Calcium in PDB 8blj: Crystal Structure of the Ligand-Binding Domain (Lbd) of Human Iglur Delta-1 (GLUD1), Apo State
Protein crystallography data
The structure of Crystal Structure of the Ligand-Binding Domain (Lbd) of Human Iglur Delta-1 (GLUD1), Apo State, PDB code: 8blj
was solved by
C.Heroven,
T.Malinauskas,
A.R.Aricescu,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
62.59 /
2.18
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
86.29,
107.569,
98.559,
90,
94.08,
90
|
R / Rfree (%)
|
20.6 /
24.4
|
Other elements in 8blj:
The structure of Crystal Structure of the Ligand-Binding Domain (Lbd) of Human Iglur Delta-1 (GLUD1), Apo State also contains other interesting chemical elements:
Calcium Binding Sites:
Pages:
>>> Page 1 <<<
Page 2, Binding sites: 11 -
11;
Binding sites:
The binding sites of Calcium atom in the Crystal Structure of the Ligand-Binding Domain (Lbd) of Human Iglur Delta-1 (GLUD1), Apo State
(pdb code 8blj). This binding sites where shown within
5.0 Angstroms radius around Calcium atom.
In total 11 binding sites of Calcium where determined in the
Crystal Structure of the Ligand-Binding Domain (Lbd) of Human Iglur Delta-1 (GLUD1), Apo State, PDB code: 8blj:
Jump to Calcium binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
10;
Calcium binding site 1 out
of 11 in 8blj
Go back to
Calcium Binding Sites List in 8blj
Calcium binding site 1 out
of 11 in the Crystal Structure of the Ligand-Binding Domain (Lbd) of Human Iglur Delta-1 (GLUD1), Apo State
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 the Ligand-Binding Domain (Lbd) of Human Iglur Delta-1 (GLUD1), Apo State within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca901
b:40.0
occ:1.00
|
O
|
A:HOH1004
|
2.3
|
29.6
|
1.0
|
O
|
A:GLU527
|
2.3
|
22.5
|
1.0
|
OD1
|
A:ASP531
|
2.4
|
24.9
|
1.0
|
OE2
|
A:GLU527
|
2.5
|
30.6
|
1.0
|
O
|
A:VAL530
|
2.6
|
23.9
|
1.0
|
O
|
B:HOH1032
|
2.7
|
30.4
|
1.0
|
HA
|
A:ASP531
|
3.3
|
34.2
|
1.0
|
HG3
|
A:GLU527
|
3.5
|
38.5
|
1.0
|
CG
|
A:ASP531
|
3.5
|
28.7
|
1.0
|
CD
|
A:GLU527
|
3.5
|
35.6
|
1.0
|
C
|
A:GLU527
|
3.5
|
20.2
|
1.0
|
C
|
A:VAL530
|
3.5
|
26.3
|
1.0
|
ND1
|
A:HIS776
|
3.9
|
33.4
|
1.0
|
CA
|
A:ASP531
|
4.0
|
27.8
|
1.0
|
HA
|
A:SER528
|
4.0
|
27.6
|
1.0
|
CG
|
A:GLU527
|
4.0
|
31.3
|
1.0
|
N
|
A:ASP531
|
4.1
|
25.4
|
1.0
|
HA
|
A:GLU527
|
4.1
|
31.5
|
1.0
|
HE1
|
A:HIS776
|
4.1
|
48.1
|
1.0
|
CB
|
A:ASP531
|
4.3
|
20.6
|
1.0
|
OD2
|
A:ASP531
|
4.3
|
34.0
|
1.0
|
H
|
A:VAL530
|
4.4
|
28.2
|
1.0
|
CA
|
A:GLU527
|
4.4
|
25.5
|
1.0
|
CE1
|
A:HIS776
|
4.4
|
39.3
|
1.0
|
C
|
A:SER528
|
4.4
|
23.7
|
1.0
|
N
|
A:SER528
|
4.5
|
21.9
|
1.0
|
N
|
A:VAL530
|
4.5
|
22.7
|
1.0
|
CA
|
A:SER528
|
4.5
|
22.2
|
1.0
|
HH12
|
A:ARG781
|
4.5
|
41.8
|
1.0
|
OE1
|
A:GLU527
|
4.5
|
30.0
|
1.0
|
O
|
B:HOH1017
|
4.5
|
28.3
|
1.0
|
CA
|
A:VAL530
|
4.6
|
19.3
|
1.0
|
O
|
A:SER528
|
4.6
|
28.7
|
1.0
|
HH22
|
A:ARG781
|
4.7
|
64.7
|
1.0
|
HB3
|
A:ASP531
|
4.7
|
25.7
|
1.0
|
HA
|
A:HIS776
|
4.8
|
31.5
|
1.0
|
HG2
|
A:GLU527
|
4.8
|
38.5
|
1.0
|
N
|
A:VAL529
|
4.8
|
23.5
|
1.0
|
CB
|
A:GLU527
|
4.8
|
23.5
|
1.0
|
HA
|
A:VAL530
|
4.8
|
24.1
|
1.0
|
H
|
A:ASP531
|
4.9
|
31.4
|
1.0
|
OE1
|
B:GLN786
|
4.9
|
20.2
|
1.0
|
H
|
A:PHE532
|
5.0
|
32.7
|
1.0
|
H
|
A:VAL529
|
5.0
|
29.1
|
1.0
|
|
Calcium binding site 2 out
of 11 in 8blj
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Calcium Binding Sites List in 8blj
Calcium binding site 2 out
of 11 in the Crystal Structure of the Ligand-Binding Domain (Lbd) of Human Iglur Delta-1 (GLUD1), Apo State
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 the Ligand-Binding Domain (Lbd) of Human Iglur Delta-1 (GLUD1), Apo State within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca902
b:62.9
occ:1.00
|
OD2
|
A:ASP742
|
3.0
|
44.4
|
1.0
|
O
|
A:HOH1038
|
3.4
|
30.0
|
1.0
|
O
|
A:ALA519
|
3.7
|
25.3
|
1.0
|
HB3
|
A:ALA519
|
3.7
|
31.6
|
1.0
|
HB1
|
A:ALA519
|
3.9
|
31.6
|
1.0
|
HE1
|
A:TYR770
|
4.0
|
19.4
|
1.0
|
OH
|
A:TYR492
|
4.1
|
33.3
|
1.0
|
CG
|
A:ASP742
|
4.1
|
36.2
|
1.0
|
HH
|
A:TYR492
|
4.1
|
40.9
|
1.0
|
HH
|
A:TYR770
|
4.2
|
34.1
|
1.0
|
CB
|
A:ALA519
|
4.3
|
25.6
|
1.0
|
CZ
|
A:TYR492
|
4.3
|
36.9
|
1.0
|
O
|
A:HOH1006
|
4.3
|
34.0
|
1.0
|
HE2
|
A:TYR539
|
4.4
|
22.6
|
1.0
|
OD1
|
A:ASP742
|
4.5
|
42.3
|
1.0
|
HZ2
|
A:TRP741
|
4.6
|
26.6
|
1.0
|
HG23
|
A:THR521
|
4.6
|
28.3
|
1.0
|
CE1
|
A:TYR492
|
4.6
|
46.9
|
1.0
|
HG21
|
A:VAL745
|
4.7
|
26.9
|
1.0
|
HE1
|
A:TYR492
|
4.7
|
57.1
|
1.0
|
HG2
|
A:GLU446
|
4.7
|
44.0
|
1.0
|
C
|
A:ALA519
|
4.7
|
21.9
|
1.0
|
CE2
|
A:TYR492
|
4.7
|
32.4
|
1.0
|
CD
|
A:GLU446
|
4.8
|
40.2
|
1.0
|
OE2
|
A:GLU446
|
4.8
|
43.1
|
1.0
|
CE1
|
A:TYR770
|
4.9
|
15.4
|
1.0
|
HE2
|
A:TYR492
|
4.9
|
39.8
|
1.0
|
HE1
|
A:TRP741
|
4.9
|
29.4
|
1.0
|
OE1
|
A:GLU446
|
4.9
|
42.8
|
1.0
|
HB2
|
A:ALA519
|
5.0
|
31.6
|
1.0
|
|
Calcium binding site 3 out
of 11 in 8blj
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Calcium Binding Sites List in 8blj
Calcium binding site 3 out
of 11 in the Crystal Structure of the Ligand-Binding Domain (Lbd) of Human Iglur Delta-1 (GLUD1), Apo State
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 3 of Crystal Structure of the Ligand-Binding Domain (Lbd) of Human Iglur Delta-1 (GLUD1), Apo State within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca903
b:59.5
occ:1.00
|
O
|
A:PRO698
|
3.5
|
24.4
|
1.0
|
HA
|
A:LEU699
|
4.1
|
34.5
|
1.0
|
HA
|
A:GLN701
|
4.4
|
45.0
|
1.0
|
O
|
A:GLU700
|
4.6
|
34.8
|
1.0
|
C
|
A:PRO698
|
4.7
|
25.0
|
1.0
|
O
|
A:LEU699
|
4.8
|
31.5
|
1.0
|
HG2
|
A:GLN701
|
4.8
|
64.8
|
1.0
|
CA
|
A:LEU699
|
4.9
|
28.0
|
1.0
|
C
|
A:LEU699
|
4.9
|
29.2
|
1.0
|
|
Calcium binding site 4 out
of 11 in 8blj
Go back to
Calcium Binding Sites List in 8blj
Calcium binding site 4 out
of 11 in the Crystal Structure of the Ligand-Binding Domain (Lbd) of Human Iglur Delta-1 (GLUD1), Apo State
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 4 of Crystal Structure of the Ligand-Binding Domain (Lbd) of Human Iglur Delta-1 (GLUD1), Apo State within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca901
b:46.9
occ:1.00
|
O
|
B:GLU527
|
2.1
|
35.5
|
1.0
|
OE2
|
B:GLU527
|
2.3
|
42.0
|
1.0
|
O
|
B:VAL530
|
2.3
|
33.6
|
1.0
|
OD1
|
B:ASP531
|
2.3
|
32.4
|
1.0
|
O
|
B:HOH1016
|
2.4
|
36.0
|
1.0
|
O
|
B:HOH1013
|
2.4
|
36.8
|
1.0
|
HA
|
B:ASP531
|
2.9
|
42.9
|
1.0
|
CD
|
B:GLU527
|
3.2
|
35.1
|
1.0
|
HG3
|
B:GLU527
|
3.3
|
39.7
|
1.0
|
C
|
B:VAL530
|
3.3
|
30.4
|
1.0
|
CG
|
B:ASP531
|
3.3
|
35.9
|
1.0
|
C
|
B:GLU527
|
3.3
|
33.6
|
1.0
|
CA
|
B:ASP531
|
3.6
|
35.0
|
1.0
|
CG
|
B:GLU527
|
3.7
|
32.3
|
1.0
|
HA
|
B:GLU527
|
3.8
|
37.5
|
1.0
|
N
|
B:ASP531
|
3.8
|
31.6
|
1.0
|
CB
|
B:ASP531
|
4.0
|
37.5
|
1.0
|
CA
|
B:GLU527
|
4.1
|
30.5
|
1.0
|
HA
|
B:SER528
|
4.1
|
45.7
|
1.0
|
OE1
|
B:GLU527
|
4.1
|
32.2
|
1.0
|
HH12
|
B:ARG781
|
4.2
|
42.4
|
1.0
|
OD2
|
B:ASP531
|
4.2
|
43.0
|
1.0
|
ND1
|
B:HIS776
|
4.3
|
46.7
|
1.0
|
H
|
B:VAL530
|
4.3
|
41.0
|
1.0
|
N
|
B:SER528
|
4.4
|
34.6
|
1.0
|
O
|
A:HOH1019
|
4.4
|
30.2
|
1.0
|
N
|
B:VAL530
|
4.4
|
33.4
|
1.0
|
CA
|
B:VAL530
|
4.4
|
30.5
|
1.0
|
HB3
|
B:ASP531
|
4.5
|
45.9
|
1.0
|
CB
|
B:GLU527
|
4.5
|
29.3
|
1.0
|
HG2
|
B:GLU527
|
4.5
|
39.7
|
1.0
|
H
|
B:PHE532
|
4.5
|
37.3
|
1.0
|
CA
|
B:SER528
|
4.5
|
37.3
|
1.0
|
C
|
B:SER528
|
4.6
|
40.6
|
1.0
|
H
|
B:ASP531
|
4.6
|
38.9
|
1.0
|
HE1
|
B:HIS776
|
4.6
|
60.6
|
1.0
|
HA
|
B:VAL530
|
4.8
|
37.5
|
1.0
|
HB2
|
B:ASP531
|
4.8
|
45.9
|
1.0
|
HA
|
B:HIS776
|
4.8
|
40.6
|
1.0
|
N
|
B:VAL529
|
4.8
|
38.7
|
1.0
|
CE1
|
B:HIS776
|
4.9
|
49.8
|
1.0
|
HH22
|
B:ARG781
|
4.9
|
65.9
|
1.0
|
C
|
B:ASP531
|
4.9
|
28.1
|
1.0
|
O
|
B:SER528
|
4.9
|
47.5
|
1.0
|
NH1
|
B:ARG781
|
4.9
|
34.5
|
1.0
|
H
|
B:VAL529
|
4.9
|
47.4
|
1.0
|
OE1
|
A:GLN786
|
5.0
|
30.7
|
1.0
|
|
Calcium binding site 5 out
of 11 in 8blj
Go back to
Calcium Binding Sites List in 8blj
Calcium binding site 5 out
of 11 in the Crystal Structure of the Ligand-Binding Domain (Lbd) of Human Iglur Delta-1 (GLUD1), Apo State
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 5 of Crystal Structure of the Ligand-Binding Domain (Lbd) of Human Iglur Delta-1 (GLUD1), Apo State within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca902
b:65.6
occ:1.00
|
OE1
|
B:GLU747
|
2.6
|
57.7
|
1.0
|
O
|
B:HOH1041
|
3.0
|
56.5
|
1.0
|
CD
|
B:GLU747
|
3.4
|
63.6
|
1.0
|
HE3
|
B:MET537
|
3.5
|
44.6
|
1.0
|
HA
|
B:ALA744
|
3.6
|
39.6
|
1.0
|
HE1
|
B:MET537
|
3.6
|
44.6
|
1.0
|
OE2
|
B:GLU747
|
3.6
|
76.1
|
1.0
|
CE
|
B:MET537
|
3.9
|
36.4
|
1.0
|
HE2
|
B:MET537
|
4.0
|
44.6
|
1.0
|
HG12
|
B:VAL743
|
4.0
|
49.9
|
1.0
|
CG
|
B:TRP805
|
4.1
|
25.4
|
1.0
|
CD1
|
B:TRP805
|
4.1
|
30.1
|
1.0
|
HB3
|
B:TRP805
|
4.1
|
38.6
|
1.0
|
HB3
|
B:GLU747
|
4.3
|
44.5
|
1.0
|
HB2
|
B:ALA744
|
4.3
|
38.6
|
1.0
|
HD1
|
B:TRP805
|
4.3
|
37.1
|
1.0
|
CD2
|
B:TRP805
|
4.4
|
25.9
|
1.0
|
HB2
|
B:TRP805
|
4.4
|
38.6
|
1.0
|
NE1
|
B:TRP805
|
4.4
|
30.3
|
1.0
|
CB
|
B:TRP805
|
4.5
|
31.4
|
1.0
|
CA
|
B:ALA744
|
4.5
|
32.2
|
1.0
|
CE2
|
B:TRP805
|
4.6
|
25.8
|
1.0
|
CG
|
B:GLU747
|
4.6
|
48.9
|
1.0
|
O
|
B:HOH1029
|
4.6
|
30.1
|
1.0
|
HB2
|
B:GLU747
|
4.7
|
44.5
|
1.0
|
CB
|
B:GLU747
|
4.7
|
36.3
|
1.0
|
CB
|
B:ALA744
|
4.8
|
31.4
|
1.0
|
HB1
|
B:ALA744
|
4.8
|
38.6
|
1.0
|
HE1
|
B:TRP805
|
4.8
|
37.3
|
1.0
|
HG2
|
B:GLU747
|
4.8
|
59.6
|
1.0
|
CG1
|
B:VAL743
|
4.9
|
40.8
|
1.0
|
CE3
|
B:TRP805
|
5.0
|
29.6
|
1.0
|
|
Calcium binding site 6 out
of 11 in 8blj
Go back to
Calcium Binding Sites List in 8blj
Calcium binding site 6 out
of 11 in the Crystal Structure of the Ligand-Binding Domain (Lbd) of Human Iglur Delta-1 (GLUD1), Apo State
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 6 of Crystal Structure of the Ligand-Binding Domain (Lbd) of Human Iglur Delta-1 (GLUD1), Apo State within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Ca901
b:50.2
occ:1.00
|
OD1
|
C:ASP531
|
2.2
|
46.8
|
1.0
|
O
|
C:HOH1013
|
2.2
|
51.4
|
1.0
|
O
|
C:VAL530
|
2.3
|
41.7
|
1.0
|
O
|
C:GLU527
|
2.3
|
47.2
|
1.0
|
O
|
C:HOH1038
|
2.7
|
50.7
|
1.0
|
OE2
|
C:GLU527
|
2.9
|
56.3
|
1.0
|
HA
|
C:ASP531
|
3.1
|
59.6
|
1.0
|
C
|
C:VAL530
|
3.3
|
42.4
|
1.0
|
HG3
|
C:GLU527
|
3.4
|
45.8
|
1.0
|
CG
|
C:ASP531
|
3.4
|
54.7
|
1.0
|
C
|
C:GLU527
|
3.5
|
47.0
|
1.0
|
CD
|
C:GLU527
|
3.6
|
46.3
|
1.0
|
CA
|
C:ASP531
|
3.8
|
48.9
|
1.0
|
N
|
C:ASP531
|
3.9
|
46.0
|
1.0
|
CG
|
C:GLU527
|
4.0
|
37.4
|
1.0
|
HA
|
C:GLU527
|
4.0
|
54.2
|
1.0
|
HA
|
C:SER528
|
4.2
|
54.6
|
1.0
|
CB
|
C:ASP531
|
4.2
|
47.2
|
1.0
|
H
|
C:VAL530
|
4.2
|
56.2
|
1.0
|
ND1
|
C:HIS776
|
4.3
|
61.3
|
1.0
|
CA
|
C:GLU527
|
4.3
|
44.5
|
1.0
|
N
|
C:VAL530
|
4.3
|
46.0
|
1.0
|
OD2
|
C:ASP531
|
4.3
|
56.2
|
1.0
|
CA
|
C:VAL530
|
4.4
|
46.5
|
1.0
|
C
|
C:SER528
|
4.5
|
44.6
|
1.0
|
HH12
|
C:ARG781
|
4.5
|
57.3
|
1.0
|
OE1
|
C:GLU527
|
4.5
|
45.7
|
1.0
|
N
|
C:SER528
|
4.5
|
46.5
|
1.0
|
O
|
C:SER528
|
4.5
|
44.0
|
1.0
|
CA
|
C:SER528
|
4.6
|
44.8
|
1.0
|
HE1
|
C:HIS776
|
4.6
|
56.7
|
1.0
|
HA
|
C:VAL530
|
4.6
|
56.7
|
1.0
|
HB3
|
C:ASP531
|
4.7
|
57.5
|
1.0
|
H
|
C:ASP531
|
4.7
|
56.1
|
1.0
|
CB
|
C:GLU527
|
4.8
|
36.0
|
1.0
|
HG2
|
C:GLU527
|
4.8
|
45.8
|
1.0
|
HH22
|
C:ARG781
|
4.8
|
79.2
|
1.0
|
HA
|
C:HIS776
|
4.8
|
52.3
|
1.0
|
N
|
C:VAL529
|
4.8
|
46.1
|
1.0
|
OE1
|
D:GLN786
|
4.8
|
37.9
|
1.0
|
H
|
C:PHE532
|
4.8
|
59.0
|
1.0
|
CE1
|
C:HIS776
|
4.9
|
46.5
|
1.0
|
C
|
C:VAL529
|
4.9
|
49.3
|
1.0
|
HB2
|
C:ASP531
|
5.0
|
57.5
|
1.0
|
|
Calcium binding site 7 out
of 11 in 8blj
Go back to
Calcium Binding Sites List in 8blj
Calcium binding site 7 out
of 11 in the Crystal Structure of the Ligand-Binding Domain (Lbd) of Human Iglur Delta-1 (GLUD1), Apo State
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 7 of Crystal Structure of the Ligand-Binding Domain (Lbd) of Human Iglur Delta-1 (GLUD1), Apo State within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Ca902
b:43.5
occ:1.00
|
OG
|
C:SER757
|
2.2
|
21.3
|
1.0
|
OD1
|
C:ASP755
|
2.3
|
39.1
|
1.0
|
OD2
|
C:ASP753
|
2.6
|
34.4
|
1.0
|
O
|
C:HOH1008
|
2.9
|
26.1
|
1.0
|
CG
|
C:ASP755
|
3.3
|
37.0
|
1.0
|
CG
|
C:ASP753
|
3.4
|
31.4
|
1.0
|
CB
|
C:SER757
|
3.4
|
26.7
|
1.0
|
H
|
C:ASP755
|
3.4
|
38.5
|
1.0
|
O
|
C:HOH1053
|
3.5
|
18.8
|
1.0
|
HB3
|
C:SER757
|
3.5
|
33.0
|
1.0
|
OD1
|
C:ASP753
|
3.5
|
25.8
|
1.0
|
H
|
C:SER757
|
3.6
|
37.0
|
1.0
|
O
|
C:HOH1017
|
3.7
|
30.3
|
1.0
|
OD2
|
C:ASP755
|
3.9
|
34.6
|
1.0
|
HB2
|
C:SER757
|
3.9
|
33.0
|
1.0
|
O
|
C:LYS733
|
4.0
|
27.2
|
1.0
|
HB3
|
C:LYS733
|
4.3
|
35.1
|
1.0
|
N
|
C:ASP755
|
4.3
|
31.4
|
1.0
|
H
|
C:ASP754
|
4.3
|
45.0
|
1.0
|
N
|
C:SER757
|
4.3
|
30.1
|
1.0
|
HB2
|
C:ASP754
|
4.3
|
48.5
|
1.0
|
HG13
|
C:VAL758
|
4.4
|
34.1
|
1.0
|
CA
|
C:SER757
|
4.4
|
29.1
|
1.0
|
CB
|
C:ASP755
|
4.5
|
35.0
|
1.0
|
HB3
|
C:ASP755
|
4.6
|
42.9
|
1.0
|
CA
|
C:ASP755
|
4.8
|
28.9
|
1.0
|
N
|
C:ASP754
|
4.8
|
36.7
|
1.0
|
CB
|
C:ASP753
|
4.8
|
34.1
|
1.0
|
H
|
C:CYS756
|
4.8
|
41.7
|
1.0
|
HA
|
C:LYS733
|
4.9
|
37.3
|
1.0
|
C
|
C:ASP755
|
4.9
|
33.2
|
1.0
|
HD3
|
C:LYS733
|
5.0
|
34.1
|
1.0
|
N
|
C:CYS756
|
5.0
|
34.0
|
1.0
|
HB3
|
C:ASP753
|
5.0
|
41.8
|
1.0
|
|
Calcium binding site 8 out
of 11 in 8blj
Go back to
Calcium Binding Sites List in 8blj
Calcium binding site 8 out
of 11 in the Crystal Structure of the Ligand-Binding Domain (Lbd) of Human Iglur Delta-1 (GLUD1), Apo State
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 8 of Crystal Structure of the Ligand-Binding Domain (Lbd) of Human Iglur Delta-1 (GLUD1), Apo State within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Ca901
b:51.6
occ:1.00
|
O
|
D:GLU527
|
2.4
|
46.8
|
1.0
|
OE2
|
D:GLU527
|
2.4
|
43.1
|
1.0
|
O
|
D:VAL530
|
2.4
|
34.1
|
1.0
|
OD1
|
D:ASP531
|
2.5
|
45.8
|
1.0
|
HA
|
D:ASP531
|
3.2
|
59.6
|
1.0
|
CD
|
D:GLU527
|
3.3
|
45.1
|
1.0
|
C
|
D:VAL530
|
3.4
|
39.4
|
1.0
|
HG3
|
D:GLU527
|
3.4
|
51.3
|
1.0
|
O
|
C:HOH1016
|
3.5
|
42.2
|
1.0
|
C
|
D:GLU527
|
3.6
|
39.8
|
1.0
|
CG
|
D:ASP531
|
3.7
|
44.9
|
1.0
|
CG
|
D:GLU527
|
3.9
|
42.0
|
1.0
|
CA
|
D:ASP531
|
4.0
|
48.9
|
1.0
|
N
|
D:ASP531
|
4.0
|
36.3
|
1.0
|
HA
|
D:GLU527
|
4.0
|
50.8
|
1.0
|
ND1
|
D:HIS776
|
4.1
|
57.4
|
1.0
|
H
|
D:VAL530
|
4.1
|
50.0
|
1.0
|
HA
|
D:SER528
|
4.2
|
51.2
|
1.0
|
OE1
|
D:GLU527
|
4.2
|
37.0
|
1.0
|
CA
|
D:GLU527
|
4.3
|
41.5
|
1.0
|
N
|
D:VAL530
|
4.3
|
40.9
|
1.0
|
O
|
C:HOH1011
|
4.4
|
34.2
|
1.0
|
HE1
|
D:HIS776
|
4.4
|
63.9
|
1.0
|
CB
|
D:ASP531
|
4.4
|
49.8
|
1.0
|
CA
|
D:VAL530
|
4.4
|
41.0
|
1.0
|
HH12
|
D:ARG781
|
4.5
|
60.9
|
1.0
|
HH22
|
D:ARG781
|
4.5
|
53.5
|
1.0
|
N
|
D:SER528
|
4.6
|
39.6
|
1.0
|
C
|
D:SER528
|
4.6
|
37.7
|
1.0
|
OD2
|
D:ASP531
|
4.6
|
46.5
|
1.0
|
HG2
|
D:GLU527
|
4.7
|
51.3
|
1.0
|
CE1
|
D:HIS776
|
4.7
|
52.5
|
1.0
|
CA
|
D:SER528
|
4.7
|
41.9
|
1.0
|
HA
|
D:VAL530
|
4.7
|
50.1
|
1.0
|
CB
|
D:GLU527
|
4.7
|
37.3
|
1.0
|
OE1
|
C:GLN786
|
4.7
|
37.9
|
1.0
|
HA
|
D:HIS776
|
4.8
|
58.5
|
1.0
|
O
|
D:SER528
|
4.8
|
46.2
|
1.0
|
H
|
D:ASP531
|
4.8
|
44.5
|
1.0
|
HB3
|
D:ASP531
|
4.9
|
60.6
|
1.0
|
H
|
D:PHE532
|
4.9
|
57.3
|
1.0
|
N
|
D:VAL529
|
4.9
|
37.1
|
1.0
|
|
Calcium binding site 9 out
of 11 in 8blj
Go back to
Calcium Binding Sites List in 8blj
Calcium binding site 9 out
of 11 in the Crystal Structure of the Ligand-Binding Domain (Lbd) of Human Iglur Delta-1 (GLUD1), Apo State
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 9 of Crystal Structure of the Ligand-Binding Domain (Lbd) of Human Iglur Delta-1 (GLUD1), Apo State within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Ca901
b:53.0
occ:1.00
|
O
|
E:GLU527
|
2.4
|
40.4
|
1.0
|
OD1
|
E:ASP531
|
2.5
|
49.9
|
1.0
|
OE2
|
E:GLU527
|
2.5
|
41.0
|
1.0
|
O
|
E:VAL530
|
2.7
|
40.6
|
1.0
|
HG3
|
E:GLU527
|
3.4
|
45.7
|
1.0
|
HA
|
E:ASP531
|
3.5
|
52.8
|
1.0
|
CD
|
E:GLU527
|
3.6
|
45.7
|
1.0
|
C
|
E:GLU527
|
3.6
|
39.3
|
1.0
|
CG
|
E:ASP531
|
3.7
|
51.3
|
1.0
|
C
|
E:VAL530
|
3.7
|
45.3
|
1.0
|
ND1
|
E:HIS776
|
3.7
|
65.4
|
1.0
|
HE1
|
E:HIS776
|
3.8
|
80.8
|
1.0
|
CG
|
E:GLU527
|
4.0
|
37.3
|
1.0
|
HA
|
E:SER528
|
4.1
|
48.7
|
1.0
|
O
|
E:HOH1011
|
4.1
|
44.2
|
1.0
|
CE1
|
E:HIS776
|
4.1
|
66.6
|
1.0
|
HA
|
E:GLU527
|
4.2
|
43.1
|
1.0
|
CA
|
E:ASP531
|
4.2
|
43.3
|
1.0
|
N
|
E:ASP531
|
4.3
|
39.6
|
1.0
|
H
|
E:VAL530
|
4.4
|
57.4
|
1.0
|
OD2
|
E:ASP531
|
4.5
|
52.2
|
1.0
|
CA
|
E:GLU527
|
4.5
|
35.1
|
1.0
|
CB
|
E:ASP531
|
4.6
|
49.9
|
1.0
|
N
|
E:VAL530
|
4.6
|
47.1
|
1.0
|
N
|
E:SER528
|
4.6
|
42.1
|
1.0
|
HH22
|
E:ARG781
|
4.6
|
70.3
|
1.0
|
C
|
E:SER528
|
4.6
|
44.5
|
1.0
|
CA
|
E:SER528
|
4.6
|
39.8
|
1.0
|
OE1
|
E:GLU527
|
4.6
|
35.5
|
1.0
|
HH12
|
E:ARG781
|
4.7
|
59.5
|
1.0
|
O
|
F:HOH1052
|
4.7
|
28.1
|
1.0
|
CA
|
E:VAL530
|
4.7
|
43.5
|
1.0
|
OE1
|
F:GLN786
|
4.7
|
35.9
|
1.0
|
HG2
|
E:GLU527
|
4.7
|
45.7
|
1.0
|
HA
|
E:HIS776
|
4.8
|
55.5
|
1.0
|
O
|
E:SER528
|
4.8
|
51.0
|
1.0
|
CB
|
E:GLU527
|
4.9
|
26.2
|
1.0
|
N
|
E:VAL529
|
4.9
|
43.1
|
1.0
|
HB3
|
F:ASP782
|
4.9
|
38.5
|
1.0
|
HA
|
E:VAL530
|
4.9
|
53.2
|
1.0
|
CG
|
E:HIS776
|
5.0
|
52.2
|
1.0
|
HB3
|
E:ASP531
|
5.0
|
60.7
|
1.0
|
|
Calcium binding site 10 out
of 11 in 8blj
Go back to
Calcium Binding Sites List in 8blj
Calcium binding site 10 out
of 11 in the Crystal Structure of the Ligand-Binding Domain (Lbd) of Human Iglur Delta-1 (GLUD1), Apo State
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 10 of Crystal Structure of the Ligand-Binding Domain (Lbd) of Human Iglur Delta-1 (GLUD1), Apo State within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Ca901
b:47.2
occ:1.00
|
OD1
|
F:ASP531
|
2.2
|
39.2
|
1.0
|
O
|
F:GLU527
|
2.3
|
44.2
|
1.0
|
OE2
|
F:GLU527
|
2.3
|
41.4
|
1.0
|
O
|
F:HOH1023
|
2.4
|
37.0
|
1.0
|
O
|
F:VAL530
|
2.5
|
38.7
|
1.0
|
O
|
F:HOH1039
|
2.7
|
37.2
|
1.0
|
HA
|
F:ASP531
|
2.9
|
41.0
|
1.0
|
CD
|
F:GLU527
|
3.1
|
40.8
|
1.0
|
HG3
|
F:GLU527
|
3.2
|
43.5
|
1.0
|
CG
|
F:ASP531
|
3.3
|
39.9
|
1.0
|
C
|
F:VAL530
|
3.5
|
36.6
|
1.0
|
C
|
F:GLU527
|
3.5
|
37.9
|
1.0
|
HD1
|
F:HIS776
|
3.5
|
54.5
|
1.0
|
CA
|
F:ASP531
|
3.7
|
33.4
|
1.0
|
CG
|
F:GLU527
|
3.7
|
35.5
|
1.0
|
HA
|
F:GLU527
|
3.9
|
37.6
|
1.0
|
N
|
F:ASP531
|
3.9
|
34.9
|
1.0
|
OE1
|
F:GLU527
|
4.0
|
43.3
|
1.0
|
CB
|
F:ASP531
|
4.1
|
40.0
|
1.0
|
HA
|
F:SER528
|
4.2
|
49.5
|
1.0
|
CA
|
F:GLU527
|
4.2
|
30.6
|
1.0
|
OD2
|
F:ASP531
|
4.2
|
45.1
|
1.0
|
HH12
|
F:ARG781
|
4.3
|
58.2
|
1.0
|
ND1
|
F:HIS776
|
4.4
|
44.6
|
1.0
|
HG2
|
F:GLU527
|
4.5
|
43.5
|
1.0
|
H
|
F:VAL530
|
4.5
|
37.1
|
1.0
|
HH22
|
F:ARG781
|
4.5
|
69.5
|
1.0
|
N
|
F:SER528
|
4.5
|
37.7
|
1.0
|
O
|
E:HOH1009
|
4.5
|
43.8
|
1.0
|
HB3
|
F:ASP531
|
4.5
|
49.0
|
1.0
|
H
|
F:PHE532
|
4.5
|
42.0
|
1.0
|
CB
|
F:GLU527
|
4.6
|
32.1
|
1.0
|
OE1
|
E:GLN786
|
4.6
|
39.7
|
1.0
|
N
|
F:VAL530
|
4.6
|
30.1
|
1.0
|
CA
|
F:VAL530
|
4.6
|
31.6
|
1.0
|
CA
|
F:SER528
|
4.7
|
40.5
|
1.0
|
H
|
F:ASP531
|
4.7
|
42.7
|
1.0
|
C
|
F:SER528
|
4.8
|
37.5
|
1.0
|
HA
|
F:HIS776
|
4.8
|
42.6
|
1.0
|
HE1
|
F:HIS776
|
4.8
|
67.7
|
1.0
|
HB2
|
F:ASP531
|
4.8
|
49.0
|
1.0
|
HA
|
F:VAL530
|
4.9
|
38.8
|
1.0
|
C
|
F:ASP531
|
4.9
|
30.2
|
1.0
|
N
|
F:VAL529
|
5.0
|
36.3
|
1.0
|
H
|
F:VAL529
|
5.0
|
44.5
|
1.0
|
NH1
|
F:ARG781
|
5.0
|
47.8
|
1.0
|
|
Reference:
C.Heroven,
T.Malinauskas,
A.R.Aricescu.
Crystal Structure of the Ligand-Binding Domain (Lbd) of Human Iglur Delta-1 (GLUD1), Apo State To Be Published.
Page generated: Fri Jul 19 07:21:19 2024
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