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

Enzymatic activity of 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;

Protein crystallography data

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

Calcium Binding Sites:

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 6ry5

Go back to Calcium Binding Sites List in 6ry5
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 6ry5

Go back to Calcium Binding Sites List in 6ry5
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

Reference:

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
Page generated: Sat Dec 12 07:31:26 2020

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