Calcium in PDB 6ry2: Crystal Structure of DFG5 From Chaetomium Thermophilum in Complex with Alpha-1,2-Mannobiose

All present enzymatic activity of Crystal Structure of DFG5 From Chaetomium Thermophilum in Complex with Alpha-1,2-Mannobiose:
3.2.1.101;

The structure of Crystal Structure of DFG5 From Chaetomium Thermophilum in Complex with Alpha-1,2-Mannobiose, PDB code: 6ry2 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)	41.86 / 1.30
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	83.715, 54.863, 80.128, 90.00, 90.45, 90.00
R / Rfree (%)	10.5 / 12.9

The binding sites of Calcium atom in the Crystal Structure of DFG5 From Chaetomium Thermophilum in Complex with Alpha-1,2-Mannobiose (pdb code 6ry2). 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-1,2-Mannobiose, PDB code: 6ry2:
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-1,2-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-1,2-Mannobiose within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca702 b:13.4 occ:0.58 O A:HOH879 2.0 23.5 1.0 OD1 A:ASP79 2.2 14.0 1.0 O A:HOH1181 2.3 25.6 1.0 O A:HOH1045 2.3 44.7 1.0 O A:HOH1197 2.4 32.9 1.0 O A:HIS391 2.5 15.3 1.0 CG A:ASP79 3.4 12.2 1.0 HA A:THR392 3.6 14.2 1.0 C A:HIS391 3.6 14.1 1.0 HB3 A:HIS391 3.7 20.9 1.0 HA A:ASP79 3.9 12.9 1.0 O A:HOH1290 4.1 47.3 1.0 OD2 A:ASP79 4.2 12.7 1.0 O A:HOH1260 4.2 42.8 1.0 HB3 A:ASP79 4.3 13.1 1.0 CB A:ASP79 4.3 10.9 1.0 O A:HOH892 4.3 24.9 1.0 HG22 A:THR392 4.3 15.3 1.0 CB A:HIS391 4.4 17.4 1.0 O A:HOH931 4.4 26.5 1.0 CA A:THR392 4.5 11.8 1.0 HB2 A:HIS391 4.5 20.9 1.0 N A:THR392 4.5 12.3 1.0 CA A:HIS391 4.5 14.6 1.0 HA A:HIS391 4.6 17.5 1.0 CA A:ASP79 4.6 10.8 1.0 O A:HOH1409 4.8 29.2 0.4 O A:HOH1133 4.9 27.6 1.0 HB3 A:PRO73 4.9 20.8 1.0 O A:HOH1220 4.9 42.2 1.0

Calcium binding site 2 out of 2 in the Crystal Structure of DFG5 From Chaetomium Thermophilum in Complex with Alpha-1,2-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-1,2-Mannobiose within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca703 b:13.5 occ:0.66 O A:HOH1187 2.2 20.8 1.0 O A:HOH924 2.3 17.4 1.0 OD1 A:ASP135 2.4 14.1 1.0 O A:HOH1213 2.4 39.8 1.0 O A:HOH1320 2.5 41.7 1.0 OD2 A:ASP135 2.6 13.8 1.0 CG A:ASP135 2.8 12.1 1.0 O A:HOH888 2.9 42.2 1.0 O A:SER130 3.3 26.8 0.7 H A:GLY132 3.6 16.2 1.0 HA A:SER130 3.6 28.1 0.7 HE22 A:GLN189 3.8 23.7 1.0 O A:HOH1065 3.9 21.1 0.4 C A:SER130 3.9 23.9 0.7 HA3 A:GLY132 4.0 14.3 1.0 N A:GLY132 4.2 13.5 1.0 CA A:SER130 4.2 23.4 0.7 OD1 A:ASP134 4.2 11.1 1.0 HB3 A:SER130 4.2 30.5 0.7 CB A:ASP135 4.2 10.0 1.0 O A:HOH829 4.3 12.3 1.0 HE1 A:TRP188 4.4 15.0 1.0 O A:HOH1065 4.5 37.9 0.6 HB2 A:ASP135 4.5 12.0 1.0 H A:ASP135 4.5 9.8 1.0 O A:HOH994 4.5 28.1 0.6 NE2 A:GLN189 4.6 19.7 1.0 OD2 A:ASP134 4.6 12.4 1.0 CA A:GLY132 4.6 12.0 1.0 HB3 A:ASP135 4.6 12.0 1.0 O A:HOH1236 4.7 32.1 1.0 HZ2 A:TRP188 4.7 16.9 1.0 CB A:SER130 4.7 25.4 0.7 CG A:ASP134 4.7 10.9 1.0 O A:HOH1335 4.8 45.5 1.0 N A:LEU131 4.8 22.1 0.8 NE1 A:TRP188 4.9 12.5 1.0 OE1 A:GLN189 4.9 16.9 1.0 HD1 A:TRP83 4.9 14.9 1.0

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