Cobalt in PDB 1c23: E. Coli Methionine Aminopeptidase: Methionine Phosphonate Complex

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

The structure of E. Coli Methionine Aminopeptidase: Methionine Phosphonate Complex, PDB code: 1c23 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)	32.20 / 2.00
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	39.221, 67.518, 48.823, 90.00, 111.20, 90.00
R / Rfree (%)	n/a / n/a

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

Sodium

(Na)

1 atom

The binding sites of Cobalt atom in the E. Coli Methionine Aminopeptidase: Methionine Phosphonate Complex (pdb code 1c23). 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 Phosphonate Complex, PDB code: 1c23:
Jump to Cobalt binding site number: 1; 2;

Cobalt binding site 1 out of 2 in the E. Coli Methionine Aminopeptidase: Methionine Phosphonate 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 Phosphonate Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Co401 b:15.6 occ:1.00 OD1 A:ASP108 1.9 10.3 1.0 OE1 A:GLU235 2.1 14.7 1.0 NE2 A:HIS171 2.1 11.3 1.0 O1 A:MPH300 2.1 16.8 1.0 OE2 A:GLU204 2.4 12.2 1.0 O2 A:MPH300 2.5 15.4 1.0 P A:MPH300 2.7 13.4 1.0 CG A:ASP108 2.9 11.9 1.0 CE1 A:HIS171 3.1 14.5 1.0 CD A:GLU235 3.1 14.3 1.0 CD2 A:HIS171 3.1 13.6 1.0 CD A:GLU204 3.2 19.0 1.0 CO A:CO402 3.3 15.6 1.0 OE1 A:GLU204 3.4 15.4 1.0 OE2 A:GLU235 3.5 11.9 1.0 OD2 A:ASP108 3.5 12.4 1.0 O3 A:MPH300 3.8 11.1 1.0 OG1 A:THR202 3.9 9.9 1.0 N A:MPH300 4.0 9.7 1.0 CA A:MPH300 4.0 10.7 1.0 CB A:ASP108 4.1 12.2 1.0 CG2 A:THR202 4.2 6.9 1.0 ND1 A:HIS171 4.2 10.3 1.0 CG A:HIS171 4.3 11.0 1.0 NE2 A:HIS178 4.4 20.1 1.0 CB A:THR202 4.4 6.3 1.0 CG A:GLU235 4.5 9.9 1.0 CG A:GLU204 4.6 11.8 1.0 O A:HOH582 4.7 37.3 1.0 CD2 A:HIS178 4.8 16.8 1.0 CE1 A:PHE177 4.9 14.2 1.0

Cobalt binding site 2 out of 2 in the E. Coli Methionine Aminopeptidase: Methionine Phosphonate 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 Phosphonate Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Co402 b:15.6 occ:1.00 OD2 A:ASP108 2.1 12.4 1.0 OD1 A:ASP97 2.1 12.8 1.0 O1 A:MPH300 2.1 16.8 1.0 OE2 A:GLU235 2.2 11.9 1.0 N A:MPH300 2.3 9.7 1.0 OD2 A:ASP97 2.4 12.7 1.0 CG A:ASP97 2.5 9.8 1.0 CG A:ASP108 3.0 11.9 1.0 CA A:MPH300 3.0 10.7 1.0 CD A:GLU235 3.1 14.3 1.0 P A:MPH300 3.2 13.4 1.0 OD1 A:ASP108 3.2 10.3 1.0 CO A:CO401 3.3 15.6 1.0 OE1 A:GLU235 3.3 14.7 1.0 O A:HOH502 4.0 15.7 1.0 OG1 A:THR99 4.0 9.3 1.0 CB A:ASP97 4.0 8.0 1.0 O2 A:MPH300 4.0 15.4 1.0 OE1 A:GLU204 4.1 15.4 1.0 O A:HOH505 4.2 22.6 1.0 CB A:ASP108 4.3 12.2 1.0 O A:HOH583 4.3 26.7 1.0 O3 A:MPH300 4.3 11.1 1.0 N A:THR109 4.4 5.8 1.0 CG A:GLU235 4.5 9.9 1.0 CB A:MPH300 4.5 15.1 1.0 O A:THR109 4.6 11.3 1.0 C A:ASP108 4.7 13.4 1.0 O A:VAL98 4.7 15.1 1.0 CA A:ASP108 4.8 15.1 1.0 OE2 A:GLU204 4.8 12.2 1.0 CD A:GLU204 4.8 19.0 1.0 C A:THR109 4.8 10.6 1.0 CA A:ASP97 4.9 7.5 1.0 CB A:GLU235 4.9 10.1 1.0 C A:ASP97 5.0 8.2 1.0 N A:VAL98 5.0 8.0 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