Nickel in PDB 3pke: M. Tuberculosis Metap with Bengamide Analog Y10, in Ni Form

All present enzymatic activity of M. Tuberculosis Metap with Bengamide Analog Y10, in Ni Form:
3.4.11.18;

The structure of M. Tuberculosis Metap with Bengamide Analog Y10, in Ni Form, PDB code: 3pke 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)	25.06 / 1.60
Space group	P 63
Cell size a, b, c (Å), α, β, γ (°)	105.454, 105.454, 50.124, 90.00, 90.00, 120.00
R / Rfree (%)	17.3 / 20.8

The structure of M. Tuberculosis Metap with Bengamide Analog Y10, in Ni Form also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Nickel atom in the M. Tuberculosis Metap with Bengamide Analog Y10, in Ni Form (pdb code 3pke). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 2 binding sites of Nickel where determined in the M. Tuberculosis Metap with Bengamide Analog Y10, in Ni Form, PDB code: 3pke:
Jump to Nickel binding site number: 1; 2;

Nickel binding site 1 out of 2 in the M. Tuberculosis Metap with Bengamide Analog Y10, in Ni Form


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of M. Tuberculosis Metap with Bengamide Analog Y10, in Ni Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni287 b:6.8 occ:1.00 OD1 A:ASP142 2.0 5.0 1.0 O3 A:Y10286 2.1 4.6 1.0 OE1 A:GLU269 2.1 4.6 1.0 NE2 A:HIS205 2.1 4.0 1.0 OE2 A:GLU238 2.3 4.0 1.0 O2 A:Y10286 2.4 5.7 1.0 CG A:ASP142 3.0 6.5 1.0 C05 A:Y10286 3.1 8.5 1.0 CD2 A:HIS205 3.1 5.1 1.0 CD A:GLU238 3.1 5.5 1.0 CE1 A:HIS205 3.1 5.9 1.0 CD A:GLU269 3.2 5.8 1.0 NI A:NI288 3.2 7.2 1.0 C06 A:Y10286 3.3 8.1 1.0 OE1 A:GLU238 3.3 6.4 1.0 OD2 A:ASP142 3.4 4.9 1.0 OE2 A:GLU269 3.6 5.5 1.0 C04 A:Y10286 3.6 7.3 1.0 C07 A:Y10286 3.9 6.5 1.0 OG1 A:THR236 3.9 4.7 1.0 O1 A:Y10286 4.0 6.7 1.0 CG2 A:THR236 4.1 3.0 1.0 CB A:ASP142 4.2 6.1 1.0 ND1 A:HIS205 4.2 5.0 1.0 CG A:HIS205 4.3 3.6 1.0 CB A:THR236 4.3 5.9 1.0 CG A:GLU238 4.5 4.7 1.0 CG A:GLU269 4.5 4.9 1.0 NE2 A:HIS212 4.6 6.7 1.0 CE1 A:PHE211 4.7 3.8 1.0 O5 A:Y10286 4.8 8.5 1.0 OD2 A:ASP131 4.9 6.0 1.0 CD2 A:HIS212 5.0 5.0 1.0 C11 A:Y10286 5.0 9.5 1.0

Nickel binding site 2 out of 2 in the M. Tuberculosis Metap with Bengamide Analog Y10, in Ni Form


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of M. Tuberculosis Metap with Bengamide Analog Y10, in Ni Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni288 b:7.2 occ:1.00 OD2 A:ASP142 2.0 4.9 1.0 O3 A:Y10286 2.0 4.6 1.0 OE2 A:GLU269 2.1 5.5 1.0 O1 A:Y10286 2.1 6.7 1.0 OD1 A:ASP131 2.1 7.3 1.0 OD2 A:ASP131 2.2 6.0 1.0 CG A:ASP131 2.5 6.4 1.0 CG A:ASP142 2.9 6.5 1.0 CD A:GLU269 3.0 5.8 1.0 C04 A:Y10286 3.0 7.3 1.0 C05 A:Y10286 3.0 8.5 1.0 OE1 A:GLU269 3.2 4.6 1.0 NI A:NI287 3.2 6.8 1.0 OD1 A:ASP142 3.2 5.0 1.0 O A:HOH397 3.7 10.6 1.0 OE1 A:GLU238 3.9 6.4 1.0 CB A:ASP131 4.0 3.3 1.0 ND2 A:ASN144 4.1 5.3 1.0 OG1 A:THR133 4.2 7.2 1.0 C03 A:Y10286 4.3 6.8 1.0 CG A:GLU269 4.3 4.9 1.0 CB A:ASP142 4.3 6.1 1.0 C06 A:Y10286 4.4 8.1 1.0 N A:THR143 4.4 2.9 1.0 O2 A:Y10286 4.5 5.7 1.0 O A:THR143 4.5 5.9 1.0 O A:HOH324 4.6 8.0 1.0 CD A:GLU238 4.6 5.5 1.0 CB A:ASN144 4.6 4.7 1.0 OE2 A:GLU238 4.6 4.0 1.0 C A:THR143 4.7 5.0 1.0 C A:ASP142 4.7 5.9 1.0 CB A:GLU269 4.8 5.4 1.0 CA A:ASP131 4.8 5.4 1.0 CA A:ASP142 4.8 4.9 1.0 CG A:ASN144 4.9 4.2 1.0 C A:ASP131 5.0 5.3 1.0

J.P.Lu, X.H.Yuan, H.Yuan, W.L.Wang, B.Wan, S.G.Franzblau, Q.Z.Ye. Inhibition of Mycobacterium Tuberculosis Methionine Aminopeptidases By Bengamide Derivatives. Chemmedchem V. 6 1041 2011.
ISSN: ISSN 1860-7179
PubMed: 21465667
DOI: 10.1002/CMDC.201100003