Cobalt in PDB 8kho: Crystal Structure of Human Methionine Aminopeptidase 12 (MAP12) in Complex with Two Cobalt Ions and Methionine

All present enzymatic activity of Crystal Structure of Human Methionine Aminopeptidase 12 (MAP12) in Complex with Two Cobalt Ions and Methionine:
3.4.11.18;

The structure of Crystal Structure of Human Methionine Aminopeptidase 12 (MAP12) in Complex with Two Cobalt Ions and Methionine, PDB code: 8kho was solved by Y.Lee, E.Lee, H.Hahn, H.Kim, Y.Heo, D.M.Jang, H.J.Kim, H.S.Kim, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	28.02 / 1.45
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	79.36, 81.07, 49.02, 90, 102.32, 90
R / Rfree (%)	18.3 / 20.9

The binding sites of Cobalt atom in the Crystal Structure of Human Methionine Aminopeptidase 12 (MAP12) in Complex with Two Cobalt Ions and Methionine (pdb code 8kho). 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 12 (MAP12) in Complex with Two Cobalt Ions and Methionine, PDB code: 8kho:
Jump to Cobalt binding site number: 1; 2;

Cobalt binding site 1 out of 2 in the Crystal Structure of Human Methionine Aminopeptidase 12 (MAP12) in Complex with Two Cobalt Ions and Methionine


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 12 (MAP12) in Complex with Two Cobalt Ions and Methionine within 5.0Å range: probe atom residue distance (Å) B Occ A:Co402 b:14.7 occ:1.00 OE2 A:GLU315 1.9 12.2 1.0 OXT A:MET401 2.0 16.3 1.0 NE2 A:HIS252 2.1 13.3 1.0 OE2 A:GLU284 2.1 13.3 1.0 OD2 A:ASP189 2.2 12.6 1.0 C A:MET401 2.9 23.7 1.0 CD A:GLU315 2.9 15.2 1.0 CD A:GLU284 3.0 18.1 1.0 CD2 A:HIS252 3.0 12.1 1.0 O A:MET401 3.0 21.0 1.0 CE1 A:HIS252 3.1 13.9 1.0 CG A:ASP189 3.1 12.4 1.0 OE1 A:GLU284 3.3 25.2 1.0 CO A:CO403 3.3 14.1 1.0 OE1 A:GLU315 3.4 13.9 1.0 OD1 A:ASP189 3.6 11.7 1.0 OG1 A:THR282 3.6 13.7 1.0 CG2 A:THR282 3.8 13.8 1.0 CB A:THR282 4.0 12.7 1.0 ND1 A:HIS252 4.2 13.9 1.0 CG A:HIS252 4.2 12.9 1.0 CG A:GLU315 4.2 13.6 1.0 CA A:MET401 4.2 17.4 1.0 CB A:ASP189 4.3 11.7 1.0 N A:MET401 4.3 14.1 1.0 CG A:GLU284 4.4 16.4 1.0 O A:HOH510 4.7 32.4 1.0 NE2 A:HIS259 4.8 16.4 1.0

Cobalt binding site 2 out of 2 in the Crystal Structure of Human Methionine Aminopeptidase 12 (MAP12) in Complex with Two Cobalt Ions and Methionine


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 12 (MAP12) in Complex with Two Cobalt Ions and Methionine within 5.0Å range: probe atom residue distance (Å) B Occ A:Co403 b:14.1 occ:1.00 OD1 A:ASP189 2.1 11.7 1.0 OXT A:MET401 2.1 16.3 1.0 OD1 A:ASP178 2.1 12.9 1.0 OE1 A:GLU315 2.2 13.9 1.0 N A:MET401 2.3 14.1 1.0 OD2 A:ASP178 2.3 16.5 1.0 CG A:ASP178 2.5 13.6 1.0 C A:MET401 2.9 23.7 1.0 CG A:ASP189 2.9 12.4 1.0 CA A:MET401 3.0 17.4 1.0 CD A:GLU315 3.0 15.2 1.0 OD2 A:ASP189 3.2 12.6 1.0 OE2 A:GLU315 3.2 12.2 1.0 CO A:CO402 3.3 14.7 1.0 OG1 A:THR180 3.9 12.4 1.0 O A:HOH570 4.0 15.4 1.0 O A:MET401 4.0 21.0 1.0 CB A:ASP178 4.1 11.1 1.0 O A:HOH598 4.3 19.3 1.0 CB A:ASP189 4.3 11.7 1.0 OE1 A:GLU284 4.4 25.2 1.0 CG A:GLU315 4.4 13.6 1.0 CB A:MET401 4.4 23.9 1.0 N A:THR190 4.6 9.8 1.0 O A:HOH510 4.6 32.4 1.0 O A:HOH568 4.6 16.8 1.0 O A:VAL179 4.7 14.1 1.0 OE2 A:GLU284 4.8 13.3 1.0 C A:ASP189 4.8 11.3 1.0 CA A:ASP189 4.8 11.8 1.0 O A:THR190 4.8 10.6 1.0 CA A:ASP178 4.8 13.5 1.0 CB A:GLU315 4.9 12.7 1.0 CD A:GLU284 4.9 18.1 1.0 C A:ASP178 4.9 14.2 1.0 C A:THR190 5.0 12.1 1.0

Y.Lee, H.Kim, E.Lee, H.Hahn, Y.Heo, D.M.Jang, K.Kwak, H.J.Kim, H.S.Kim. Structural Insights Into N-Terminal Methionine Cleavage By the Human Mitochondrial Methionine Aminopeptidase, METAP1D. Sci Rep V. 13 22326 2023.
ISSN: ESSN 2045-2322
PubMed: 38102161
DOI: 10.1038/S41598-023-49332-6