Manganese in PDB 3pkb: M. Tuberculosis Metap with Bengamide Analog Y16, in Mn Form

All present enzymatic activity of M. Tuberculosis Metap with Bengamide Analog Y16, in Mn Form:
3.4.11.18;

The structure of M. Tuberculosis Metap with Bengamide Analog Y16, in Mn Form, PDB code: 3pkb 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)	33.84 / 1.25
Space group	P 63
Cell size a, b, c (Å), α, β, γ (°)	105.952, 105.952, 50.131, 90.00, 90.00, 120.00
R / Rfree (%)	16.8 / 18.1

The structure of M. Tuberculosis Metap with Bengamide Analog Y16, in Mn Form also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Manganese atom in the M. Tuberculosis Metap with Bengamide Analog Y16, in Mn Form (pdb code 3pkb). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 2 binding sites of Manganese where determined in the M. Tuberculosis Metap with Bengamide Analog Y16, in Mn Form, PDB code: 3pkb:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in the M. Tuberculosis Metap with Bengamide Analog Y16, in Mn Form


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of M. Tuberculosis Metap with Bengamide Analog Y16, in Mn Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn287 b:8.5 occ:1.00 OD1 A:ASP142 2.1 8.8 1.0 NE2 A:HIS205 2.2 8.5 1.0 O3 A:Y16286 2.2 8.7 1.0 OE2 A:GLU238 2.3 8.8 1.0 OE1 A:GLU269 2.3 8.2 1.0 O2 A:Y16286 2.3 9.8 1.0 CD2 A:HIS205 3.1 8.2 1.0 CD A:GLU238 3.1 9.7 1.0 CG A:ASP142 3.1 8.6 1.0 C05 A:Y16286 3.2 9.0 1.0 CE1 A:HIS205 3.2 8.7 1.0 C06 A:Y16286 3.2 9.5 1.0 CD A:GLU269 3.3 7.3 1.0 OE1 A:GLU238 3.3 10.8 1.0 MN A:MN288 3.4 8.7 1.0 OD2 A:ASP142 3.6 9.4 1.0 OE2 A:GLU269 3.7 9.8 1.0 C04 A:Y16286 3.8 10.6 1.0 C07 A:Y16286 3.9 10.7 1.0 OG1 A:THR236 3.9 8.5 1.0 CG2 A:THR236 4.0 9.3 1.0 O1 A:Y16286 4.1 10.8 1.0 CB A:ASP142 4.3 9.6 1.0 CG A:HIS205 4.3 7.9 1.0 CB A:THR236 4.3 7.3 1.0 ND1 A:HIS205 4.3 8.5 1.0 CG A:GLU238 4.5 9.5 1.0 NE2 A:HIS212 4.5 10.8 1.0 CG A:GLU269 4.6 7.9 1.0 CE1 A:PHE211 4.7 9.6 1.0 C11 A:Y16286 4.8 12.0 1.0 O6 A:Y16286 4.9 11.4 1.0

Manganese binding site 2 out of 2 in the M. Tuberculosis Metap with Bengamide Analog Y16, in Mn Form


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of M. Tuberculosis Metap with Bengamide Analog Y16, in Mn Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn288 b:8.7 occ:1.00 OD2 A:ASP142 2.1 9.4 1.0 OE2 A:GLU269 2.1 9.8 1.0 O1 A:Y16286 2.1 10.8 1.0 O3 A:Y16286 2.2 8.7 1.0 OD1 A:ASP131 2.2 8.9 1.0 OD2 A:ASP131 2.3 9.3 1.0 CG A:ASP131 2.6 9.7 1.0 CG A:ASP142 3.0 8.6 1.0 CD A:GLU269 3.0 7.3 1.0 C05 A:Y16286 3.1 9.0 1.0 C04 A:Y16286 3.1 10.6 1.0 OE1 A:GLU269 3.2 8.2 1.0 OD1 A:ASP142 3.2 8.8 1.0 MN A:MN287 3.4 8.5 1.0 O A:HOH312 3.8 13.3 1.0 OE1 A:GLU238 4.0 10.8 1.0 CB A:ASP131 4.1 8.8 1.0 ND2 A:ASN144 4.1 8.8 1.0 OG1 A:THR133 4.2 12.5 1.0 CG A:GLU269 4.4 7.9 1.0 CB A:ASP142 4.4 9.6 1.0 C06 A:Y16286 4.4 9.5 1.0 C03 A:Y16286 4.4 10.5 1.0 N A:THR143 4.4 7.1 1.0 O A:THR143 4.5 8.2 1.0 O2 A:Y16286 4.5 9.8 1.0 O A:HOH330 4.5 10.7 1.0 CB A:ASN144 4.7 8.9 1.0 C A:THR143 4.7 6.8 1.0 C A:ASP142 4.7 8.3 1.0 OE2 A:GLU238 4.7 8.8 1.0 CD A:GLU238 4.8 9.7 1.0 CA A:ASP131 4.8 7.5 1.0 CB A:GLU269 4.8 7.5 1.0 CA A:ASP142 4.9 7.3 1.0 CG A:ASN144 4.9 7.8 1.0 CA A:THR143 5.0 8.2 1.0 C A:ASP131 5.0 7.8 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