Calcium in PDB 6ry5: Crystal Structure of DFG5 From Chaetomium Thermophilum in Complex with Alpha-1,6-Mannobiose

All present enzymatic activity of Crystal Structure of DFG5 From Chaetomium Thermophilum in Complex with Alpha-1,6-Mannobiose:
3.2.1.101;

The structure of Crystal Structure of DFG5 From Chaetomium Thermophilum in Complex with Alpha-1,6-Mannobiose, PDB code: 6ry5 was solved by L.-O.Essen, M.S.Vogt, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.93 / 1.30
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	83.415, 55.019, 80.119, 90.00, 90.37, 90.00
R / Rfree (%)	10.2 / 12.3

The binding sites of Calcium atom in the Crystal Structure of DFG5 From Chaetomium Thermophilum in Complex with Alpha-1,6-Mannobiose (pdb code 6ry5). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Crystal Structure of DFG5 From Chaetomium Thermophilum in Complex with Alpha-1,6-Mannobiose, PDB code: 6ry5:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Crystal Structure of DFG5 From Chaetomium Thermophilum in Complex with Alpha-1,6-Mannobiose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of DFG5 From Chaetomium Thermophilum in Complex with Alpha-1,6-Mannobiose within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca501 b:18.6 occ:0.63 O A:HOH645 2.2 34.0 1.0 O A:HOH857 2.2 36.5 1.0 OD1 A:ASP79 2.2 19.4 1.0 O A:HOH881 2.4 38.8 1.0 O A:HIS391 2.5 20.1 1.0 CG A:ASP79 3.5 16.9 1.0 HA A:THR392 3.6 18.1 1.0 C A:HIS391 3.6 17.2 1.0 HB3 A:HIS391 3.7 26.1 1.0 HA A:ASP79 4.0 16.4 1.0 OD2 A:ASP79 4.2 17.3 1.0 HG22 A:THR392 4.3 19.9 1.0 O A:HOH672 4.3 36.8 1.0 HB3 A:ASP79 4.3 17.6 1.0 CB A:HIS391 4.4 21.7 1.0 HB2 A:HIS391 4.4 26.1 1.0 CB A:ASP79 4.4 14.7 1.0 CA A:THR392 4.4 15.1 1.0 N A:THR392 4.5 14.9 1.0 CA A:HIS391 4.5 18.1 1.0 O A:HOH666 4.5 25.7 1.0 HA A:HIS391 4.6 21.7 1.0 CA A:ASP79 4.7 13.7 1.0 O A:HOH927 4.8 29.0 0.4 O A:HOH862 4.9 42.8 1.0 O A:HOH858 4.9 38.8 1.0

Calcium binding site 2 out of 2 in the Crystal Structure of DFG5 From Chaetomium Thermophilum in Complex with Alpha-1,6-Mannobiose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of DFG5 From Chaetomium Thermophilum in Complex with Alpha-1,6-Mannobiose within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca502 b:14.2 occ:0.50 O A:HOH677 2.2 26.1 1.0 O A:HOH885 2.3 39.6 1.0 OD1 A:ASP135 2.4 17.4 1.0 O A:HOH894 2.4 31.0 1.0 HO2 B:BMA1 2.5 24.0 0.6 OD2 A:ASP135 2.5 16.7 1.0 O2 B:BMA1 2.5 20.0 0.6 O1 B:BMA1 2.5 20.2 0.6 O A:HOH784 2.6 35.2 1.0 CG A:ASP135 2.8 14.8 1.0 HO1 B:BMA1 3.2 24.2 0.6 C2 B:BMA1 3.4 20.0 0.6 C1 B:BMA1 3.4 20.0 0.6 H2 B:BMA1 3.5 24.0 0.6 HE22 A:GLN189 3.6 29.5 1.0 HA A:SER130 3.9 19.9 0.6 HA3 A:GLY132 3.9 16.4 1.0 O5 B:BMA1 3.9 20.1 0.6 H A:GLY132 4.1 19.2 1.0 OD1 A:ASP134 4.1 15.6 1.0 O A:HOH615 4.2 30.0 0.7 HE1 A:TRP188 4.2 25.0 1.0 CB A:ASP135 4.3 12.5 1.0 O A:SER130 4.3 16.7 0.6 HZ2 A:TRP188 4.3 27.1 1.0 H1 B:BMA1 4.4 24.0 0.6 O A:HOH640 4.4 14.0 1.0 NE2 A:GLN189 4.4 24.6 1.0 H A:ASP135 4.5 12.3 1.0 OD2 A:ASP134 4.5 17.3 1.0 N A:GLY132 4.5 16.0 1.0 HB2 A:ASP135 4.6 15.0 1.0 C A:SER130 4.6 16.6 0.6 NE1 A:TRP188 4.6 20.8 1.0 CA A:GLY132 4.6 13.6 1.0 HG A:SER130 4.6 25.3 0.6 CA A:SER130 4.7 16.6 0.6 CG A:ASP134 4.7 14.3 1.0 HB3 A:ASP135 4.7 15.0 1.0 CZ2 A:TRP188 4.7 22.6 1.0 CE2 A:TRP188 4.9 19.1 1.0 C3 B:BMA1 4.9 20.0 0.6 OE1 A:GLN189 4.9 22.0 1.0 HE21 A:GLN189 4.9 29.5 1.0 HD1 A:TRP83 5.0 16.3 1.0 O A:ALA129 5.0 23.8 0.8

M.S.Vogt, G.F.Schmitz, D.Varon Silva, H.U.Mosch, L.O.Essen. Structural Base For the Transfer of Gpi-Anchored Glycoproteins Into Fungal Cell Walls. Proc.Natl.Acad.Sci.Usa V. 117 22061 2020.
ISSN: ESSN 1091-6490
PubMed: 32839341
DOI: 10.1073/PNAS.2010661117