Cobalt in PDB 2b3k: Crystal Structure of Human Methionine Aminopeptidase Type I in the Holo Form

All present enzymatic activity of Crystal Structure of Human Methionine Aminopeptidase Type I in the Holo Form:
3.4.11.18;

The structure of Crystal Structure of Human Methionine Aminopeptidase Type I in the Holo Form, PDB code: 2b3k was solved by A.Addlagatta, X.Hu, J.O.Liu, B.W.Matthews, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 1.55
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	47.432, 77.522, 48.308, 90.00, 90.60, 90.00
R / Rfree (%)	19 / 21.5

The structure of Crystal Structure of Human Methionine Aminopeptidase Type I in the Holo Form also contains other interesting chemical elements:

Potassium

(K)

1 atom

The binding sites of Cobalt atom in the Crystal Structure of Human Methionine Aminopeptidase Type I in the Holo Form (pdb code 2b3k). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 2 binding sites of Cobalt where determined in the Crystal Structure of Human Methionine Aminopeptidase Type I in the Holo Form, PDB code: 2b3k:
Jump to Cobalt binding site number: 1; 2;

Cobalt binding site 1 out of 2 in the Crystal Structure of Human Methionine Aminopeptidase Type I in the Holo Form


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 1 of Crystal Structure of Human Methionine Aminopeptidase Type I in the Holo Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Co401 b:15.4 occ:1.00 OE2 A:GLU367 2.0 15.9 1.0 O A:HOH500 2.0 19.5 1.0 OD2 A:ASP240 2.0 12.7 1.0 NE2 A:HIS303 2.1 10.2 1.0 OE1 A:GLU336 2.3 19.6 1.0 CD A:GLU367 3.0 18.4 1.0 CE1 A:HIS303 3.0 15.9 1.0 CG A:ASP240 3.0 13.5 1.0 CD2 A:HIS303 3.1 20.0 1.0 CO A:CO402 3.1 13.9 1.0 CD A:GLU336 3.2 31.3 1.0 OE1 A:GLU367 3.3 14.7 1.0 OE2 A:GLU336 3.4 24.7 1.0 OD1 A:ASP240 3.5 12.0 1.0 OG1 A:THR334 3.7 16.9 1.0 O A:HOH502 3.9 34.0 1.0 CG2 A:THR334 4.0 12.9 1.0 ND1 A:HIS303 4.2 14.9 1.0 CB A:THR334 4.2 13.5 1.0 CG A:HIS303 4.2 12.0 1.0 CB A:ASP240 4.2 14.8 1.0 O A:HOH501 4.2 22.3 1.0 CG A:GLU367 4.3 15.8 1.0 CG A:GLU336 4.5 17.4 1.0 NE2 A:HIS310 4.6 19.9 1.0 CD2 A:HIS310 4.9 20.5 1.0 CB A:GLU336 5.0 14.5 1.0

Cobalt binding site 2 out of 2 in the Crystal Structure of Human Methionine Aminopeptidase Type I in the Holo Form


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 2 of Crystal Structure of Human Methionine Aminopeptidase Type I in the Holo Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Co402 b:13.9 occ:1.00 OD1 A:ASP240 2.0 12.0 1.0 O A:HOH500 2.0 19.5 1.0 OE1 A:GLU367 2.1 14.7 1.0 OD1 A:ASP229 2.1 20.4 1.0 O A:HOH501 2.2 22.3 1.0 OD2 A:ASP229 2.5 28.5 1.0 CG A:ASP229 2.6 13.0 1.0 CG A:ASP240 2.8 13.5 1.0 OD2 A:ASP240 3.0 12.7 1.0 CD A:GLU367 3.0 18.4 1.0 CO A:CO401 3.1 15.4 1.0 OE2 A:GLU367 3.2 15.9 1.0 OG1 A:THR231 4.0 15.4 1.0 O A:HOH502 4.1 34.0 1.0 ND2 A:ASN242 4.1 13.1 1.0 CB A:ASP229 4.2 9.5 1.0 CB A:ASP240 4.3 14.8 1.0 O A:LEU241 4.4 10.0 1.0 OE2 A:GLU336 4.4 24.7 1.0 N A:LEU241 4.4 11.7 1.0 CG A:GLU367 4.4 15.8 1.0 O A:HOH516 4.5 23.0 1.0 O A:ILE230 4.5 11.7 1.0 C A:LEU241 4.6 12.5 1.0 OE1 A:GLU336 4.6 19.6 1.0 C A:ASP240 4.7 11.7 1.0 CD A:GLU336 4.8 31.3 1.0 CA A:LEU241 4.8 11.3 1.0 CA A:ASP240 4.9 12.8 1.0 O A:HOH729 4.9 46.5 1.0 CB A:GLU367 4.9 11.8 1.0 CA A:ASP229 4.9 11.7 1.0 CB A:ASN242 4.9 12.7 1.0 N A:ILE230 4.9 9.0 1.0

A.Addlagatta, X.Hu, J.O.Liu, B.W.Matthews. Structural Basis For the Functional Differences Between Type I and Type II Human Methionine Aminopeptidases(,). Biochemistry V. 44 14741 2005.
ISSN: ISSN 0006-2960
PubMed: 16274222
DOI: 10.1021/BI051691K