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Magnesium in PDB 2b8j: Crystal Structure of Apha Class B Acid Phosphatase/Phosphotransferase Ternary Complex with Adenosine and Phosphate at 2 A Resolution

Enzymatic activity of Crystal Structure of Apha Class B Acid Phosphatase/Phosphotransferase Ternary Complex with Adenosine and Phosphate at 2 A Resolution

All present enzymatic activity of Crystal Structure of Apha Class B Acid Phosphatase/Phosphotransferase Ternary Complex with Adenosine and Phosphate at 2 A Resolution:
3.1.3.2;

Protein crystallography data

The structure of Crystal Structure of Apha Class B Acid Phosphatase/Phosphotransferase Ternary Complex with Adenosine and Phosphate at 2 A Resolution, PDB code: 2b8j was solved by V.Calderone, C.Forleo, M.Benvenuti, M.C.Thaller, G.M.Rossolini, S.Mangani, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.39 / 2.03
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 89.966, 66.544, 91.544, 90.00, 124.02, 90.00
R / Rfree (%) 17.1 / 22.3

Other elements in 2b8j:

The structure of Crystal Structure of Apha Class B Acid Phosphatase/Phosphotransferase Ternary Complex with Adenosine and Phosphate at 2 A Resolution also contains other interesting chemical elements:

Gold (Au) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Apha Class B Acid Phosphatase/Phosphotransferase Ternary Complex with Adenosine and Phosphate at 2 A Resolution (pdb code 2b8j). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of Apha Class B Acid Phosphatase/Phosphotransferase Ternary Complex with Adenosine and Phosphate at 2 A Resolution, PDB code: 2b8j:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 2b8j

Go back to Magnesium Binding Sites List in 2b8j
Magnesium binding site 1 out of 2 in the Crystal Structure of Apha Class B Acid Phosphatase/Phosphotransferase Ternary Complex with Adenosine and Phosphate at 2 A Resolution


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 Apha Class B Acid Phosphatase/Phosphotransferase Ternary Complex with Adenosine and Phosphate at 2 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg311

b:13.7
occ:1.00
 OD1 A:ASP167 2.0 12.4 1.0
O A:ASP46 2.1 10.9 1.0
OD2 A:ASP44 2.1 13.8 1.0
O A:HOH737 2.1 11.3 1.0
O A:HOH757 2.1 9.0 1.0
O A:HOH670 2.2 10.7 1.0
CG A:ASP167 3.0 11.9 1.0
CG A:ASP44 3.1 13.3 1.0
C A:ASP46 3.3 11.5 1.0
OD2 A:ASP167 3.3 11.4 1.0
OD1 A:ASP44 3.4 13.8 1.0
OG1 A:THR48 3.8 11.4 1.0
OG A:SER168 3.9 15.6 1.0
CA A:ASP46 4.0 10.8 1.0
OD2 A:ASP171 4.0 11.4 1.0
N A:ASP46 4.1 11.5 1.0
CB A:ASP46 4.2 10.7 1.0
O1 A:PO4301 4.2 30.4 1.0
O A:HOH756 4.2 12.6 1.0
CB A:ASP167 4.3 11.2 1.0
CB A:ASP44 4.4 11.6 1.0
N A:ASP47 4.4 11.2 1.0
O3 A:PO4301 4.4 30.9 1.0
N A:ASP167 4.4 11.1 1.0
CB A:ASP47 4.5 10.9 1.0
O2 A:PO4301 4.7 26.7 1.0
N A:SER168 4.7 10.5 1.0
P A:PO4301 4.7 32.1 1.0
N A:THR48 4.7 10.5 1.0
CA A:ASP47 4.7 11.1 1.0
C A:ASP47 4.7 11.4 1.0
CB A:SER168 4.8 12.5 1.0
O A:HOH660 4.8 12.6 1.0
CA A:ASP167 4.8 10.9 1.0
C A:ILE45 4.8 11.3 1.0
CB A:THR48 4.8 11.2 1.0

Magnesium binding site 2 out of 2 in 2b8j

Go back to Magnesium Binding Sites List in 2b8j
Magnesium binding site 2 out of 2 in the Crystal Structure of Apha Class B Acid Phosphatase/Phosphotransferase Ternary Complex with Adenosine and Phosphate at 2 A Resolution


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 Apha Class B Acid Phosphatase/Phosphotransferase Ternary Complex with Adenosine and Phosphate at 2 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg312

b:11.5
occ:1.00
 OD2 B:ASP44 2.0 11.8 1.0
OD1 B:ASP167 2.0 11.9 1.0
O B:HOH348 2.1 16.3 1.0
O B:ASP46 2.1 10.1 1.0
O B:HOH352 2.1 10.2 1.0
O B:HOH350 2.1 10.0 1.0
CG B:ASP44 2.9 11.8 1.0
CG B:ASP167 3.0 13.2 1.0
C B:ASP46 3.2 9.9 1.0
OD1 B:ASP44 3.2 12.6 1.0
OD2 B:ASP167 3.4 13.9 1.0
CA B:ASP46 3.8 10.2 1.0
N B:ASP46 4.0 9.9 1.0
OG1 B:THR48 4.0 10.4 1.0
OD2 B:ASP171 4.0 13.4 1.0
OG B:SER168 4.0 10.2 1.0
CB B:ASP46 4.1 10.5 1.0
O B:HOH422 4.2 13.2 1.0
CB B:ASP44 4.3 12.3 1.0
N B:ASP47 4.3 10.1 1.0
O B:HOH381 4.4 22.1 1.0
CB B:ASP167 4.4 11.5 1.0
CB B:ASP47 4.5 10.9 1.0
N B:ASP167 4.5 11.3 1.0
CA B:ASP47 4.7 10.2 1.0
C B:ASP47 4.7 11.3 1.0
N B:THR48 4.7 10.5 1.0
N B:SER168 4.8 10.7 1.0
C B:ILE45 4.8 11.2 1.0
CB B:SER168 4.8 11.3 1.0
O B:HOH336 4.9 13.3 1.0
O B:HOH346 4.9 12.7 1.0
O4' B:ADN331 4.9 42.9 1.0
CA B:ASP167 4.9 11.1 1.0
CB B:THR48 4.9 10.2 1.0

Reference:

V.Calderone, C.Forleo, M.Benvenuti, M.C.Thaller, G.M.Rossolini, S.Mangani. A Structure-Based Proposal For the Catalytic Mechanism of the Bacterial Acid Phosphatase Apha Belonging to the Dddd Superfamily of Phosphohydrolases J.Mol.Biol. V. 355 708 2006.
ISSN: ISSN 0022-2836
PubMed: 16330049
DOI: 10.1016/J.JMB.2005.10.068
Page generated: Tue Aug 13 21:47:11 2024

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