Magnesium in PDB 6rcz: The Structure of Burkholderia Pseudomallei Trehalose-6-Phosphatase

Enzymatic activity of The Structure of Burkholderia Pseudomallei Trehalose-6-Phosphatase

All present enzymatic activity of The Structure of Burkholderia Pseudomallei Trehalose-6-Phosphatase:
3.1.3.12;

Protein crystallography data

The structure of The Structure of Burkholderia Pseudomallei Trehalose-6-Phosphatase, PDB code: 6rcz was solved by L.J.Gourlay, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 59.68 / 1.74
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 75.926, 83.843, 84.978, 90.00, 90.00, 90.00
R / Rfree (%) 19.1 / 22.9

Other elements in 6rcz:

The structure of The Structure of Burkholderia Pseudomallei Trehalose-6-Phosphatase also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Magnesium Binding Sites:

The binding sites of Magnesium atom in the The Structure of Burkholderia Pseudomallei Trehalose-6-Phosphatase (pdb code 6rcz). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the The Structure of Burkholderia Pseudomallei Trehalose-6-Phosphatase, PDB code: 6rcz:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 6rcz

Go back to Magnesium Binding Sites List in 6rcz
Magnesium binding site 1 out of 2 in the The Structure of Burkholderia Pseudomallei Trehalose-6-Phosphatase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of The Structure of Burkholderia Pseudomallei Trehalose-6-Phosphatase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg301

b:16.9
occ:1.00
O A:HOH431 2.0 16.7 1.0
O A:HOH459 2.1 20.7 1.0
OD1 A:ASP216 2.1 22.6 1.0
OD2 A:ASP37 2.1 21.4 1.0
O A:ASP39 2.1 21.4 1.0
O A:HOH422 2.1 22.2 1.0
CG A:ASP216 3.1 21.1 1.0
CG A:ASP37 3.1 21.5 1.0
C A:ASP39 3.3 20.6 1.0
OD2 A:ASP216 3.4 22.9 1.0
OD1 A:ASP37 3.5 22.2 1.0
OD2 A:ASP220 4.0 21.6 1.0
O A:HOH479 4.1 15.9 1.0
OG1 A:THR41 4.2 15.5 1.0
CA A:ASP39 4.2 22.5 1.0
O A:HOH402 4.2 32.0 1.0
N A:GLY40 4.2 20.1 1.0
O A:HOH500 4.3 42.9 1.0
N A:ASP39 4.3 19.4 1.0
CA A:GLY40 4.3 17.9 1.0
CB A:ASP39 4.4 24.6 1.0
CB A:ASP216 4.4 18.4 1.0
CB A:ASP37 4.4 19.0 1.0
CB A:ASP217 4.5 19.7 1.0
C A:GLY40 4.6 21.1 1.0
N A:ASP216 4.7 15.1 1.0
N A:THR41 4.7 18.4 1.0
N A:ASP217 4.8 18.7 1.0
O A:HOH401 4.8 15.1 1.0
C A:PHE38 4.9 18.9 1.0
CA A:ASP216 5.0 16.8 1.0
CG A:ASP220 5.0 16.5 1.0

Magnesium binding site 2 out of 2 in 6rcz

Go back to Magnesium Binding Sites List in 6rcz
Magnesium binding site 2 out of 2 in the The Structure of Burkholderia Pseudomallei Trehalose-6-Phosphatase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of The Structure of Burkholderia Pseudomallei Trehalose-6-Phosphatase within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg301

b:23.8
occ:1.00
OD2 E:ASP37 1.9 29.7 1.0
O E:HOH414 2.0 23.5 1.0
OD1 E:ASP216 2.1 32.4 1.0
O E:ASP39 2.2 23.2 1.0
O E:HOH462 2.2 28.5 1.0
O E:HOH433 2.3 28.8 1.0
CG E:ASP37 2.9 27.8 1.0
CG E:ASP216 3.2 29.3 1.0
OD1 E:ASP37 3.2 27.9 1.0
C E:ASP39 3.4 20.9 1.0
OD2 E:ASP216 3.6 32.4 1.0
OD2 E:ASP220 4.0 24.7 1.0
O E:HOH468 4.0 45.0 1.0
OG1 E:THR41 4.1 22.0 1.0
O E:HOH445 4.1 32.9 1.0
CA E:ASP39 4.2 25.7 1.0
CB E:ASP37 4.2 22.7 1.0
N E:ASP39 4.3 28.6 1.0
OD2 E:ASP217 4.3 37.0 1.0
N E:GLY40 4.3 26.6 1.0
O E:HOH405 4.4 28.1 1.0
CB E:ASP39 4.4 32.8 1.0
CB E:ASP216 4.5 23.9 1.0
CA E:GLY40 4.5 27.0 1.0
CG E:ASP217 4.5 34.0 1.0
NZ E:LYS193 4.5 22.2 1.0
OD1 E:ASP217 4.6 33.6 1.0
N E:ASP216 4.6 21.9 1.0
N E:THR41 4.7 19.5 1.0
C E:GLY40 4.7 24.1 1.0
C E:PHE38 4.8 27.4 1.0
CG E:ASP220 4.9 28.1 1.0
N E:ASP217 4.9 25.3 1.0
N E:PHE38 4.9 16.2 1.0
CB E:THR41 4.9 16.8 1.0
O E:HOH413 5.0 51.6 1.0
OD1 E:ASP220 5.0 26.6 1.0
CA E:ASP216 5.0 21.8 1.0

Reference:

S.Suthisawat, L.J.Gourlay, M.Bolognesi, U.Boonyuen, M.Vanaporn. Functional and Structural Analysis of Trehalose-6-Phosphate Phosphatase From Burkholderia Pseudomallei: Insights Into the Catalytic Mechanism. Biochem.Biophys.Res.Commun. 2020.
ISSN: ESSN 1090-2104
PubMed: 31973820
DOI: 10.1016/J.BBRC.2019.12.088
Page generated: Mon Dec 14 23:56:36 2020

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