Nickel in PDB 3iu8: M. Tuberculosis Methionine Aminopeptidase with Ni Inhibitor T03

All present enzymatic activity of M. Tuberculosis Methionine Aminopeptidase with Ni Inhibitor T03:
3.4.11.18;

The structure of M. Tuberculosis Methionine Aminopeptidase with Ni Inhibitor T03, PDB code: 3iu8 was solved by Q.Z.Ye, J.P.Lu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	36.49 / 1.85
Space group	P 63
Cell size a, b, c (Å), α, β, γ (°)	105.728, 105.728, 50.427, 90.00, 90.00, 120.00
R / Rfree (%)	16.5 / 20

The structure of M. Tuberculosis Methionine Aminopeptidase with Ni Inhibitor T03 also contains other interesting chemical elements:

Fluorine	(F)	1 atom
Chlorine	(Cl)	2 atoms

The binding sites of Nickel atom in the M. Tuberculosis Methionine Aminopeptidase with Ni Inhibitor T03 (pdb code 3iu8). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 3 binding sites of Nickel where determined in the M. Tuberculosis Methionine Aminopeptidase with Ni Inhibitor T03, PDB code: 3iu8:
Jump to Nickel binding site number: 1; 2; 3;

Nickel binding site 1 out of 3 in the M. Tuberculosis Methionine Aminopeptidase with Ni Inhibitor T03


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of M. Tuberculosis Methionine Aminopeptidase with Ni Inhibitor T03 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni286 b:8.9 occ:1.00 N3 A:T03289 1.9 14.0 1.0 OE2 A:GLU269 1.9 8.9 1.0 OD2 A:ASP142 2.0 9.3 1.0 OD1 A:ASP131 2.1 10.2 1.0 OD2 A:ASP131 2.5 13.3 1.0 CG A:ASP131 2.6 8.2 1.0 N2 A:T03289 2.8 10.0 1.0 CD A:GLU269 2.9 14.8 1.0 CG A:ASP142 2.9 10.6 1.0 C9 A:T03289 3.1 17.4 1.0 OD1 A:ASP142 3.1 15.0 1.0 OE1 A:GLU269 3.1 17.0 1.0 NI A:NI287 3.3 8.4 1.0 O A:HOH423 3.8 23.7 1.0 S A:T03289 3.9 17.1 1.0 C8 A:T03289 4.0 16.9 1.0 CB A:ASP131 4.1 8.9 1.0 ND2 A:ASN144 4.1 8.5 1.0 N1 A:T03289 4.1 15.1 1.0 OG1 A:THR133 4.1 10.8 1.0 CG A:GLU269 4.2 10.6 1.0 N A:THR143 4.2 7.7 1.0 CB A:ASP142 4.3 7.0 1.0 O A:THR143 4.4 8.0 1.0 OE1 A:GLU238 4.5 14.3 1.0 C A:THR143 4.6 7.5 1.0 C A:ASP142 4.6 8.3 1.0 CB A:ASN144 4.6 7.0 1.0 C7 A:T03289 4.6 22.1 1.0 OE2 A:GLU238 4.7 13.0 1.0 O A:HOH354 4.7 12.8 1.0 CA A:ASP131 4.7 8.0 1.0 CB A:GLU269 4.8 9.8 1.0 CA A:THR143 4.8 7.1 1.0 CA A:ASP142 4.8 7.7 1.0 N A:VAL132 4.9 7.9 1.0 CG A:ASN144 4.9 8.1 1.0 CD A:GLU238 4.9 11.8 1.0 C A:ASP131 4.9 7.6 1.0 O A:VAL132 5.0 7.4 1.0

Nickel binding site 2 out of 3 in the M. Tuberculosis Methionine Aminopeptidase with Ni Inhibitor T03


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of M. Tuberculosis Methionine Aminopeptidase with Ni Inhibitor T03 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni287 b:8.4 occ:1.00 OE1 A:GLU269 1.9 17.0 1.0 OE2 A:GLU238 2.0 13.0 1.0 N2 A:T03289 2.0 10.0 1.0 NE2 A:HIS205 2.0 8.4 1.0 OD1 A:ASP142 2.1 15.0 1.0 CD A:GLU238 2.9 11.8 1.0 CD A:GLU269 2.9 14.8 1.0 N3 A:T03289 3.0 14.0 1.0 C8 A:T03289 3.0 16.9 1.0 CD2 A:HIS205 3.0 8.4 1.0 CE1 A:HIS205 3.0 12.2 1.0 CG A:ASP142 3.1 10.6 1.0 OE1 A:GLU238 3.2 14.3 1.0 NI A:NI286 3.3 8.9 1.0 OE2 A:GLU269 3.4 8.9 1.0 OD2 A:ASP142 3.6 9.3 1.0 OG1 A:THR236 3.7 8.7 1.0 CG2 A:THR236 3.9 5.4 1.0 C9 A:T03289 4.1 17.4 1.0 CB A:THR236 4.1 6.9 1.0 N1 A:T03289 4.1 15.1 1.0 ND1 A:HIS205 4.1 10.3 1.0 CG A:HIS205 4.2 9.8 1.0 CG A:GLU269 4.2 10.6 1.0 CG A:GLU238 4.3 8.3 1.0 CB A:ASP142 4.3 7.0 1.0 CB A:GLU238 4.8 7.6 1.0 CE1 A:PHE211 4.9 14.5 1.0

Nickel binding site 3 out of 3 in the M. Tuberculosis Methionine Aminopeptidase with Ni Inhibitor T03


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 3 of M. Tuberculosis Methionine Aminopeptidase with Ni Inhibitor T03 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni288 b:19.4 occ:1.00 O A:HOH447 2.0 29.2 1.0 N1 A:T03289 2.0 15.1 1.0 NE2 A:HIS114 2.1 14.3 1.0 CL A:CL292 2.4 30.0 1.0 C8 A:T03289 2.9 16.9 1.0 CE1 A:HIS114 3.0 18.1 1.0 CD2 A:HIS114 3.0 13.9 1.0 C9 A:T03289 3.1 17.4 1.0 C6 A:T03289 3.4 26.6 1.0 C5 A:T03289 3.6 24.5 1.0 S A:T03289 3.7 17.1 1.0 C1 A:T03289 4.0 22.6 1.0 N2 A:T03289 4.1 10.0 1.0 ND1 A:HIS114 4.1 15.2 1.0 CG A:HIS114 4.2 15.7 1.0 O A:HOH372 4.2 19.6 1.0 N3 A:T03289 4.2 14.0 1.0 O A:HOH354 4.3 12.8 1.0 C4 A:T03289 4.4 27.8 1.0 C7 A:T03289 4.5 22.1 1.0 C2 A:T03289 4.7 26.4 1.0 SG A:CYS113 4.9 16.1 1.0 C3 A:T03289 4.9 25.4 1.0 CD2 A:PHE202 4.9 15.5 1.0 OE1 A:GLU238 4.9 14.3 1.0

J.P.Lu, S.C.Chai, Q.Z.Ye. Catalysis and Inhibition of Mycobacterium Tuberculosis Methionine Aminopeptidase J.Med.Chem. V. 53 1329 2010.
ISSN: ISSN 0022-2623
PubMed: 20038112
DOI: 10.1021/JM901624N