From Pseudomonas Aeruginosa

All present enzymatic activity of X-Ray Crystal Structure of A 2-C-Methyl-D-Erythritol 2,4- Cyclodiphosphate Synthase From Pseudomonas Aeruginosa:
4.6.1.12;

Protein crystallography data

The structure of X-Ray Crystal Structure of A 2-C-Methyl-D-Erythritol 2,4- Cyclodiphosphate Synthase From Pseudomonas Aeruginosa, PDB code: 5b8f was solved by Seattle Structural Genomics Center For Infectious Disease (Ssgcid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 36.98 / 1.45
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 80.560, 100.210, 54.810, 90.00, 90.00, 90.00
R / Rfree (%) 13.8 / 16.9

Magnesium Binding Sites:

The binding sites of Magnesium atom in the X-Ray Crystal Structure of A 2-C-Methyl-D-Erythritol 2,4- Cyclodiphosphate Synthase From Pseudomonas Aeruginosa (pdb code 5b8f). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the X-Ray Crystal Structure of A 2-C-Methyl-D-Erythritol 2,4- Cyclodiphosphate Synthase From Pseudomonas Aeruginosa, PDB code: 5b8f:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 5b8f

Go back to Magnesium Binding Sites List in 5b8f
Magnesium binding site 1 out of 3 in the X-Ray Crystal Structure of A 2-C-Methyl-D-Erythritol 2,4- Cyclodiphosphate Synthase From Pseudomonas Aeruginosa


Mono view


Stereo pair view

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

b:20.9
occ:1.00
 OD2 A:ASP8 2.1 17.3 0.6
NE2 A:HIS10 2.1 16.4 0.3
CD2 A:HIS42 2.2 16.5 0.4
ND1 A:HIS42 2.2 14.1 0.6
NE2 A:HIS10 2.3 24.4 0.7
NE2 A:HIS42 2.6 16.9 0.4
CG A:HIS42 2.6 15.7 0.4
CG A:ASP8 2.9 15.8 0.6
CE1 A:HIS10 3.0 16.5 0.3
OD1 A:ASP8 3.1 17.0 0.6
CE1 A:HIS42 3.1 17.2 0.4
ND1 A:HIS42 3.1 17.4 0.4
CE1 A:HIS42 3.1 13.9 0.6
CG A:HIS42 3.2 12.0 0.6
CD2 A:HIS10 3.2 16.4 0.3
CD2 A:HIS10 3.3 23.2 0.7
CE1 A:HIS10 3.3 24.4 0.7
CB A:HIS42 3.5 13.1 0.4
CB A:HIS42 3.5 10.9 0.6
ND1 A:HIS10 4.2 16.1 0.3
NE2 A:HIS42 4.2 12.9 0.6
CB A:ASP8 4.2 12.6 0.4
CB A:ASP8 4.3 13.2 0.6
CD2 A:HIS42 4.3 13.0 0.6
CG A:HIS10 4.3 15.8 0.3
ND1 A:HIS10 4.3 23.4 0.7
CG A:HIS10 4.4 21.2 0.7
CG A:ASP8 4.4 13.6 0.4
OD1 A:ASP8 4.5 15.4 0.4
O C:HOH457 4.5 23.0 1.0
O A:HOH414 4.5 33.7 1.0
CA A:HIS42 4.9 11.3 0.4
O A:HOH473 4.9 30.6 1.0
CA A:VAL39 5.0 11.7 0.4
O C:HOH437 5.0 30.6 1.0
CA A:HIS42 5.0 10.4 0.6

Magnesium binding site 2 out of 3 in 5b8f

Go back to Magnesium Binding Sites List in 5b8f
Magnesium binding site 2 out of 3 in the X-Ray Crystal Structure of A 2-C-Methyl-D-Erythritol 2,4- Cyclodiphosphate Synthase From Pseudomonas Aeruginosa


Mono view


Stereo pair view

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

b:24.9
occ:1.00
 O B:HOH491 1.9 36.0 1.0
OD2 B:ASP8 2.0 17.7 1.0
ND1 B:HIS42 2.1 13.8 0.6
NE2 B:HIS10 2.2 24.5 0.3
NE2 B:HIS10 2.2 25.4 0.7
CD2 B:HIS42 2.3 16.3 0.4
CG B:HIS42 2.7 14.4 0.4
NE2 B:HIS42 2.8 16.6 0.4
CG B:ASP8 2.9 16.0 1.0
CE1 B:HIS10 3.0 24.4 0.3
CE1 B:HIS42 3.0 13.8 0.6
CE1 B:HIS10 3.0 24.7 0.7
CG B:HIS42 3.1 11.7 0.6
OD1 B:ASP8 3.1 17.3 1.0
CD2 B:HIS10 3.2 24.2 0.7
CD2 B:HIS10 3.3 23.7 0.3
ND1 B:HIS42 3.4 15.2 0.4
CB B:HIS42 3.4 11.8 0.4
CE1 B:HIS42 3.4 16.0 0.4
CB B:HIS42 3.5 9.7 0.6
O B:HOH470 3.6 31.3 1.0
NE2 B:HIS42 4.1 13.3 0.6
ND1 B:HIS10 4.2 23.3 0.3
CD2 B:HIS42 4.2 12.5 0.6
ND1 B:HIS10 4.2 23.6 0.7
CB B:ASP8 4.3 13.5 1.0
CG B:HIS10 4.3 22.4 0.7
O B:HOH438 4.3 42.4 1.0
CG B:HIS10 4.3 22.2 0.3
O A:HOH475 4.6 29.8 1.0
CA B:VAL39 4.9 11.0 0.5
CA B:HIS42 4.9 10.3 0.4
CA B:HIS42 5.0 9.8 0.6
CA B:VAL39 5.0 9.8 0.5

Magnesium binding site 3 out of 3 in 5b8f

Go back to Magnesium Binding Sites List in 5b8f
Magnesium binding site 3 out of 3 in the X-Ray Crystal Structure of A 2-C-Methyl-D-Erythritol 2,4- Cyclodiphosphate Synthase From Pseudomonas Aeruginosa


Mono view


Stereo pair view

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

b:19.4
occ:1.00
 OD2 C:ASP8 2.0 10.9 1.0
ND1 C:HIS42 2.1 14.0 1.0
NE2 C:HIS10 2.1 14.6 1.0
CG C:ASP8 2.9 13.2 1.0
CE1 C:HIS42 3.0 15.6 1.0
CD2 C:HIS10 3.1 15.4 1.0
CG C:HIS42 3.1 12.7 1.0
CE1 C:HIS10 3.1 17.5 1.0
OD1 C:ASP8 3.2 14.0 1.0
CB C:HIS42 3.4 9.8 1.0
NE2 C:HIS42 4.1 15.0 1.0
CD2 C:HIS42 4.2 13.6 1.0
ND1 C:HIS10 4.2 18.4 1.0
CG C:HIS10 4.2 15.1 1.0
CB C:ASP8 4.3 10.9 1.0
O C:HOH318 4.4 24.2 1.0
CA C:VAL39 4.7 9.3 1.0
O B:HOH321 4.8 23.6 1.0
CA C:HIS42 4.9 9.2 1.0

Reference:

Ssgcid, J.W.Fairman, D.M.Dranow, D.Lorimer, T.E.Edwards. X-Ray Crystal Structure of A 2-C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase From Pseudomonas Aeruginosa To Be Published.
Page generated: Tue Aug 12 05:33:36 2025

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