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Magnesium in PDB 3nba: Phosphopantetheine Adenylyltranferase From Mycobacterium Tuberculosis in Complex with Adenosine-5'-[(Alpha,Beta)-Methyleno]Triphosphate (Ampcpp)

Enzymatic activity of Phosphopantetheine Adenylyltranferase From Mycobacterium Tuberculosis in Complex with Adenosine-5'-[(Alpha,Beta)-Methyleno]Triphosphate (Ampcpp)

All present enzymatic activity of Phosphopantetheine Adenylyltranferase From Mycobacterium Tuberculosis in Complex with Adenosine-5'-[(Alpha,Beta)-Methyleno]Triphosphate (Ampcpp):
2.7.7.3;

Protein crystallography data

The structure of Phosphopantetheine Adenylyltranferase From Mycobacterium Tuberculosis in Complex with Adenosine-5'-[(Alpha,Beta)-Methyleno]Triphosphate (Ampcpp), PDB code: 3nba was solved by T.J.Wubben, A.D.Mesecar, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 2.68
Space group P 3 2 1
Cell size a, b, c (Å), α, β, γ (°) 115.118, 115.118, 133.913, 90.00, 90.00, 120.00
R / Rfree (%) 19.9 / 25.6

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Phosphopantetheine Adenylyltranferase From Mycobacterium Tuberculosis in Complex with Adenosine-5'-[(Alpha,Beta)-Methyleno]Triphosphate (Ampcpp) (pdb code 3nba). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Phosphopantetheine Adenylyltranferase From Mycobacterium Tuberculosis in Complex with Adenosine-5'-[(Alpha,Beta)-Methyleno]Triphosphate (Ampcpp), PDB code: 3nba:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 3nba

Go back to Magnesium Binding Sites List in 3nba
Magnesium binding site 1 out of 3 in the Phosphopantetheine Adenylyltranferase From Mycobacterium Tuberculosis in Complex with Adenosine-5'-[(Alpha,Beta)-Methyleno]Triphosphate (Ampcpp)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Phosphopantetheine Adenylyltranferase From Mycobacterium Tuberculosis in Complex with Adenosine-5'-[(Alpha,Beta)-Methyleno]Triphosphate (Ampcpp) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg158

b:42.5
occ:1.00
O1G A:APC200 2.5 59.6 1.0
O2A A:APC200 2.5 48.5 1.0
O A:HOH177 2.8 25.1 1.0
C3A A:APC200 3.3 49.9 1.0
PA A:APC200 3.5 47.7 1.0
O A:HOH256 3.7 38.3 1.0
PG A:APC200 3.7 59.5 1.0
O3G A:APC200 4.1 58.6 1.0
PB A:APC200 4.3 52.4 1.0
O A:HOH257 4.4 34.8 1.0
O3B A:APC200 4.4 56.9 1.0
O1A A:APC200 4.4 46.4 1.0
O2B A:APC200 4.4 53.2 1.0
OG A:SER9 4.5 18.5 0.5
OG A:SER9 4.5 18.3 0.5
O5' A:APC200 4.7 47.9 1.0
CB A:SER9 4.9 18.7 0.5
O2G A:APC200 4.9 59.4 1.0

Magnesium binding site 2 out of 3 in 3nba

Go back to Magnesium Binding Sites List in 3nba
Magnesium binding site 2 out of 3 in the Phosphopantetheine Adenylyltranferase From Mycobacterium Tuberculosis in Complex with Adenosine-5'-[(Alpha,Beta)-Methyleno]Triphosphate (Ampcpp)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Phosphopantetheine Adenylyltranferase From Mycobacterium Tuberculosis in Complex with Adenosine-5'-[(Alpha,Beta)-Methyleno]Triphosphate (Ampcpp) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg158

b:48.7
occ:1.00
O1G C:APC200 2.4 61.5 1.0
O2A C:APC200 2.8 55.9 1.0
C3A C:APC200 3.3 56.1 1.0
PA C:APC200 3.6 55.6 1.0
PG C:APC200 3.8 59.1 1.0
OG C:SER9 4.0 28.0 1.0
O3G C:APC200 4.3 59.4 1.0
O C:HOH248 4.3 35.8 1.0
PB C:APC200 4.4 57.1 1.0
O3B C:APC200 4.6 59.8 1.0
O2B C:APC200 4.6 58.7 1.0
O1A C:APC200 4.6 54.0 1.0
O C:HOH249 4.9 34.3 1.0
O5' C:APC200 4.9 56.7 1.0
O2G C:APC200 4.9 58.6 1.0

Magnesium binding site 3 out of 3 in 3nba

Go back to Magnesium Binding Sites List in 3nba
Magnesium binding site 3 out of 3 in the Phosphopantetheine Adenylyltranferase From Mycobacterium Tuberculosis in Complex with Adenosine-5'-[(Alpha,Beta)-Methyleno]Triphosphate (Ampcpp)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Phosphopantetheine Adenylyltranferase From Mycobacterium Tuberculosis in Complex with Adenosine-5'-[(Alpha,Beta)-Methyleno]Triphosphate (Ampcpp) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg158

b:45.8
occ:1.00
O2A D:APC200 2.5 63.2 1.0
O1G D:APC200 2.8 72.0 1.0
C3A D:APC200 3.0 64.7 1.0
PA D:APC200 3.4 61.4 1.0
O D:HOH265 4.0 33.6 1.0
OG D:SER9 4.1 31.9 1.0
PG D:APC200 4.2 70.3 1.0
PB D:APC200 4.3 68.1 1.0
O1A D:APC200 4.4 60.4 1.0
O2B D:APC200 4.5 67.6 1.0
O5' D:APC200 4.5 60.9 1.0
O3B D:APC200 4.7 69.7 1.0
O2G D:APC200 4.7 69.7 1.0
O D:HOH252 4.9 28.9 1.0

Reference:

T.J.Wubben, A.D.Mesecar. Kinetic, Thermodynamic, and Structural Insight Into the Mechanism of Phosphopantetheine Adenylyltransferase From Mycobacterium Tuberculosis. J.Mol.Biol. V. 404 202 2010.
ISSN: ISSN 0022-2836
PubMed: 20851704
DOI: 10.1016/J.JMB.2010.09.002
Page generated: Mon Dec 14 08:28:09 2020

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