Calcium in PDB 7zlu: Catalytic Domain of Udp-Glucose Glycoprotein Glucosyltransferase From Chaetomium Thermophilum in Complex with Udp-2-Deoxy-2-Fluoro-D- Glucose
Protein crystallography data
The structure of Catalytic Domain of Udp-Glucose Glycoprotein Glucosyltransferase From Chaetomium Thermophilum in Complex with Udp-2-Deoxy-2-Fluoro-D- Glucose, PDB code: 7zlu
was solved by
P.Roversi,
N.Zitzmann,
Y.Bayo,
R.Ibba,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
41.16 /
2.05
|
Space group
|
P 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
68.159,
72.316,
72.393,
110.48,
108.33,
108.26
|
R / Rfree (%)
|
22.6 /
27
|
Other elements in 7zlu:
The structure of Catalytic Domain of Udp-Glucose Glycoprotein Glucosyltransferase From Chaetomium Thermophilum in Complex with Udp-2-Deoxy-2-Fluoro-D- Glucose also contains other interesting chemical elements:
Calcium Binding Sites:
The binding sites of Calcium atom in the Catalytic Domain of Udp-Glucose Glycoprotein Glucosyltransferase From Chaetomium Thermophilum in Complex with Udp-2-Deoxy-2-Fluoro-D- Glucose
(pdb code 7zlu). This binding sites where shown within
5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the
Catalytic Domain of Udp-Glucose Glycoprotein Glucosyltransferase From Chaetomium Thermophilum in Complex with Udp-2-Deoxy-2-Fluoro-D- Glucose, PDB code: 7zlu:
Jump to Calcium binding site number:
1;
2;
3;
Calcium binding site 1 out
of 3 in 7zlu
Go back to
Calcium Binding Sites List in 7zlu
Calcium binding site 1 out
of 3 in the Catalytic Domain of Udp-Glucose Glycoprotein Glucosyltransferase From Chaetomium Thermophilum in Complex with Udp-2-Deoxy-2-Fluoro-D- Glucose
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 1 of Catalytic Domain of Udp-Glucose Glycoprotein Glucosyltransferase From Chaetomium Thermophilum in Complex with Udp-2-Deoxy-2-Fluoro-D- Glucose within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca1503
b:26.0
occ:1.00
|
O2B
|
A:U2F1502
|
2.3
|
36.8
|
1.0
|
OD2
|
A:ASP1302
|
2.4
|
29.6
|
1.0
|
OD2
|
A:ASP1304
|
2.4
|
32.8
|
1.0
|
OD1
|
A:ASP1435
|
2.5
|
28.1
|
1.0
|
OD1
|
A:ASP1304
|
2.5
|
28.0
|
1.0
|
F1
|
A:U2F1502
|
2.6
|
38.4
|
1.0
|
O
|
A:HOH1636
|
2.7
|
32.5
|
1.0
|
CG
|
A:ASP1304
|
2.8
|
29.4
|
1.0
|
CG
|
A:ASP1302
|
3.4
|
29.6
|
1.0
|
CG
|
A:ASP1435
|
3.5
|
28.1
|
1.0
|
PB
|
A:U2F1502
|
3.6
|
38.2
|
1.0
|
C2
|
A:U2F1502
|
3.8
|
37.8
|
1.0
|
OD2
|
A:ASP1435
|
3.8
|
30.4
|
1.0
|
O1
|
A:U2F1502
|
3.9
|
38.1
|
1.0
|
C3
|
A:U2F1502
|
4.0
|
37.0
|
1.0
|
O3
|
A:U2F1502
|
4.1
|
36.4
|
1.0
|
NZ
|
A:LYS1446
|
4.1
|
47.5
|
1.0
|
CB
|
A:ASP1302
|
4.1
|
26.0
|
1.0
|
CB
|
A:ASP1304
|
4.3
|
26.5
|
1.0
|
OD1
|
A:ASP1302
|
4.3
|
32.8
|
1.0
|
C1
|
A:U2F1502
|
4.4
|
38.2
|
1.0
|
N
|
A:LEU1436
|
4.6
|
28.0
|
1.0
|
O3A
|
A:U2F1502
|
4.6
|
40.3
|
1.0
|
O2A
|
A:U2F1502
|
4.6
|
41.7
|
1.0
|
O
|
A:LEU1436
|
4.6
|
31.3
|
1.0
|
C
|
A:LEU1436
|
4.7
|
30.4
|
1.0
|
O1B
|
A:U2F1502
|
4.7
|
37.9
|
1.0
|
O1A
|
A:U2F1502
|
4.7
|
42.1
|
1.0
|
N
|
A:CYS1437
|
4.8
|
30.1
|
1.0
|
CA
|
A:CYS1437
|
4.8
|
30.8
|
1.0
|
CB
|
A:ASP1435
|
4.8
|
24.9
|
1.0
|
PA
|
A:U2F1502
|
4.9
|
41.9
|
1.0
|
CB
|
A:ALA1360
|
4.9
|
23.3
|
1.0
|
|
Calcium binding site 2 out
of 3 in 7zlu
Go back to
Calcium Binding Sites List in 7zlu
Calcium binding site 2 out
of 3 in the Catalytic Domain of Udp-Glucose Glycoprotein Glucosyltransferase From Chaetomium Thermophilum in Complex with Udp-2-Deoxy-2-Fluoro-D- Glucose
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 2 of Catalytic Domain of Udp-Glucose Glycoprotein Glucosyltransferase From Chaetomium Thermophilum in Complex with Udp-2-Deoxy-2-Fluoro-D- Glucose within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca1503
b:26.4
occ:1.00
|
OD1
|
B:ASP1304
|
2.4
|
32.5
|
1.0
|
OD2
|
B:ASP1304
|
2.4
|
36.7
|
1.0
|
OD2
|
B:ASP1302
|
2.5
|
33.9
|
1.0
|
OD1
|
B:ASP1435
|
2.5
|
23.7
|
1.0
|
O
|
B:HOH1639
|
2.6
|
48.8
|
1.0
|
O2B
|
B:U2F1501
|
2.6
|
34.1
|
1.0
|
CG
|
B:ASP1304
|
2.7
|
33.3
|
1.0
|
F1
|
B:U2F1501
|
2.7
|
34.3
|
1.0
|
CG
|
B:ASP1302
|
3.3
|
33.4
|
1.0
|
CG
|
B:ASP1435
|
3.6
|
25.6
|
1.0
|
PB
|
B:U2F1501
|
3.8
|
35.1
|
1.0
|
C2
|
B:U2F1501
|
3.9
|
34.5
|
1.0
|
O1
|
B:U2F1501
|
3.9
|
34.6
|
1.0
|
OD2
|
B:ASP1435
|
4.0
|
28.6
|
1.0
|
C3
|
B:U2F1501
|
4.1
|
34.4
|
1.0
|
CB
|
B:ASP1302
|
4.1
|
29.1
|
1.0
|
OD1
|
B:ASP1302
|
4.1
|
35.9
|
1.0
|
CB
|
B:ASP1304
|
4.1
|
29.8
|
1.0
|
O3
|
B:U2F1501
|
4.1
|
35.0
|
1.0
|
NZ
|
B:LYS1446
|
4.4
|
43.6
|
1.0
|
C1
|
B:U2F1501
|
4.5
|
34.5
|
1.0
|
O
|
B:LEU1436
|
4.6
|
30.2
|
1.0
|
O1A
|
B:U2F1501
|
4.6
|
38.8
|
1.0
|
N
|
B:LEU1436
|
4.6
|
25.5
|
1.0
|
C
|
B:LEU1436
|
4.7
|
28.9
|
1.0
|
O3A
|
B:U2F1501
|
4.8
|
37.1
|
1.0
|
N
|
B:CYS1437
|
4.8
|
29.0
|
1.0
|
O2A
|
B:U2F1501
|
4.8
|
38.3
|
1.0
|
CA
|
B:CYS1437
|
4.9
|
29.7
|
1.0
|
CB
|
B:ASP1435
|
4.9
|
22.9
|
1.0
|
O1B
|
B:U2F1501
|
4.9
|
35.0
|
1.0
|
PA
|
B:U2F1501
|
5.0
|
38.7
|
1.0
|
|
Calcium binding site 3 out
of 3 in 7zlu
Go back to
Calcium Binding Sites List in 7zlu
Calcium binding site 3 out
of 3 in the Catalytic Domain of Udp-Glucose Glycoprotein Glucosyltransferase From Chaetomium Thermophilum in Complex with Udp-2-Deoxy-2-Fluoro-D- Glucose
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 3 of Catalytic Domain of Udp-Glucose Glycoprotein Glucosyltransferase From Chaetomium Thermophilum in Complex with Udp-2-Deoxy-2-Fluoro-D- Glucose within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Ca1503
b:28.0
occ:1.00
|
O2B
|
C:U2F1501
|
2.3
|
35.5
|
1.0
|
OD1
|
C:ASP1304
|
2.3
|
38.2
|
1.0
|
OD2
|
C:ASP1302
|
2.5
|
33.9
|
1.0
|
O
|
C:HOH1607
|
2.5
|
29.6
|
1.0
|
OD1
|
C:ASP1435
|
2.6
|
26.2
|
1.0
|
OD2
|
C:ASP1304
|
2.6
|
40.4
|
1.0
|
CG
|
C:ASP1304
|
2.7
|
37.7
|
1.0
|
F1
|
C:U2F1501
|
2.8
|
37.7
|
1.0
|
CG
|
C:ASP1302
|
3.3
|
32.6
|
1.0
|
CG
|
C:ASP1435
|
3.7
|
26.5
|
1.0
|
PB
|
C:U2F1501
|
3.7
|
36.7
|
1.0
|
C2
|
C:U2F1501
|
4.0
|
37.4
|
1.0
|
CB
|
C:ASP1302
|
4.0
|
29.1
|
1.0
|
OD2
|
C:ASP1435
|
4.0
|
29.4
|
1.0
|
O1
|
C:U2F1501
|
4.0
|
36.9
|
1.0
|
OD1
|
C:ASP1302
|
4.1
|
33.6
|
1.0
|
C3
|
C:U2F1501
|
4.2
|
37.2
|
1.0
|
CB
|
C:ASP1304
|
4.2
|
32.8
|
1.0
|
NZ
|
C:LYS1446
|
4.3
|
41.9
|
1.0
|
O
|
C:LEU1436
|
4.3
|
30.6
|
1.0
|
O3
|
C:U2F1501
|
4.3
|
37.1
|
1.0
|
O1A
|
C:U2F1501
|
4.4
|
39.2
|
1.0
|
C1
|
C:U2F1501
|
4.5
|
37.3
|
1.0
|
C
|
C:LEU1436
|
4.6
|
29.9
|
1.0
|
N
|
C:LEU1436
|
4.6
|
25.2
|
1.0
|
O3A
|
C:U2F1501
|
4.7
|
38.0
|
1.0
|
O1B
|
C:U2F1501
|
4.8
|
36.5
|
1.0
|
PA
|
C:U2F1501
|
4.9
|
39.2
|
1.0
|
N
|
C:CYS1437
|
4.9
|
30.6
|
1.0
|
CA
|
C:CYS1437
|
4.9
|
32.4
|
1.0
|
CB
|
C:ASP1435
|
5.0
|
21.3
|
1.0
|
O2A
|
C:U2F1501
|
5.0
|
39.3
|
1.0
|
|
Reference:
A.T.Caputo,
R.Ibba,
J.D.Le Cornu,
B.Darlot,
M.Hensen,
C.B.Lipp,
G.Marciano,
S.Vasiljevic,
P.Roversi,
N.Zitzmann.
A Quinolin-8-Ol Sub-Millimolar Inhibitor of Uggt, the Er Glycoprotein Quality Control Checkpoint To Be Published.
Page generated: Tue Apr 4 19:21:47 2023
|