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Magnesium in PDB 2b82: Crystal Structure of Apha Class B Acid Phosphatase/Phosphotransferase Ternary Complex with Adenosine and Phosphate Bound to the Catalytic Metal at 1.2 A Resolution

Enzymatic activity of Crystal Structure of Apha Class B Acid Phosphatase/Phosphotransferase Ternary Complex with Adenosine and Phosphate Bound to the Catalytic Metal at 1.2 A Resolution

All present enzymatic activity of Crystal Structure of Apha Class B Acid Phosphatase/Phosphotransferase Ternary Complex with Adenosine and Phosphate Bound to the Catalytic Metal at 1.2 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 Bound to the Catalytic Metal at 1.2 A Resolution, PDB code: 2b82 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) 76.71 / 1.25
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 90.971, 66.868, 86.120, 90.00, 116.96, 90.00
R / Rfree (%) 16.5 / 18.9

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 Bound to the Catalytic Metal at 1.2 A Resolution (pdb code 2b82). 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 Bound to the Catalytic Metal at 1.2 A Resolution, PDB code: 2b82:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 2b82

Go back to Magnesium Binding Sites List in 2b82
Magnesium binding site 1 out of 2 in the Crystal Structure of Apha Class B Acid Phosphatase/Phosphotransferase Ternary Complex with Adenosine and Phosphate Bound to the Catalytic Metal at 1.2 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 Bound to the Catalytic Metal at 1.2 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1013

b:5.4
occ:1.00
 O3 A:PO41004 2.0 7.3 1.0
OD2 A:ASP44 2.1 6.1 1.0
O A:HOH1436 2.1 5.8 1.0
OD1 A:ASP167 2.1 5.5 1.0
O A:ASP46 2.1 5.1 1.0
O A:HOH1449 2.1 7.4 1.0
CG A:ASP44 3.0 6.5 1.0
CG A:ASP167 3.1 4.6 1.0
C A:ASP46 3.3 4.7 1.0
OD1 A:ASP44 3.3 6.8 1.0
P A:PO41004 3.5 10.1 1.0
OD2 A:ASP167 3.5 5.7 1.0
N A:ASP46 3.9 4.8 1.0
CA A:ASP46 3.9 4.8 1.0
OG1 A:THR48 4.0 5.8 1.0
OG A:SER168 4.0 7.5 1.0
OD2 A:ASP171 4.1 6.4 1.0
O2' A:ADN1001 4.1 21.1 0.5
O2 A:PO41004 4.1 9.5 1.0
CB A:ASP46 4.2 5.4 1.0
O A:HOH1025 4.2 6.8 1.0
O4 A:PO41004 4.2 10.7 1.0
CB A:ASP44 4.3 6.0 1.0
N A:ASP47 4.4 4.7 1.0
CB A:ASP167 4.5 5.2 1.0
O1 A:PO41004 4.5 12.4 1.0
N A:ASP167 4.6 5.2 1.0
CB A:ASP47 4.7 5.1 1.0
C A:ILE45 4.7 4.8 1.0
N A:THR48 4.7 4.9 1.0
CA A:ASP47 4.8 4.8 1.0
N A:SER168 4.8 5.7 1.0
C A:ASP47 4.9 5.0 1.0
CB A:THR48 4.9 5.3 1.0
CB A:SER168 5.0 6.2 1.0
N A:ILE45 5.0 5.5 1.0

Magnesium binding site 2 out of 2 in 2b82

Go back to Magnesium Binding Sites List in 2b82
Magnesium binding site 2 out of 2 in the Crystal Structure of Apha Class B Acid Phosphatase/Phosphotransferase Ternary Complex with Adenosine and Phosphate Bound to the Catalytic Metal at 1.2 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 Bound to the Catalytic Metal at 1.2 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1014

b:5.0
occ:1.00
 OD2 B:ASP44 2.0 5.2 1.0
O3 B:PO41005 2.1 6.5 1.0
O B:ASP46 2.1 4.9 1.0
O B:HOH1425 2.1 5.5 1.0
OD1 B:ASP167 2.1 5.3 1.0
O B:HOH1433 2.1 5.9 1.0
CG B:ASP44 3.0 5.6 1.0
CG B:ASP167 3.1 5.4 1.0
C B:ASP46 3.2 4.9 1.0
OD1 B:ASP44 3.3 7.1 1.0
P B:PO41005 3.4 7.0 1.0
OD2 B:ASP167 3.5 5.6 1.0
CA B:ASP46 3.9 5.0 1.0
N B:ASP46 3.9 4.7 1.0
OG1 B:THR48 4.0 5.8 1.0
O4 B:PO41005 4.0 6.7 1.0
OG B:SER168 4.0 7.2 1.0
OD2 B:ASP171 4.0 6.0 1.0
CB B:ASP46 4.1 5.4 1.0
O1 B:PO41005 4.1 6.4 1.0
O B:HOH1054 4.2 11.1 1.0
CB B:ASP44 4.3 5.2 1.0
O B:HOH1040 4.3 8.2 1.0
N B:ASP47 4.4 4.6 1.0
CB B:ASP167 4.4 5.2 1.0
O2 B:PO41005 4.5 7.2 1.0
O2' B:ADN1002 4.6 27.2 0.5
N B:ASP167 4.6 4.8 1.0
CB B:ASP47 4.7 4.8 1.0
C B:ILE45 4.7 4.5 1.0
N B:THR48 4.7 4.7 1.0
CA B:ASP47 4.8 5.0 1.0
N B:SER168 4.8 5.1 1.0
C B:ASP47 4.9 4.8 1.0
CB B:THR48 5.0 5.1 1.0
N B:ILE45 5.0 5.1 1.0
CB B:SER168 5.0 6.3 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: Sun Aug 10 09:56:39 2025

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