Manganese in PDB 2gu7: E. Coli Methionine Aminopeptidase Unliganded, 1:0.5

All present enzymatic activity of E. Coli Methionine Aminopeptidase Unliganded, 1:0.5:
3.4.11.18;

The structure of E. Coli Methionine Aminopeptidase Unliganded, 1:0.5, PDB code: 2gu7 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)	14.00 / 2.00
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	51.200, 61.980, 77.050, 90.00, 107.36, 90.00
R / Rfree (%)	20.8 / 24.4

The structure of E. Coli Methionine Aminopeptidase Unliganded, 1:0.5 also contains other interesting chemical elements:

Sodium

(Na)

2 atoms

The binding sites of Manganese atom in the E. Coli Methionine Aminopeptidase Unliganded, 1:0.5 (pdb code 2gu7). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the E. Coli Methionine Aminopeptidase Unliganded, 1:0.5, PDB code: 2gu7:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in the E. Coli Methionine Aminopeptidase Unliganded, 1:0.5


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 Unliganded, 1:0.5 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn265 b:20.8 occ:0.71 OD2 A:ASP108 2.0 23.1 1.0 OE2 A:GLU235 2.3 17.8 1.0 OE2 A:GLU204 2.4 18.7 1.0 NE2 A:HIS171 2.4 22.9 1.0 CG A:ASP108 3.1 21.7 1.0 CD A:GLU235 3.1 17.9 1.0 CD A:GLU204 3.2 21.0 1.0 CD2 A:HIS171 3.3 22.7 1.0 MN A:MN266 3.3 22.4 0.3 OE1 A:GLU235 3.3 20.2 1.0 CE1 A:HIS171 3.4 22.2 1.0 OE1 A:GLU204 3.4 23.5 1.0 O A:HOH348 3.7 25.5 1.0 OD1 A:ASP108 3.7 24.1 1.0 OG1 A:THR202 3.9 21.3 1.0 CB A:ASP108 4.1 20.2 1.0 CG2 A:THR202 4.2 20.7 1.0 CB A:THR202 4.3 19.0 1.0 CG A:HIS171 4.4 22.2 1.0 ND1 A:HIS171 4.5 23.9 1.0 CG A:GLU204 4.5 20.7 1.0 CG A:GLU235 4.5 13.8 1.0 O A:HOH375 4.8 31.3 1.0 CE1 A:PHE177 4.8 27.6 1.0

Manganese binding site 2 out of 4 in the E. Coli Methionine Aminopeptidase Unliganded, 1:0.5


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 Unliganded, 1:0.5 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn266 b:22.4 occ:0.28 OE1 A:GLU235 2.1 20.2 1.0 OD1 A:ASP97 2.2 21.9 1.0 OD1 A:ASP108 2.4 24.1 1.0 OD2 A:ASP97 2.6 29.8 1.0 CG A:ASP97 2.7 20.8 1.0 CG A:ASP108 3.1 21.7 1.0 OD2 A:ASP108 3.1 23.1 1.0 CD A:GLU235 3.2 17.9 1.0 MN A:MN265 3.3 20.8 0.7 O A:HOH272 3.4 15.5 1.0 OE2 A:GLU235 3.5 17.8 1.0 O A:HOH348 4.0 25.5 1.0 OG1 A:THR99 4.1 17.2 1.0 OE1 A:GLU204 4.2 23.5 1.0 CB A:ASP97 4.2 20.2 1.0 N A:THR109 4.4 15.6 1.0 O A:THR109 4.5 10.6 1.0 CB A:ASP108 4.5 20.2 1.0 CG A:GLU235 4.5 13.8 1.0 O A:VAL98 4.6 15.3 1.0 O A:HOH375 4.6 31.3 1.0 C A:THR109 4.7 12.7 1.0 O A:HOH352 4.8 21.8 1.0 OE2 A:GLU204 4.8 18.7 1.0 CD A:GLU204 4.8 21.0 1.0 C A:ASP108 4.8 18.1 1.0 CA A:THR109 4.9 13.5 1.0 CB A:GLU235 4.9 13.1 1.0 N A:VAL98 4.9 16.5 1.0 CA A:ASP97 4.9 17.0 1.0 CA A:ASP108 5.0 19.2 1.0

Manganese binding site 3 out of 4 in the E. Coli Methionine Aminopeptidase Unliganded, 1:0.5


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of E. Coli Methionine Aminopeptidase Unliganded, 1:0.5 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn265 b:18.4 occ:0.46 O B:HOH374 2.2 20.6 1.0 OE2 B:GLU235 2.2 17.6 1.0 OD2 B:ASP108 2.2 17.5 1.0 OE2 B:GLU204 2.5 15.8 1.0 NE2 B:HIS171 2.6 16.7 1.0 CD B:GLU235 3.0 13.3 1.0 CG B:ASP108 3.1 16.7 1.0 OE1 B:GLU235 3.2 12.8 1.0 MN B:MN266 3.2 19.1 0.3 CD B:GLU204 3.3 12.9 1.0 OE1 B:GLU204 3.4 16.3 1.0 OD1 B:ASP108 3.4 18.7 1.0 CE1 B:HIS171 3.5 14.4 1.0 CD2 B:HIS171 3.6 13.4 1.0 OG1 B:THR202 3.9 12.8 1.0 CG2 B:THR202 4.2 13.5 1.0 CB B:ASP108 4.3 13.2 1.0 CB B:THR202 4.4 12.8 1.0 CG B:GLU235 4.4 12.7 1.0 ND1 B:HIS171 4.6 14.1 1.0 CG B:GLU204 4.6 11.9 1.0 CE1 B:PHE177 4.7 25.8 1.0 CG B:HIS171 4.7 15.3 1.0 NE2 B:HIS178 4.9 28.4 1.0

Manganese binding site 4 out of 4 in the E. Coli Methionine Aminopeptidase Unliganded, 1:0.5


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of E. Coli Methionine Aminopeptidase Unliganded, 1:0.5 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn266 b:19.1 occ:0.31 OD1 B:ASP108 2.1 18.7 1.0 OE1 B:GLU235 2.4 12.8 1.0 OD1 B:ASP97 2.5 21.9 1.0 OD2 B:ASP97 2.8 23.4 1.0 CG B:ASP108 3.0 16.7 1.0 CG B:ASP97 3.0 19.3 1.0 O B:HOH374 3.2 20.6 1.0 MN B:MN265 3.2 18.4 0.5 OD2 B:ASP108 3.3 17.5 1.0 CD B:GLU235 3.3 13.3 1.0 OE2 B:GLU235 3.6 17.6 1.0 OG1 B:THR99 3.7 20.4 1.0 O B:HOH268 3.8 10.9 1.0 CB B:ASP108 4.5 13.2 1.0 N B:THR109 4.5 13.0 1.0 CB B:ASP97 4.5 17.3 1.0 O B:THR109 4.6 10.0 1.0 O B:VAL98 4.6 16.2 1.0 OE1 B:GLU204 4.7 16.3 1.0 CG B:GLU235 4.7 12.7 1.0 C B:ASP108 4.8 13.5 1.0 C B:THR109 4.9 12.3 1.0 CA B:ASP108 4.9 14.8 1.0

Q.Z.Ye, S.X.Xie, Z.Q.Ma, M.Huang, R.P.Hanzlik. Structural Basis of Catalysis By Monometalated Methionine Aminopeptidase. Proc.Natl.Acad.Sci.Usa V. 103 9470 2006.
ISSN: ISSN 0027-8424
PubMed: 16769889
DOI: 10.1073/PNAS.0602433103