Cobalt in PDB 1c24: E. Coli Methionine Aminopeptidase: Methionine Phosphinate Complex

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

The structure of E. Coli Methionine Aminopeptidase: Methionine Phosphinate Complex, PDB code: 1c24 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)	24.60 / 1.70
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	39.293, 67.633, 48.865, 90.00, 111.15, 90.00
R / Rfree (%)	n/a / n/a

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

Sodium

(Na)

1 atom

The binding sites of Cobalt atom in the E. Coli Methionine Aminopeptidase: Methionine Phosphinate Complex (pdb code 1c24). 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 Phosphinate Complex, PDB code: 1c24:
Jump to Cobalt binding site number: 1; 2;

Cobalt binding site 1 out of 2 in the E. Coli Methionine Aminopeptidase: Methionine Phosphinate 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 Phosphinate Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Co401 b:17.6 occ:0.99 OD1 A:ASP108 1.9 14.0 1.0 O2 A:MPJ300 2.0 13.7 0.6 OE1 A:GLU235 2.1 15.5 1.0 NE2 A:HIS171 2.1 9.6 1.0 O1 A:MPJ300 2.3 29.3 0.7 OE2 A:GLU204 2.4 14.6 1.0 O2 A:MPJ300 2.6 18.7 0.7 P A:MPJ300 2.8 35.5 0.6 CG A:ASP108 2.9 14.7 1.0 P A:MPJ300 2.9 18.7 0.7 CD A:GLU235 3.0 21.1 1.0 CE1 A:HIS171 3.1 18.3 1.0 CD2 A:HIS171 3.1 17.1 1.0 CD A:GLU204 3.2 19.3 1.0 CO A:CO402 3.2 16.1 1.0 OE2 A:GLU235 3.4 14.2 1.0 OE1 A:GLU204 3.4 20.1 1.0 OD2 A:ASP108 3.4 15.3 1.0 OG1 A:THR202 3.9 14.2 1.0 O1 A:MPJ300 3.9 12.4 0.6 N A:MPJ300 4.1 13.3 1.0 CB A:ASP108 4.1 12.5 1.0 CA A:MPJ300 4.1 17.0 1.0 CG2 A:THR202 4.2 11.3 1.0 ND1 A:HIS171 4.3 10.8 1.0 CG A:HIS171 4.3 13.8 1.0 CB A:THR202 4.4 9.9 1.0 CG A:GLU235 4.4 14.3 1.0 CG A:GLU204 4.5 14.1 1.0 NE2 A:HIS178 4.6 22.7 1.0 CE1 A:PHE177 5.0 19.1 1.0 CD2 A:HIS178 5.0 20.1 1.0

Cobalt binding site 2 out of 2 in the E. Coli Methionine Aminopeptidase: Methionine Phosphinate 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 Phosphinate Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Co402 b:16.1 occ:0.96 O2 A:MPJ300 2.0 13.7 0.6 OD2 A:ASP108 2.0 15.3 1.0 OE2 A:GLU235 2.1 14.2 1.0 OD1 A:ASP97 2.1 13.8 1.0 N A:MPJ300 2.3 13.3 1.0 O1 A:MPJ300 2.3 29.3 0.7 OD2 A:ASP97 2.4 15.3 1.0 CG A:ASP97 2.5 8.7 1.0 CG A:ASP108 2.9 14.7 1.0 CA A:MPJ300 3.1 17.0 1.0 CD A:GLU235 3.1 21.1 1.0 OD1 A:ASP108 3.1 14.0 1.0 P A:MPJ300 3.1 35.5 0.6 CO A:CO401 3.2 17.6 1.0 P A:MPJ300 3.2 18.7 0.7 OE1 A:GLU235 3.3 15.5 1.0 O A:HOH502 3.9 19.7 1.0 OG1 A:THR99 4.0 15.1 1.0 CB A:ASP97 4.0 9.5 1.0 O2 A:MPJ300 4.1 18.7 0.7 OE1 A:GLU204 4.1 20.1 1.0 O A:HOH570 4.2 33.2 1.0 O1 A:MPJ300 4.3 12.4 0.6 CB A:ASP108 4.3 12.5 1.0 O A:HOH552 4.4 27.0 1.0 CG A:GLU235 4.4 14.3 1.0 N A:THR109 4.5 8.3 1.0 CB A:MPJ300 4.5 21.5 1.0 O A:VAL98 4.7 16.8 1.0 C A:ASP108 4.7 15.8 1.0 O A:THR109 4.7 12.3 1.0 OE2 A:GLU204 4.8 14.6 1.0 CD A:GLU204 4.8 19.3 1.0 CA A:ASP108 4.8 13.5 1.0 CA A:ASP97 4.8 10.5 1.0 C A:THR109 4.9 12.9 1.0 CB A:GLU235 4.9 9.6 1.0 C A:ASP97 5.0 12.6 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