Cobalt in PDB 1c27: E. Coli Methionine Aminopeptidase:Norleucine Phosphonate Complex

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

The structure of E. Coli Methionine Aminopeptidase:Norleucine Phosphonate Complex, PDB code: 1c27 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)	36.60 / 1.95
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	39.298, 67.206, 49.104, 90.00, 111.52, 90.00
R / Rfree (%)	n/a / n/a

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

Sodium

(Na)

1 atom

The binding sites of Cobalt atom in the E. Coli Methionine Aminopeptidase:Norleucine Phosphonate Complex (pdb code 1c27). 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:Norleucine Phosphonate Complex, PDB code: 1c27:
Jump to Cobalt binding site number: 1; 2;

Cobalt binding site 1 out of 2 in the E. Coli Methionine Aminopeptidase:Norleucine 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:Norleucine Phosphonate Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Co401 b:23.8 occ:1.00 OD1 A:ASP108 1.9 18.2 1.0 OE1 A:GLU235 2.1 20.4 1.0 NE2 A:HIS171 2.1 17.2 1.0 O1 A:NLP300 2.2 25.9 1.0 OE2 A:GLU204 2.3 16.0 1.0 O2 A:NLP300 2.6 30.2 1.0 P A:NLP300 2.9 23.6 1.0 CG A:ASP108 2.9 18.6 1.0 CD A:GLU235 3.1 30.3 1.0 CE1 A:HIS171 3.1 17.1 1.0 CD2 A:HIS171 3.1 17.6 1.0 CD A:GLU204 3.2 34.2 1.0 CO A:CO402 3.2 24.0 1.0 OE2 A:GLU235 3.4 17.3 1.0 OE1 A:GLU204 3.4 25.0 1.0 OD2 A:ASP108 3.4 16.9 1.0 OG1 A:THR202 3.8 17.7 1.0 O3 A:NLP300 4.0 27.2 1.0 N A:NLP300 4.0 25.5 1.0 CA A:NLP300 4.1 28.3 1.0 CB A:ASP108 4.1 13.8 1.0 CG2 A:THR202 4.2 13.6 1.0 ND1 A:HIS171 4.2 15.6 1.0 CG A:HIS171 4.3 15.9 1.0 CB A:THR202 4.4 12.1 1.0 CG A:GLU235 4.5 16.0 1.0 NE2 A:HIS178 4.5 34.3 1.0 CG A:GLU204 4.5 23.5 1.0 CE1 A:PHE177 4.8 22.5 1.0 CD2 A:HIS178 4.9 31.8 1.0

Cobalt binding site 2 out of 2 in the E. Coli Methionine Aminopeptidase:Norleucine 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:Norleucine Phosphonate Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Co402 b:24.0 occ:1.00 OD2 A:ASP108 2.0 16.9 1.0 OE2 A:GLU235 2.2 17.3 1.0 OD1 A:ASP97 2.2 17.9 1.0 O1 A:NLP300 2.3 25.9 1.0 OD2 A:ASP97 2.3 18.2 1.0 N A:NLP300 2.4 25.5 1.0 CG A:ASP97 2.6 16.9 1.0 CG A:ASP108 2.9 18.6 1.0 OD1 A:ASP108 3.1 18.2 1.0 CD A:GLU235 3.1 30.3 1.0 CO A:CO401 3.2 23.8 1.0 CA A:NLP300 3.3 28.3 1.0 P A:NLP300 3.3 23.6 1.0 OE1 A:GLU235 3.4 20.4 1.0 O A:HOH502 3.7 21.5 1.0 OG1 A:THR99 4.0 17.9 1.0 CB A:ASP97 4.1 14.7 1.0 O2 A:NLP300 4.2 30.2 1.0 CB A:ASP108 4.2 13.8 1.0 OE1 A:GLU204 4.3 25.0 1.0 O A:HOH578 4.3 38.4 1.0 O A:HOH577 4.4 43.8 1.0 N A:THR109 4.4 9.6 1.0 CG A:GLU235 4.5 16.0 1.0 O3 A:NLP300 4.6 27.2 1.0 O A:THR109 4.6 13.6 1.0 O A:VAL98 4.6 15.9 1.0 C A:ASP108 4.7 20.4 1.0 CB A:NLP300 4.7 34.7 1.0 OE2 A:GLU204 4.7 16.0 1.0 CA A:ASP108 4.8 18.0 1.0 CD A:GLU204 4.8 34.2 1.0 C A:THR109 4.8 11.6 1.0 CB A:GLU235 4.9 11.2 1.0 CA A:ASP97 4.9 11.5 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