Cobalt in PDB 2mat: E.Coli Methionine Aminopeptidase at 1.9 Angstrom Resolution

All present enzymatic activity of E.Coli Methionine Aminopeptidase at 1.9 Angstrom Resolution:
3.4.11.18;

The structure of E.Coli Methionine Aminopeptidase at 1.9 Angstrom Resolution, PDB code: 2mat was solved by W.T.Lowther, A.M.Orville, D.T.Madden, S.Lim, D.H.Rich, B.W.Matthews, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	35.50 / 1.90
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	39.299, 67.683, 48.863, 90.00, 111.24, 90.00
R / Rfree (%)	n/a / n/a

The structure of E.Coli Methionine Aminopeptidase at 1.9 Angstrom Resolution also contains other interesting chemical elements:

Sodium

(Na)

1 atom

The binding sites of Cobalt atom in the E.Coli Methionine Aminopeptidase at 1.9 Angstrom Resolution (pdb code 2mat). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 3 binding sites of Cobalt where determined in the E.Coli Methionine Aminopeptidase at 1.9 Angstrom Resolution, PDB code: 2mat:
Jump to Cobalt binding site number: 1; 2; 3;

Cobalt binding site 1 out of 3 in the E.Coli Methionine Aminopeptidase at 1.9 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 1 of E.Coli Methionine Aminopeptidase at 1.9 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Co401 b:16.5 occ:1.00 OD2 A:ASP108 1.9 10.9 1.0 OE2 A:GLU235 2.0 12.4 1.0 OE2 A:GLU204 2.1 8.7 1.0 O A:HOH502 2.1 12.0 1.0 NE2 A:HIS171 2.2 12.3 1.0 CG A:ASP108 2.9 15.1 1.0 CD A:GLU235 3.0 19.0 1.0 CD A:GLU204 3.1 19.0 1.0 CE1 A:HIS171 3.1 16.6 1.0 CD2 A:HIS171 3.1 13.8 1.0 CO A:CO402 3.2 14.2 1.0 OE1 A:GLU204 3.3 15.0 1.0 OE1 A:GLU235 3.3 11.7 1.0 OD1 A:ASP108 3.4 12.0 1.0 OG1 A:THR202 3.5 11.0 1.0 O A:HOH505 3.6 16.8 1.0 CG2 A:THR202 3.8 6.4 1.0 CB A:THR202 4.1 7.7 1.0 CB A:ASP108 4.1 10.8 1.0 ND1 A:HIS171 4.3 12.7 1.0 CG A:HIS171 4.3 12.4 1.0 CG A:GLU235 4.3 14.2 1.0 O A:HOH503 4.3 11.4 1.0 CG A:GLU204 4.3 13.5 1.0 NE2 A:HIS178 4.9 24.8 1.0 CB A:GLU204 4.9 4.5 1.0 CE1 A:PHE177 5.0 20.1 1.0 OD2 A:ASP97 5.0 15.2 1.0

Cobalt binding site 2 out of 3 in the E.Coli Methionine Aminopeptidase at 1.9 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 2 of E.Coli Methionine Aminopeptidase at 1.9 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Co402 b:14.2 occ:1.00 OD1 A:ASP108 2.0 12.0 1.0 O A:HOH502 2.1 12.0 1.0 OD1 A:ASP97 2.1 11.6 1.0 OE1 A:GLU235 2.1 11.7 1.0 O A:HOH503 2.2 11.4 1.0 OD2 A:ASP97 2.4 15.2 1.0 CG A:ASP97 2.5 9.6 1.0 CG A:ASP108 3.0 15.1 1.0 CD A:GLU235 3.1 19.0 1.0 OD2 A:ASP108 3.2 10.9 1.0 CO A:CO401 3.2 16.5 1.0 OE2 A:GLU235 3.3 12.4 1.0 O A:HOH590 3.8 12.4 1.0 OG1 A:THR99 3.9 12.3 1.0 O A:HOH505 4.0 16.8 1.0 CB A:ASP97 4.1 8.6 1.0 OE1 A:GLU204 4.2 15.0 1.0 CB A:ASP108 4.3 10.8 1.0 O A:HOH506 4.3 32.6 1.0 CG A:GLU235 4.4 14.2 1.0 N A:THR109 4.4 9.3 1.0 OE2 A:GLU204 4.5 8.7 1.0 O A:VAL98 4.6 15.7 1.0 O A:THR109 4.6 14.2 1.0 O A:HOH504 4.6 17.3 1.0 C A:ASP108 4.7 18.3 1.0 CD A:GLU204 4.7 19.0 1.0 CA A:ASP108 4.8 13.4 1.0 C A:THR109 4.8 9.8 1.0 CA A:ASP97 4.9 8.3 1.0 CB A:GLU235 4.9 11.5 1.0 N A:VAL98 5.0 9.6 1.0 C A:ASP97 5.0 12.6 1.0 CA A:THR109 5.0 7.3 1.0

Cobalt binding site 3 out of 3 in the E.Coli Methionine Aminopeptidase at 1.9 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 3 of E.Coli Methionine Aminopeptidase at 1.9 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Co403 b:56.9 occ:1.00 NE2 A:HIS54 2.2 47.1 1.0 O A:HOH554 2.3 28.4 1.0 O A:HOH556 2.5 36.6 1.0 O A:HOH555 2.7 40.3 1.0 CE1 A:HIS54 3.2 45.8 1.0 CD2 A:HIS54 3.2 43.7 1.0 O A:GLU52 4.0 21.4 1.0 O A:HOH539 4.0 22.9 1.0 ND1 A:HIS54 4.3 43.6 1.0 CG A:HIS54 4.4 41.6 1.0 O A:ASN51 4.4 24.5 1.0 C A:GLU52 4.8 17.9 1.0 CA A:GLU52 5.0 15.3 1.0

W.T.Lowther, A.M.Orville, D.T.Madden, S.Lim, D.H.Rich, B.W.Matthews. Escherichia Coli Methionine Aminopeptidase: Implications of Crystallographic Analyses of the Native, Mutant, and Inhibited Enzymes For the Mechanism of Catalysis. Biochemistry V. 38 7678 1999.
ISSN: ISSN 0006-2960
PubMed: 10387007
DOI: 10.1021/BI990684R