Manganese in PDB 8onx: High Resolution Structure of Chaetomium Thermophilum MAP2

The structure of High Resolution Structure of Chaetomium Thermophilum MAP2, PDB code: 8onx was solved by M.A.Klein, K.Wild, M.Kisonaite, I.Sinning, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	41.02 / 1.30
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	59.938, 73.806, 82.049, 90, 90, 90
R / Rfree (%)	16.1 / 17.7

The binding sites of Manganese atom in the High Resolution Structure of Chaetomium Thermophilum MAP2 (pdb code 8onx). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 2 binding sites of Manganese where determined in the High Resolution Structure of Chaetomium Thermophilum MAP2, PDB code: 8onx:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in the High Resolution Structure of Chaetomium Thermophilum MAP2


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of High Resolution Structure of Chaetomium Thermophilum MAP2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn501 b:40.4 occ:1.00 OD1 A:ASP228 2.0 24.0 1.0 OD1 A:ASP217 2.2 18.9 1.0 OE1 A:GLU425 2.2 26.8 1.0 OD2 A:ASP217 2.2 19.5 1.0 CG A:ASP217 2.5 17.2 1.0 CG A:ASP228 2.7 19.6 1.0 OD2 A:ASP228 2.9 35.4 1.0 CD A:GLU425 3.0 20.0 1.0 OE2 A:GLU425 3.3 21.1 1.0 MN A:MN502 3.3 47.9 1.0 HZ A:PHE185 3.4 19.5 1.0 HE22 A:GLN423 3.4 21.8 1.0 HB1 A:ALA230 3.6 17.5 1.0 O A:HOH979 3.6 38.2 1.0 O A:HOH653 3.8 38.8 1.0 CZ A:PHE185 3.9 16.2 1.0 NE2 A:GLN423 4.0 18.2 1.0 CB A:ASP217 4.1 17.0 1.0 HE21 A:GLN423 4.1 21.8 1.0 CB A:ASP228 4.2 18.4 1.0 HE1 A:PHE185 4.3 19.1 1.0 OE1 A:GLU330 4.3 26.6 1.0 CG A:GLU425 4.3 15.7 1.0 HB3 A:GLU425 4.4 20.1 1.0 CE1 A:PHE185 4.4 15.9 1.0 HB2 A:ASP217 4.4 20.4 1.0 HG2 A:GLU425 4.5 18.9 1.0 HB3 A:ASP217 4.5 20.4 1.0 CB A:ALA230 4.5 14.6 1.0 O A:HOH646 4.5 21.9 1.0 HB3 A:ASP228 4.5 22.0 1.0 HA A:ASP228 4.5 19.1 1.0 HA A:ASP217 4.6 17.4 1.0 HB3 A:ALA230 4.6 17.5 1.0 C A:ASP228 4.6 15.3 1.0 N A:SER229 4.6 15.3 1.0 H A:SER229 4.7 18.3 1.0 CA A:ASP228 4.7 15.9 1.0 HB2 A:ASP228 4.7 22.0 1.0 CB A:GLU425 4.8 16.8 1.0 HB2 A:GLU425 4.8 20.1 1.0 CE2 A:PHE185 4.8 16.9 1.0 CA A:ASP217 4.8 14.5 1.0 HE2 A:PHE185 4.9 20.3 1.0 HB2 A:ALA230 5.0 17.5 1.0 C A:SER229 5.0 14.5 1.0 HA A:SER229 5.0 21.0 1.0 CD A:GLU330 5.0 29.1 1.0

Manganese binding site 2 out of 2 in the High Resolution Structure of Chaetomium Thermophilum MAP2


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of High Resolution Structure of Chaetomium Thermophilum MAP2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn502 b:47.9 occ:1.00 OE2 A:GLU425 2.2 21.1 1.0 OD2 A:ASP228 2.4 35.4 1.0 NE2 A:HIS297 2.7 29.8 1.0 OE2 A:GLU330 3.0 37.0 1.0 HB1 A:ALA328 3.1 24.4 1.0 CD A:GLU425 3.2 20.0 1.0 MN A:MN501 3.3 40.4 1.0 CG A:ASP228 3.3 19.6 1.0 CD A:GLU330 3.4 29.1 1.0 OE1 A:GLU425 3.4 26.8 1.0 CD2 A:HIS297 3.6 27.6 1.0 CE1 A:HIS297 3.6 26.4 1.0 OE1 A:GLU330 3.6 26.6 1.0 HB3 A:ALA328 3.6 24.4 1.0 O A:HOH653 3.7 38.8 1.0 HD2 A:HIS297 3.7 33.1 1.0 CB A:ALA328 3.7 20.3 1.0 HE1 A:HIS297 3.7 31.6 1.0 OD1 A:ASP228 3.8 24.0 1.0 HB2 A:ALA328 3.9 24.4 1.0 O A:HOH979 3.9 38.2 1.0 HG2 A:GLU330 4.1 35.1 1.0 HE1 A:HIS305 4.2 67.8 1.0 HB3 A:ASP228 4.2 22.0 1.0 CG A:GLU330 4.3 29.2 1.0 HB3 A:GLU330 4.3 28.8 1.0 CB A:ASP228 4.4 18.4 1.0 HD11 A:ILE304 4.5 31.9 1.0 CG A:GLU425 4.6 15.7 1.0 HG13 A:ILE304 4.6 37.1 1.0 HB2 A:ASP228 4.7 22.0 1.0 ND1 A:HIS297 4.7 26.8 1.0 CG A:HIS297 4.7 25.9 1.0 HG3 A:GLU425 4.7 18.9 1.0 HA2 A:GLY296 4.8 24.0 1.0 CB A:GLU330 4.9 24.0 1.0 OD2 A:ASP217 4.9 19.5 1.0 HG2 A:GLU425 5.0 18.9 1.0 HG12 A:ILE304 5.0 37.1 1.0

M.A.Klein, K.Wild, M.Kisonaite, I.Sinning. Methionine Aminopeptidase 2 and Its Autoproteolysis Product Have Different Binding Sites on the Ribosome. Nat Commun V. 15 716 2024.
ISSN: ESSN 2041-1723
PubMed: 38267453
DOI: 10.1038/S41467-024-44862-7