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Magnesium in PDB 1rmy: Crystal Structure of Apha Class B Acid Phosphatase/Phosphotransferase Ternary Complex with Deoxycytosine and Phosphate Bound to the Catalytic Metal

Enzymatic activity of Crystal Structure of Apha Class B Acid Phosphatase/Phosphotransferase Ternary Complex with Deoxycytosine and Phosphate Bound to the Catalytic Metal

All present enzymatic activity of Crystal Structure of Apha Class B Acid Phosphatase/Phosphotransferase Ternary Complex with Deoxycytosine and Phosphate Bound to the Catalytic Metal:
3.1.3.2;

Protein crystallography data

The structure of Crystal Structure of Apha Class B Acid Phosphatase/Phosphotransferase Ternary Complex with Deoxycytosine and Phosphate Bound to the Catalytic Metal, PDB code: 1rmy was solved by V.Calderone, C.Forleo, M.Benvenuti, G.M.Rossolini, M.C.Thaller, S.Mangani, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.57 / 1.75
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 91.882, 66.393, 90.018, 90.00, 119.66, 90.00
R / Rfree (%) 15.3 / 19.4

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Apha Class B Acid Phosphatase/Phosphotransferase Ternary Complex with Deoxycytosine and Phosphate Bound to the Catalytic Metal (pdb code 1rmy). 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 Deoxycytosine and Phosphate Bound to the Catalytic Metal, PDB code: 1rmy:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 1rmy

Go back to Magnesium Binding Sites List in 1rmy
Magnesium binding site 1 out of 2 in the Crystal Structure of Apha Class B Acid Phosphatase/Phosphotransferase Ternary Complex with Deoxycytosine and Phosphate Bound to the Catalytic Metal


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 Deoxycytosine and Phosphate Bound to the Catalytic Metal within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg813

b:7.2
occ:1.00
 OD2 A:ASP44 2.0 7.3 1.0
OD1 A:ASP167 2.0 7.2 1.0
O A:ASP46 2.0 5.5 1.0
O A:HOH995 2.1 7.3 1.0
O A:HOH1204 2.1 8.9 1.0
O A:HOH1195 2.1 11.2 1.0
CG A:ASP44 3.0 10.9 1.0
CG A:ASP167 3.1 9.3 1.0
C A:ASP46 3.2 6.0 1.0
OD1 A:ASP44 3.3 9.6 1.0
OD2 A:ASP167 3.4 7.0 1.0
OG1 A:THR48 3.9 7.5 1.0
CA A:ASP46 4.0 6.2 1.0
N A:ASP46 4.0 6.0 1.0
OD2 A:ASP171 4.0 8.9 1.0
OG A:SER168 4.1 9.9 1.0
O A:HOH992 4.2 26.9 1.0
O A:HOH1006 4.2 10.0 1.0
CB A:ASP46 4.2 6.0 1.0
CB A:ASP44 4.3 8.4 1.0
N A:ASP47 4.3 6.4 1.0
O A:HOH866 4.3 15.6 1.0
CB A:ASP167 4.4 6.3 1.0
CB A:ASP47 4.5 6.3 1.0
N A:ASP167 4.5 6.9 1.0
N A:THR48 4.6 5.8 1.0
C A:ASP47 4.7 7.6 1.0
CA A:ASP47 4.7 6.5 1.0
N A:SER168 4.7 8.2 1.0
C A:ILE45 4.8 6.5 1.0
O A:HOH817 4.8 9.3 1.0
CB A:THR48 4.8 6.9 1.0
O A:HOH873 4.9 12.6 1.0
CA A:ASP167 4.9 8.2 1.0
CB A:SER168 4.9 8.8 1.0

Magnesium binding site 2 out of 2 in 1rmy

Go back to Magnesium Binding Sites List in 1rmy
Magnesium binding site 2 out of 2 in the Crystal Structure of Apha Class B Acid Phosphatase/Phosphotransferase Ternary Complex with Deoxycytosine and Phosphate Bound to the Catalytic Metal


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 Deoxycytosine and Phosphate Bound to the Catalytic Metal within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg814

b:6.5
occ:1.00
 OD2 B:ASP44 2.0 6.3 1.0
O B:HOH1190 2.0 10.2 1.0
O3 B:PO4800 2.1 11.1 1.0
O B:ASP46 2.1 5.9 1.0
OD1 B:ASP167 2.1 6.8 1.0
O B:HOH1209 2.2 15.0 1.0
CG B:ASP44 2.9 9.5 1.0
CG B:ASP167 3.2 9.4 1.0
C B:ASP46 3.2 6.2 1.0
OD1 B:ASP44 3.3 10.2 1.0
P B:PO4800 3.5 8.5 0.5
OD2 B:ASP167 3.5 7.5 1.0
N B:ASP46 3.9 6.5 1.0
CA B:ASP46 3.9 5.0 1.0
OG B:SER168 3.9 11.9 1.0
OG1 B:THR48 3.9 7.2 1.0
OD2 B:ASP171 4.0 9.1 1.0
O2 B:PO4800 4.0 12.3 1.0
O4 B:PO4800 4.1 13.3 1.0
CB B:ASP46 4.1 7.3 1.0
O B:HOH843 4.2 9.5 1.0
CB B:ASP44 4.2 7.8 1.0
N B:ASP47 4.3 6.0 1.0
O B:HOH991 4.3 25.8 1.0
CB B:ASP167 4.5 8.1 1.0
CB B:ASP47 4.6 5.5 1.0
O1 B:PO4800 4.6 15.6 1.0
N B:ASP167 4.6 7.3 1.0
N B:THR48 4.7 6.3 1.0
C B:ILE45 4.7 7.5 1.0
CA B:ASP47 4.7 6.7 1.0
C B:ASP47 4.8 6.5 1.0
N B:SER168 4.8 8.2 1.0
CB B:THR48 4.9 6.1 1.0
N B:ILE45 5.0 6.9 1.0

Reference:

V.Calderone, C.Forleo, M.Benvenuti, G.M.Rossolini, M.C.Thaller, S.Mangani. Insights in the Catalytic Mechanism of Apha From Escherichia Coli To Be Published.
Page generated: Mon Dec 14 06:42:52 2020

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