Nickel in PDB 3nbk: Phosphopantetheine Adenylyltransferase From Mycobacterium Tuberculosis in Complex with 4'-Phosphopantetheine

All present enzymatic activity of Phosphopantetheine Adenylyltransferase From Mycobacterium Tuberculosis in Complex with 4'-Phosphopantetheine:
2.7.7.3;

The structure of Phosphopantetheine Adenylyltransferase From Mycobacterium Tuberculosis in Complex with 4'-Phosphopantetheine, PDB code: 3nbk 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)	135.21 / 1.58
Space group	P 3 2 1
Cell size a, b, c (Å), α, β, γ (°)	114.627, 114.627, 135.206, 90.00, 90.00, 120.00
R / Rfree (%)	18.3 / 19.9

The binding sites of Nickel atom in the Phosphopantetheine Adenylyltransferase From Mycobacterium Tuberculosis in Complex with 4'-Phosphopantetheine (pdb code 3nbk). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 2 binding sites of Nickel where determined in the Phosphopantetheine Adenylyltransferase From Mycobacterium Tuberculosis in Complex with 4'-Phosphopantetheine, PDB code: 3nbk:
Jump to Nickel binding site number: 1; 2;

Nickel binding site 1 out of 2 in the Phosphopantetheine Adenylyltransferase From Mycobacterium Tuberculosis in Complex with 4'-Phosphopantetheine


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Phosphopantetheine Adenylyltransferase From Mycobacterium Tuberculosis in Complex with 4'-Phosphopantetheine within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni162 b:34.7 occ:1.00 O B:HIS0 2.4 20.0 1.0 OD1 A:ASP29 2.5 19.8 1.0 OD1 B:ASP29 2.7 19.0 1.0 CG A:ASP29 3.3 15.7 1.0 O A:HIS0 3.4 20.0 1.0 OD2 A:ASP29 3.4 19.5 1.0 C B:HIS0 3.4 20.0 1.0 CG B:ASP29 3.5 14.8 1.0 OD2 B:ASP29 3.5 21.3 1.0 CB B:HIS0 4.1 20.0 1.0 N B:MET1 4.2 25.6 1.0 CA B:MET1 4.3 24.8 1.0 C A:HIS0 4.3 20.0 1.0 CA B:HIS0 4.3 20.0 1.0 CA A:MET1 4.5 24.8 1.0 N B:THR2 4.7 19.1 1.0 N A:THR2 4.7 19.0 1.0 CB A:ASP29 4.7 12.9 1.0 N A:MET1 4.8 25.8 1.0 CB B:ASP29 4.9 12.2 1.0 C B:MET1 4.9 22.7 1.0 CG2 B:THR2 4.9 14.6 1.0 SD B:MET1 4.9 38.9 1.0 CG2 A:THR2 4.9 16.1 1.0

Nickel binding site 2 out of 2 in the Phosphopantetheine Adenylyltransferase From Mycobacterium Tuberculosis in Complex with 4'-Phosphopantetheine


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Phosphopantetheine Adenylyltransferase From Mycobacterium Tuberculosis in Complex with 4'-Phosphopantetheine within 5.0Å range: probe atom residue distance (Å) B Occ C:Ni162 b:6.7 occ:1.00 O D:HOH255 2.6 17.8 1.0 O D:ARG-3 2.6 20.8 1.0 O C:ARG-3 2.7 24.9 1.0 OD1 D:ASP29 2.7 15.2 1.0 OD1 C:ASP29 2.8 13.4 1.0 OD2 D:ASP29 2.8 17.2 1.0 O D:HIS0 2.8 19.4 1.0 O C:HIS0 2.9 19.1 1.0 OD2 C:ASP29 3.0 14.3 1.0 CG D:ASP29 3.2 15.5 1.0 CG C:ASP29 3.3 12.2 1.0 C D:ARG-3 3.8 20.9 1.0 C C:ARG-3 3.9 25.6 1.0 C D:HIS0 3.9 20.6 1.0 C C:HIS0 4.0 20.6 1.0 CA D:GLY-2 4.4 20.8 1.0 CA C:GLY-2 4.4 24.6 1.0 N C:HIS0 4.5 22.7 1.0 N D:HIS0 4.6 21.6 1.0 N D:GLY-2 4.6 20.9 1.0 CA D:MET1 4.6 19.6 1.0 N C:GLY-2 4.6 25.2 1.0 N C:SER-1 4.7 24.1 1.0 CB D:ASP29 4.7 14.4 1.0 CA C:MET1 4.7 19.3 1.0 N D:MET1 4.7 19.8 1.0 C C:GLY-2 4.7 24.7 1.0 N C:MET1 4.8 19.6 1.0 C D:GLY-2 4.8 21.6 1.0 N D:SER-1 4.8 21.6 1.0 CB C:ASP29 4.8 11.9 1.0 N D:THR2 4.8 17.8 1.0 CA C:HIS0 4.9 21.8 1.0 CA D:HIS0 4.9 20.8 1.0 CA D:ARG-3 4.9 21.7 1.0 N C:THR2 5.0 16.9 1.0

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