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Manganese in PDB 2p9a: E. Coli Methionine Aminopeptidase Dimetalated with Inhibitor YE6

Enzymatic activity of E. Coli Methionine Aminopeptidase Dimetalated with Inhibitor YE6

All present enzymatic activity of E. Coli Methionine Aminopeptidase Dimetalated with Inhibitor YE6:
3.4.11.18;

Protein crystallography data

The structure of E. Coli Methionine Aminopeptidase Dimetalated with Inhibitor YE6, PDB code: 2p9a was solved by Q.Ye, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 1.60
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 37.986, 60.649, 50.486, 90.00, 104.82, 90.00
R / Rfree (%) 20.6 / 23.1

Other elements in 2p9a:

The structure of E. Coli Methionine Aminopeptidase Dimetalated with Inhibitor YE6 also contains other interesting chemical elements:

Chlorine (Cl) 1 atom
Sodium (Na) 1 atom

Manganese Binding Sites:

The binding sites of Manganese atom in the E. Coli Methionine Aminopeptidase Dimetalated with Inhibitor YE6 (pdb code 2p9a). 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 Dimetalated with Inhibitor YE6, PDB code: 2p9a:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in 2p9a

Go back to Manganese Binding Sites List in 2p9a
Manganese binding site 1 out of 2 in the E. Coli Methionine Aminopeptidase Dimetalated with Inhibitor YE6


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 Dimetalated with Inhibitor YE6 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn264

b:11.9
occ:1.00
O A:HOH276 2.2 14.2 1.0
OD1 A:ASP97 2.2 11.5 1.0
OD1 A:ASP108 2.2 12.9 1.0
O A:HOH442 2.3 12.5 1.0
OE1 A:GLU235 2.3 10.7 1.0
OD2 A:ASP97 2.4 13.1 1.0
CG A:ASP97 2.6 11.6 1.0
CG A:ASP108 3.1 11.4 1.0
CD A:GLU235 3.2 9.6 1.0
OD2 A:ASP108 3.2 10.5 1.0
MN A:MN265 3.3 12.2 1.0
OE2 A:GLU235 3.4 9.2 1.0
O A:HOH269 3.8 9.2 1.0
OG1 A:THR99 3.9 15.4 1.0
O A:HOH441 4.1 18.9 1.0
CB A:ASP97 4.1 10.9 1.0
OAO A:YE6267 4.4 19.7 1.0
O A:VAL98 4.4 11.6 1.0
OE1 A:GLU204 4.4 14.7 1.0
N A:THR109 4.5 10.7 1.0
CB A:ASP108 4.5 13.0 1.0
CG A:GLU235 4.6 9.9 1.0
O A:HOH295 4.6 13.3 1.0
O A:HOH277 4.6 34.1 1.0
O A:THR109 4.8 11.4 1.0
OE2 A:GLU204 4.8 13.3 1.0
C A:ASP108 4.8 10.6 1.0
CD A:GLU204 4.9 13.2 1.0
CA A:ASP97 4.9 9.0 1.0
C A:THR109 4.9 10.5 1.0
N A:VAL98 4.9 11.0 1.0
CA A:ASP108 4.9 11.2 1.0
C A:ASP97 5.0 11.3 1.0

Manganese binding site 2 out of 2 in 2p9a

Go back to Manganese Binding Sites List in 2p9a
Manganese binding site 2 out of 2 in the E. Coli Methionine Aminopeptidase Dimetalated with Inhibitor YE6


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 Dimetalated with Inhibitor YE6 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn265

b:12.2
occ:1.00
O A:HOH276 2.1 14.2 1.0
OE2 A:GLU235 2.1 9.2 1.0
OD2 A:ASP108 2.1 10.5 1.0
OE2 A:GLU204 2.2 13.3 1.0
NE2 A:HIS171 2.3 12.0 1.0
CD A:GLU204 3.0 13.2 1.0
CD A:GLU235 3.1 9.6 1.0
CG A:ASP108 3.1 11.4 1.0
CD2 A:HIS171 3.2 13.3 1.0
CE1 A:HIS171 3.2 11.9 1.0
OE1 A:GLU204 3.3 14.7 1.0
MN A:MN264 3.3 11.9 1.0
OE1 A:GLU235 3.4 10.7 1.0
OD1 A:ASP108 3.6 12.9 1.0
OG1 A:THR202 3.7 14.1 1.0
O A:HOH441 3.8 18.9 1.0
CG2 A:THR202 4.1 11.6 1.0
CB A:THR202 4.2 12.6 1.0
CB A:ASP108 4.2 13.0 1.0
ND1 A:HIS171 4.3 11.6 1.0
CG A:HIS171 4.3 11.4 1.0
CG A:GLU204 4.4 14.1 1.0
CG A:GLU235 4.4 9.9 1.0
O A:HOH442 4.6 12.5 1.0
CE1 A:PHE177 4.7 15.8 1.0
CE1 A:HIS178 4.8 26.5 1.0
NE2 A:HIS178 4.8 24.5 1.0
CB A:GLU204 4.9 11.5 1.0

Reference:

M.Huang, S.X.Xie, Z.Q.Ma, Q.Q.Huang, F.J.Nan, Q.Z.Ye. Inhibition of Monometalated Methionine Aminopeptidase: Inhibitor Discovery and Crystallographic Analysis. J.Med.Chem. V. 50 5735 2007.
ISSN: ISSN 0022-2623
PubMed: 17948983
DOI: 10.1021/JM700930K
Page generated: Tue Dec 15 04:04:24 2020

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