Manganese in PDB 2q93: E. Coli Methionine Aminopeptidase Mn-Form with Inhibitor B21

All present enzymatic activity of E. Coli Methionine Aminopeptidase Mn-Form with Inhibitor B21:
3.4.11.18;

The structure of E. Coli Methionine Aminopeptidase Mn-Form with Inhibitor B21, PDB code: 2q93 was solved by Q.-Z.Ye, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.94 / 1.60
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	39.107, 62.340, 52.441, 90.00, 108.80, 90.00
R / Rfree (%)	22.6 / 25.1

The structure of E. Coli Methionine Aminopeptidase Mn-Form with Inhibitor B21 also contains other interesting chemical elements:

Sodium

(Na)

1 atom

The binding sites of Manganese atom in the E. Coli Methionine Aminopeptidase Mn-Form with Inhibitor B21 (pdb code 2q93). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 2 binding sites of Manganese where determined in the E. Coli Methionine Aminopeptidase Mn-Form with Inhibitor B21, PDB code: 2q93:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in the E. Coli Methionine Aminopeptidase Mn-Form with Inhibitor B21


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of E. Coli Methionine Aminopeptidase Mn-Form with Inhibitor B21 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn301 b:7.7 occ:1.00 OE2 A:GLU235 2.2 11.5 1.0 OD2 A:ASP108 2.2 5.1 1.0 OE2 A:GLU204 2.2 6.3 1.0 OAO A:B21400 2.3 6.9 1.0 NE2 A:HIS171 2.3 6.6 1.0 OAN A:B21400 2.4 6.6 1.0 CAE A:B21400 2.6 9.9 1.0 CD A:GLU204 2.9 11.5 1.0 OE1 A:GLU204 3.0 16.7 1.0 CG A:ASP108 3.1 7.1 1.0 CD2 A:HIS171 3.2 7.7 1.0 CD A:GLU235 3.2 5.7 1.0 CE1 A:HIS171 3.3 4.2 1.0 MN A:MN302 3.5 8.2 1.0 OD1 A:ASP108 3.5 5.2 1.0 OE1 A:GLU235 3.7 8.1 1.0 OG1 A:THR202 3.8 9.7 1.0 CAA A:B21400 4.1 11.3 1.0 CG2 A:THR202 4.2 8.4 1.0 CB A:ASP108 4.3 7.7 1.0 CB A:THR202 4.3 9.9 1.0 CG A:GLU204 4.4 10.0 1.0 CG A:HIS171 4.4 5.7 1.0 ND1 A:HIS171 4.4 7.9 1.0 CG A:GLU235 4.5 8.0 1.0 CE1 A:PHE177 4.6 10.4 1.0 NE2 A:HIS178 4.6 9.1 1.0 O A:HOH505 4.7 10.4 1.0 O A:HOH558 4.8 15.3 1.0 CD2 A:HIS178 4.9 7.7 1.0 OAM A:B21400 5.0 10.0 1.0

Manganese binding site 2 out of 2 in the E. Coli Methionine Aminopeptidase Mn-Form with Inhibitor B21


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of E. Coli Methionine Aminopeptidase Mn-Form with Inhibitor B21 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn302 b:8.2 occ:1.00 OAN A:B21400 2.1 6.6 1.0 OE1 A:GLU235 2.1 8.1 1.0 OD1 A:ASP108 2.2 5.2 1.0 OD1 A:ASP97 2.2 8.2 1.0 O A:HOH505 2.3 10.4 1.0 OD2 A:ASP97 2.5 7.6 1.0 CG A:ASP97 2.6 8.2 1.0 CD A:GLU235 2.9 5.7 1.0 CG A:ASP108 3.1 7.1 1.0 OE2 A:GLU235 3.2 11.5 1.0 CAE A:B21400 3.2 9.9 1.0 OD2 A:ASP108 3.4 5.1 1.0 MN A:MN301 3.5 7.7 1.0 O A:HOH512 3.8 6.4 1.0 OG1 A:THR99 3.8 8.8 1.0 CAC A:B21400 3.9 11.3 1.0 CAA A:B21400 4.0 11.3 1.0 CB A:ASP97 4.1 8.5 1.0 OAO A:B21400 4.2 6.9 1.0 OE1 A:GLU204 4.2 16.7 1.0 O A:VAL98 4.3 7.9 1.0 CG A:GLU235 4.3 8.0 1.0 N A:THR109 4.4 7.5 1.0 O A:HOH573 4.4 14.0 1.0 CB A:ASP108 4.5 7.7 1.0 O A:THR109 4.5 7.8 1.0 C A:THR109 4.7 9.1 1.0 N A:VAL98 4.7 7.7 1.0 O A:HOH538 4.7 8.1 1.0 C A:ASP108 4.7 7.2 1.0 O A:HOH558 4.8 15.3 1.0 CA A:ASP108 4.8 7.9 1.0 CA A:ASP97 4.9 7.4 1.0 C A:VAL98 4.9 7.5 1.0 CB A:GLU235 4.9 7.2 1.0 CA A:THR109 4.9 6.3 1.0 C A:ASP97 4.9 8.3 1.0 CD A:GLU204 5.0 11.5 1.0

Z.Q.Ma, S.X.Xie, Q.Q.Huang, F.J.Nan, T.D.Hurley, Q.Z.Ye. Structural Analysis of Inhibition of E. Coli Methionine Aminopeptidase: Implication of Loop Flexibility in Selective Inhibition of Bacterial Enzymes. Bmc Struct.Biol. V. 7 84 2007.
ISSN: ESSN 1472-6807
PubMed: 18093325
DOI: 10.1186/1472-6807-7-84