Cobalt in PDB 1c21: E. Coli Methionine Aminopeptidase: Methionine Complex

All present enzymatic activity of E. Coli Methionine Aminopeptidase: Methionine Complex:
3.4.11.18;

The structure of E. Coli Methionine Aminopeptidase: Methionine Complex, PDB code: 1c21 was solved by W.T.Lowther, Y.Zhang, P.B.Sampson, J.F.Honek, B.W.Matthews, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	24.80 / 1.80
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	39.242, 67.588, 48.927, 90.00, 111.20, 90.00
R / Rfree (%)	n/a / n/a

The structure of E. Coli Methionine Aminopeptidase: Methionine Complex also contains other interesting chemical elements:

Sodium

(Na)

1 atom

The binding sites of Cobalt atom in the E. Coli Methionine Aminopeptidase: Methionine Complex (pdb code 1c21). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 2 binding sites of Cobalt where determined in the E. Coli Methionine Aminopeptidase: Methionine Complex, PDB code: 1c21:
Jump to Cobalt binding site number: 1; 2;

Cobalt binding site 1 out of 2 in the E. Coli Methionine Aminopeptidase: Methionine Complex


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: Methionine Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Co401 b:20.4 occ:1.00 OE1 A:GLU235 2.0 15.6 1.0 OD1 A:ASP108 2.0 17.7 1.0 O A:MET300 2.0 17.4 1.0 OE2 A:GLU204 2.1 14.2 1.0 NE2 A:HIS171 2.1 15.9 1.0 C A:MET300 2.9 38.8 1.0 CD A:GLU235 3.0 24.0 1.0 CG A:ASP108 3.0 16.2 1.0 CD A:GLU204 3.0 25.5 1.0 CE1 A:HIS171 3.1 17.9 1.0 CD2 A:HIS171 3.1 18.4 1.0 OXT A:MET300 3.2 27.8 1.0 OE1 A:GLU204 3.2 24.5 1.0 CO A:CO402 3.3 21.6 1.0 OE2 A:GLU235 3.3 17.6 1.0 OD2 A:ASP108 3.5 16.3 1.0 OG1 A:THR202 3.6 14.7 1.0 CG2 A:THR202 3.9 13.8 1.0 CB A:THR202 4.1 12.3 1.0 CA A:MET300 4.2 37.1 1.0 CB A:ASP108 4.2 14.0 1.0 ND1 A:HIS171 4.2 17.0 1.0 CG A:HIS171 4.3 16.8 1.0 CG A:GLU204 4.3 18.6 1.0 CG A:GLU235 4.4 18.3 1.0 N A:MET300 4.4 19.0 1.0 O A:HOH598 4.7 50.6 1.0 NE2 A:HIS178 4.9 28.6 1.0 CB A:GLU204 4.9 10.6 1.0

Cobalt binding site 2 out of 2 in the E. Coli Methionine Aminopeptidase: Methionine Complex


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: Methionine Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Co402 b:21.6 occ:1.00 OD2 A:ASP108 2.1 16.3 1.0 OD1 A:ASP97 2.2 15.9 1.0 OE2 A:GLU235 2.2 17.6 1.0 N A:MET300 2.2 19.0 1.0 O A:MET300 2.2 17.4 1.0 OD2 A:ASP97 2.3 16.4 1.0 CG A:ASP97 2.6 12.7 1.0 CA A:MET300 2.9 37.1 1.0 C A:MET300 2.9 38.8 1.0 CG A:ASP108 3.0 16.2 1.0 OD1 A:ASP108 3.2 17.7 1.0 CD A:GLU235 3.2 24.0 1.0 CO A:CO401 3.3 20.4 1.0 OE1 A:GLU235 3.4 15.6 1.0 O A:HOH504 3.8 17.2 1.0 OG1 A:THR99 3.9 19.4 1.0 CB A:ASP97 4.1 10.2 1.0 OXT A:MET300 4.2 27.8 1.0 CB A:ASP108 4.3 14.0 1.0 O A:HOH598 4.4 50.6 1.0 OE1 A:GLU204 4.4 24.5 1.0 N A:THR109 4.4 8.9 1.0 CB A:MET300 4.4 42.9 1.0 CG A:GLU235 4.5 18.3 1.0 O A:VAL98 4.6 15.3 1.0 O A:HOH553 4.6 19.7 1.0 C A:ASP108 4.6 14.8 1.0 O A:THR109 4.7 14.9 1.0 OE2 A:GLU204 4.8 14.2 1.0 CA A:ASP108 4.8 14.9 1.0 C A:THR109 4.8 13.9 1.0 CD A:GLU204 4.9 25.5 1.0 CA A:ASP97 4.9 8.9 1.0 N A:VAL98 4.9 13.9 1.0 CB A:GLU235 5.0 9.3 1.0 CA A:THR109 5.0 7.5 1.0

W.T.Lowther, Y.Zhang, P.B.Sampson, J.F.Honek, B.W.Matthews. Insights Into the Mechanism of Escherichia Coli Methionine Aminopeptidase From the Structural Analysis of Reaction Products and Phosphorus-Based Transition-State Analogues. Biochemistry V. 38 14810 1999.
ISSN: ISSN 0006-2960
PubMed: 10555963
DOI: 10.1021/BI991711G