Calcium in PDB 8q5u: Endoglycosidase S2 in Complex with IGG1 Fc
Protein crystallography data
The structure of Endoglycosidase S2 in Complex with IGG1 Fc, PDB code: 8q5u
was solved by
A.S.L.Sudol,
I.Tews,
M.Crispin,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
|
Resolution Low / High (Å)
|
49.91 /
3.00
|
|
Space group
|
P 43 21 2
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
228.775,
228.775,
161.629,
90,
90,
90
|
|
R / Rfree (%)
|
21.6 /
25.2
|
Calcium Binding Sites:
The binding sites of Calcium atom in the Endoglycosidase S2 in Complex with IGG1 Fc
(pdb code 8q5u). This binding sites where shown within
5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the
Endoglycosidase S2 in Complex with IGG1 Fc, PDB code: 8q5u:
Jump to Calcium binding site number:
1;
2;
3;
Calcium binding site 1 out
of 3 in 8q5u
Go back to
Calcium Binding Sites List in 8q5u
Calcium binding site 1 out
of 3 in the Endoglycosidase S2 in Complex with IGG1 Fc
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 1 of Endoglycosidase S2 in Complex with IGG1 Fc within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Ca905
b:135.8
occ:1.00
|
O
|
D:LYS699
|
2.4
|
93.5
|
1.0
|
|
O
|
D:THR824
|
2.5
|
77.8
|
1.0
|
|
O
|
D:GLU704
|
2.7
|
98.8
|
1.0
|
|
OD1
|
D:ASP702
|
2.8
|
80.3
|
1.0
|
|
HA
|
D:LYS705
|
3.4
|
88.9
|
1.0
|
|
OE1
|
D:GLU825
|
3.4
|
81.8
|
1.0
|
|
OD2
|
D:ASP702
|
3.4
|
81.2
|
1.0
|
|
CG
|
D:ASP702
|
3.5
|
81.7
|
1.0
|
|
O
|
D:ASP707
|
3.5
|
80.9
|
1.0
|
|
C
|
D:GLU704
|
3.5
|
93.2
|
1.0
|
|
H
|
D:ASP707
|
3.6
|
82.9
|
1.0
|
|
C
|
D:LYS699
|
3.6
|
88.6
|
1.0
|
|
HB3
|
D:LYS699
|
3.6
|
86.3
|
1.0
|
|
C
|
D:THR824
|
3.7
|
78.9
|
1.0
|
|
H
|
D:SER706
|
3.7
|
84.1
|
1.0
|
|
HB
|
D:THR824
|
3.9
|
77.4
|
1.0
|
|
H
|
D:GLU704
|
3.9
|
92.2
|
1.0
|
|
HB2
|
D:GLU825
|
4.0
|
81.3
|
1.0
|
|
HA
|
D:ILE700
|
4.1
|
87.1
|
1.0
|
|
HA
|
D:THR824
|
4.1
|
77.6
|
1.0
|
|
CA
|
D:LYS705
|
4.1
|
88.3
|
1.0
|
|
HB2
|
D:GLU704
|
4.2
|
97.2
|
1.0
|
|
N
|
D:LYS705
|
4.2
|
89.5
|
1.0
|
|
H
|
D:ASP702
|
4.3
|
88.5
|
1.0
|
|
N
|
D:SER706
|
4.4
|
83.3
|
1.0
|
|
CA
|
D:GLU704
|
4.4
|
93.7
|
1.0
|
|
CA
|
D:THR824
|
4.4
|
77.6
|
1.0
|
|
N
|
D:GLU704
|
4.4
|
91.7
|
1.0
|
|
N
|
D:ASP707
|
4.4
|
83.0
|
1.0
|
|
HA
|
D:GLU825
|
4.4
|
82.7
|
1.0
|
|
HB3
|
D:ASP707
|
4.4
|
82.8
|
1.0
|
|
HB3
|
D:GLU704
|
4.4
|
96.1
|
1.0
|
|
CA
|
D:LYS699
|
4.4
|
86.8
|
1.0
|
|
C
|
D:ASP707
|
4.4
|
81.9
|
1.0
|
|
CB
|
D:LYS699
|
4.4
|
86.6
|
1.0
|
|
HA
|
D:LYS699
|
4.4
|
86.9
|
1.0
|
|
CB
|
D:GLU704
|
4.6
|
97.0
|
1.0
|
|
H
|
D:GLY703
|
4.6
|
89.3
|
1.0
|
|
CD
|
D:GLU825
|
4.6
|
83.8
|
1.0
|
|
CB
|
D:THR824
|
4.6
|
77.6
|
1.0
|
|
N
|
D:ILE700
|
4.6
|
88.2
|
1.0
|
|
C
|
D:LYS705
|
4.7
|
85.3
|
1.0
|
|
N
|
D:GLU825
|
4.7
|
81.1
|
1.0
|
|
HD11
|
D:ILE700
|
4.7
|
86.4
|
1.0
|
|
CA
|
D:ILE700
|
4.7
|
87.5
|
1.0
|
|
CB
|
D:GLU825
|
4.8
|
81.9
|
1.0
|
|
HB2
|
D:LYS699
|
4.8
|
87.2
|
1.0
|
|
CA
|
D:GLU825
|
4.8
|
82.6
|
1.0
|
|
CA
|
D:ASP707
|
4.9
|
82.3
|
1.0
|
|
CB
|
D:ASP702
|
4.9
|
83.4
|
1.0
|
|
H
|
D:LYS705
|
5.0
|
89.5
|
1.0
|
|
Calcium binding site 2 out
of 3 in 8q5u
Go back to
Calcium Binding Sites List in 8q5u
Calcium binding site 2 out
of 3 in the Endoglycosidase S2 in Complex with IGG1 Fc
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 2 of Endoglycosidase S2 in Complex with IGG1 Fc within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Ca901
b:124.7
occ:1.00
|
O
|
E:THR824
|
2.2
|
86.2
|
1.0
|
|
O
|
E:LYS699
|
2.4
|
93.3
|
1.0
|
|
O
|
E:GLU704
|
2.5
|
105.6
|
1.0
|
|
OD1
|
E:ASP702
|
2.7
|
96.1
|
1.0
|
|
OE1
|
E:GLU825
|
3.0
|
90.4
|
1.0
|
|
HA
|
E:LYS705
|
3.3
|
100.5
|
1.0
|
|
C
|
E:GLU704
|
3.4
|
104.4
|
1.0
|
|
C
|
E:THR824
|
3.4
|
86.5
|
1.0
|
|
CG
|
E:ASP702
|
3.6
|
96.8
|
1.0
|
|
HB2
|
E:GLU825
|
3.6
|
90.4
|
1.0
|
|
C
|
E:LYS699
|
3.6
|
92.0
|
1.0
|
|
H
|
E:GLU704
|
3.7
|
105.6
|
1.0
|
|
OD2
|
E:ASP702
|
3.7
|
96.6
|
1.0
|
|
O
|
E:ASP707
|
3.8
|
92.9
|
1.0
|
|
HB
|
E:THR824
|
3.8
|
87.8
|
1.0
|
|
HA
|
E:ILE700
|
3.9
|
94.2
|
1.0
|
|
HB3
|
E:LYS699
|
3.9
|
91.3
|
1.0
|
|
H
|
E:SER706
|
3.9
|
98.2
|
1.0
|
|
H
|
E:ASP707
|
4.0
|
95.6
|
1.0
|
|
HA
|
E:GLU825
|
4.0
|
90.3
|
1.0
|
|
HA
|
E:THR824
|
4.1
|
85.4
|
1.0
|
|
N
|
E:LYS705
|
4.1
|
102.2
|
1.0
|
|
CA
|
E:LYS705
|
4.1
|
100.4
|
1.0
|
|
CD
|
E:GLU825
|
4.2
|
91.6
|
1.0
|
|
HB2
|
E:GLU704
|
4.2
|
106.9
|
1.0
|
|
H
|
E:ASP702
|
4.2
|
99.2
|
1.0
|
|
N
|
E:GLU704
|
4.2
|
105.8
|
1.0
|
|
CA
|
E:GLU704
|
4.3
|
106.1
|
1.0
|
|
CA
|
E:THR824
|
4.3
|
85.8
|
1.0
|
|
CB
|
E:GLU825
|
4.3
|
91.0
|
1.0
|
|
N
|
E:GLU825
|
4.4
|
88.6
|
1.0
|
|
CA
|
E:GLU825
|
4.5
|
90.5
|
1.0
|
|
N
|
E:ILE700
|
4.5
|
93.3
|
1.0
|
|
HB3
|
E:GLU704
|
4.5
|
106.3
|
1.0
|
|
CA
|
E:LYS699
|
4.5
|
91.5
|
1.0
|
|
CB
|
E:THR824
|
4.5
|
87.8
|
1.0
|
|
CA
|
E:ILE700
|
4.5
|
94.4
|
1.0
|
|
HA
|
E:LYS699
|
4.5
|
91.8
|
1.0
|
|
CB
|
E:GLU704
|
4.6
|
106.7
|
1.0
|
|
HD11
|
E:ILE700
|
4.6
|
94.1
|
1.0
|
|
N
|
E:SER706
|
4.6
|
97.8
|
1.0
|
|
CB
|
E:LYS699
|
4.6
|
91.5
|
1.0
|
|
N
|
E:ASP707
|
4.8
|
95.5
|
1.0
|
|
C
|
E:ASP707
|
4.8
|
92.2
|
1.0
|
|
C
|
E:LYS705
|
4.8
|
98.6
|
1.0
|
|
CG
|
E:GLU825
|
4.8
|
91.9
|
1.0
|
|
C
|
E:ILE700
|
4.9
|
95.7
|
1.0
|
|
HB3
|
E:ASP707
|
4.9
|
93.6
|
1.0
|
|
H
|
E:LYS705
|
4.9
|
102.4
|
1.0
|
|
CB
|
E:ASP702
|
5.0
|
98.2
|
1.0
|
|
Calcium binding site 3 out
of 3 in 8q5u
Go back to
Calcium Binding Sites List in 8q5u
Calcium binding site 3 out
of 3 in the Endoglycosidase S2 in Complex with IGG1 Fc
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 3 of Endoglycosidase S2 in Complex with IGG1 Fc within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Ca903
b:123.4
occ:1.00
|
O
|
F:LYS699
|
2.3
|
110.1
|
1.0
|
|
O
|
F:THR824
|
2.4
|
95.9
|
1.0
|
|
O
|
F:GLU704
|
2.6
|
107.7
|
1.0
|
|
OD1
|
F:ASP702
|
2.6
|
105.8
|
1.0
|
|
OE1
|
F:GLU825
|
3.0
|
98.7
|
1.0
|
|
C
|
F:GLU704
|
3.4
|
106.4
|
1.0
|
|
CG
|
F:ASP702
|
3.4
|
105.2
|
1.0
|
|
HA
|
F:LYS705
|
3.5
|
104.7
|
1.0
|
|
C
|
F:LYS699
|
3.5
|
107.0
|
1.0
|
|
OD2
|
F:ASP702
|
3.6
|
103.7
|
1.0
|
|
C
|
F:THR824
|
3.6
|
96.0
|
1.0
|
|
HA
|
F:ILE700
|
3.7
|
104.8
|
1.0
|
|
H
|
F:GLU704
|
3.7
|
108.2
|
1.0
|
|
HB2
|
F:GLU825
|
3.7
|
98.0
|
1.0
|
|
O
|
F:ASP707
|
3.8
|
99.8
|
1.0
|
|
HB3
|
F:LYS699
|
3.8
|
105.9
|
1.0
|
|
H
|
F:SER706
|
3.9
|
103.2
|
1.0
|
|
HB
|
F:THR824
|
3.9
|
95.3
|
1.0
|
|
H
|
F:ASP707
|
4.0
|
101.8
|
1.0
|
|
HA
|
F:GLU825
|
4.1
|
98.7
|
1.0
|
|
H
|
F:ASP702
|
4.1
|
108.7
|
1.0
|
|
HB2
|
F:GLU704
|
4.1
|
112.4
|
1.0
|
|
N
|
F:GLU704
|
4.2
|
108.1
|
1.0
|
|
N
|
F:LYS705
|
4.2
|
104.1
|
1.0
|
|
HA
|
F:THR824
|
4.2
|
95.0
|
1.0
|
|
CD
|
F:GLU825
|
4.2
|
99.6
|
1.0
|
|
CA
|
F:GLU704
|
4.3
|
109.0
|
1.0
|
|
CA
|
F:LYS705
|
4.3
|
104.1
|
1.0
|
|
H
|
F:GLY703
|
4.3
|
106.7
|
1.0
|
|
CA
|
F:THR824
|
4.4
|
94.9
|
1.0
|
|
CA
|
F:LYS699
|
4.4
|
105.7
|
1.0
|
|
HA
|
F:LYS699
|
4.4
|
105.3
|
1.0
|
|
CA
|
F:ILE700
|
4.5
|
104.7
|
1.0
|
|
N
|
F:ILE700
|
4.5
|
106.0
|
1.0
|
|
CB
|
F:GLU825
|
4.5
|
98.4
|
1.0
|
|
HB3
|
F:GLU704
|
4.5
|
112.0
|
1.0
|
|
N
|
F:GLU825
|
4.5
|
97.5
|
1.0
|
|
CB
|
F:LYS699
|
4.5
|
106.4
|
1.0
|
|
CB
|
F:GLU704
|
4.6
|
112.2
|
1.0
|
|
CA
|
F:GLU825
|
4.6
|
98.6
|
1.0
|
|
N
|
F:SER706
|
4.7
|
103.2
|
1.0
|
|
CB
|
F:THR824
|
4.7
|
95.8
|
1.0
|
|
N
|
F:ASP707
|
4.8
|
101.5
|
1.0
|
|
HB3
|
F:ASP707
|
4.8
|
102.9
|
1.0
|
|
C
|
F:ASP707
|
4.8
|
100.4
|
1.0
|
|
CB
|
F:ASP702
|
4.8
|
105.7
|
1.0
|
|
N
|
F:GLY703
|
4.8
|
106.0
|
1.0
|
|
C
|
F:ILE700
|
4.9
|
106.2
|
1.0
|
|
HB2
|
F:LYS699
|
4.9
|
106.6
|
1.0
|
|
C
|
F:LYS705
|
4.9
|
103.8
|
1.0
|
|
N
|
F:ASP702
|
4.9
|
109.2
|
1.0
|
|
CG
|
F:GLU825
|
4.9
|
99.1
|
1.0
|
|
Reference:
A.S.L.Sudol,
M.Crispin,
I.Tews.
The Igg-Specific Endoglycosidases Endos and ENDOS2 Are Distinguished By Conformation and Antibody Recognition. J.Biol.Chem. 07245 2024.
ISSN: ESSN 1083-351X
PubMed: 38569940
DOI: 10.1016/J.JBC.2024.107245
Page generated: Fri Jul 19 11:16:18 2024
|
