Calcium in PDB 5aan: Crystal Structure of Drosophila Ncs-1 Bound to Penothiazine FD44
Protein crystallography data
The structure of Crystal Structure of Drosophila Ncs-1 Bound to Penothiazine FD44, PDB code: 5aan
was solved by
A.Chaves-Sanjuan,
L.Infantes,
M.J.Sanchez-Barrena,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
|
Resolution Low / High (Å)
|
40.87 /
1.60
|
|
Space group
|
P 21 21 21
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
54.052,
54.961,
61.132,
90.00,
90.00,
90.00
|
|
R / Rfree (%)
|
18.6 /
20.9
|
Calcium Binding Sites:
The binding sites of Calcium atom in the Crystal Structure of Drosophila Ncs-1 Bound to Penothiazine FD44
(pdb code 5aan). This binding sites where shown within
5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the
Crystal Structure of Drosophila Ncs-1 Bound to Penothiazine FD44, PDB code: 5aan:
Jump to Calcium binding site number:
1;
2;
3;
Calcium binding site 1 out
of 3 in 5aan
Go back to
Calcium Binding Sites List in 5aan
Calcium binding site 1 out
of 3 in the Crystal Structure of Drosophila Ncs-1 Bound to Penothiazine FD44
 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 Drosophila Ncs-1 Bound to Penothiazine FD44 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca1186
b:26.0
occ:1.00
|
O
|
A:ALA79
|
2.3
|
25.0
|
1.0
|
|
O
|
A:HOH2085
|
2.3
|
36.8
|
1.0
|
|
OD1
|
A:ASP73
|
2.3
|
28.4
|
1.0
|
|
OE1
|
A:GLU84
|
2.4
|
26.1
|
1.0
|
|
OD1
|
A:ASP77
|
2.4
|
30.9
|
1.0
|
|
OD1
|
A:ASN75
|
2.4
|
35.9
|
1.0
|
|
OE2
|
A:GLU84
|
2.5
|
31.5
|
1.0
|
|
CD
|
A:GLU84
|
2.8
|
30.2
|
1.0
|
|
HD22
|
A:ASN75
|
3.2
|
60.9
|
1.0
|
|
CG
|
A:ASP77
|
3.2
|
40.7
|
1.0
|
|
CG
|
A:ASN75
|
3.3
|
40.2
|
1.0
|
|
H
|
A:ASP77
|
3.4
|
35.8
|
1.0
|
|
HA
|
A:ASP73
|
3.4
|
25.8
|
1.0
|
|
CG
|
A:ASP73
|
3.5
|
27.5
|
1.0
|
|
H
|
A:ALA79
|
3.5
|
34.8
|
1.0
|
|
C
|
A:ALA79
|
3.5
|
22.4
|
1.0
|
|
ND2
|
A:ASN75
|
3.6
|
50.7
|
1.0
|
|
OD2
|
A:ASP77
|
3.6
|
39.6
|
1.0
|
|
HA
|
A:ILE80
|
3.7
|
27.5
|
1.0
|
|
H
|
A:ASN75
|
3.7
|
38.8
|
1.0
|
|
H
|
A:GLU81
|
3.8
|
27.5
|
1.0
|
|
CA
|
A:ASP73
|
4.1
|
21.4
|
1.0
|
|
HG2
|
A:GLU81
|
4.2
|
45.0
|
1.0
|
|
N
|
A:ASP77
|
4.2
|
29.8
|
1.0
|
|
N
|
A:ALA79
|
4.2
|
29.0
|
1.0
|
|
CB
|
A:ASP73
|
4.3
|
25.2
|
1.0
|
|
CG
|
A:GLU84
|
4.3
|
27.1
|
1.0
|
|
OD2
|
A:ASP73
|
4.3
|
27.8
|
1.0
|
|
H
|
A:ASN76
|
4.3
|
42.5
|
1.0
|
|
HB1
|
A:ALA79
|
4.4
|
40.8
|
1.0
|
|
HD21
|
A:ASN75
|
4.4
|
60.9
|
1.0
|
|
CA
|
A:ALA79
|
4.4
|
27.2
|
1.0
|
|
N
|
A:ILE80
|
4.4
|
25.2
|
1.0
|
|
CB
|
A:ASP77
|
4.4
|
37.4
|
1.0
|
|
HB2
|
A:ASP73
|
4.4
|
30.3
|
1.0
|
|
C
|
A:ASP73
|
4.4
|
30.2
|
1.0
|
|
CA
|
A:ILE80
|
4.5
|
22.9
|
1.0
|
|
H
|
A:GLY78
|
4.5
|
34.4
|
1.0
|
|
N
|
A:ASN75
|
4.5
|
32.3
|
1.0
|
|
N
|
A:GLU81
|
4.5
|
22.9
|
1.0
|
|
H
|
A:GLU74
|
4.5
|
31.4
|
1.0
|
|
CB
|
A:ASN75
|
4.6
|
36.5
|
1.0
|
|
HB3
|
A:ASP77
|
4.6
|
44.9
|
1.0
|
|
N
|
A:ASN76
|
4.6
|
35.4
|
1.0
|
|
HG3
|
A:GLU84
|
4.6
|
32.5
|
1.0
|
|
N
|
A:GLU74
|
4.7
|
26.2
|
1.0
|
|
CA
|
A:ASP77
|
4.7
|
33.5
|
1.0
|
|
HG2
|
A:GLU84
|
4.7
|
32.5
|
1.0
|
|
N
|
A:GLY78
|
4.8
|
28.7
|
1.0
|
|
HB3
|
A:GLU81
|
4.8
|
33.6
|
1.0
|
|
CD
|
A:GLU81
|
4.8
|
61.6
|
1.0
|
|
HB3
|
A:ASN75
|
4.9
|
43.8
|
1.0
|
|
HB2
|
A:GLU84
|
4.9
|
28.3
|
1.0
|
|
CA
|
A:ASN75
|
4.9
|
33.9
|
1.0
|
|
CG
|
A:GLU81
|
4.9
|
37.5
|
1.0
|
|
OE1
|
A:GLU81
|
4.9
|
49.0
|
1.0
|
|
C
|
A:ASN75
|
4.9
|
38.5
|
1.0
|
|
CB
|
A:ALA79
|
4.9
|
34.0
|
1.0
|
|
O
|
A:ASP73
|
4.9
|
31.7
|
1.0
|
|
C
|
A:ASP77
|
4.9
|
32.3
|
1.0
|
|
O
|
A:HOH2084
|
5.0
|
43.9
|
1.0
|
|
C
|
A:ILE80
|
5.0
|
20.1
|
1.0
|
|
Calcium binding site 2 out
of 3 in 5aan
Go back to
Calcium Binding Sites List in 5aan
Calcium binding site 2 out
of 3 in the Crystal Structure of Drosophila Ncs-1 Bound to Penothiazine FD44
 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 Drosophila Ncs-1 Bound to Penothiazine FD44 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca1187
b:27.4
occ:1.00
|
O
|
A:ARG162
|
2.4
|
25.8
|
1.0
|
|
O
|
A:HOH2130
|
2.4
|
31.0
|
1.0
|
|
OD1
|
A:ASN158
|
2.4
|
28.2
|
1.0
|
|
OD1
|
A:ASP156
|
2.4
|
29.0
|
1.0
|
|
OE1
|
A:GLU167
|
2.4
|
24.6
|
1.0
|
|
OD1
|
A:ASP160
|
2.4
|
32.3
|
1.0
|
|
OE2
|
A:GLU167
|
2.5
|
31.0
|
1.0
|
|
CD
|
A:GLU167
|
2.8
|
26.0
|
1.0
|
|
CG
|
A:ASP160
|
3.3
|
36.4
|
1.0
|
|
CG
|
A:ASN158
|
3.5
|
38.6
|
1.0
|
|
H
|
A:ASP160
|
3.5
|
36.1
|
1.0
|
|
CG
|
A:ASP156
|
3.5
|
28.4
|
1.0
|
|
C
|
A:ARG162
|
3.6
|
23.8
|
1.0
|
|
HA
|
A:LEU163
|
3.6
|
27.7
|
1.0
|
|
H
|
A:ASN158
|
3.6
|
41.9
|
1.0
|
|
H
|
A:ARG162
|
3.6
|
36.2
|
1.0
|
|
OD2
|
A:ASP160
|
3.6
|
44.7
|
1.0
|
|
HA
|
A:ASP156
|
3.7
|
35.7
|
1.0
|
|
HD22
|
A:ASN158
|
3.7
|
46.9
|
1.0
|
|
ND2
|
A:ASN158
|
4.0
|
39.0
|
1.0
|
|
HD21
|
A:LEU163
|
4.0
|
32.3
|
1.0
|
|
HG3
|
A:ARG162
|
4.0
|
41.6
|
1.0
|
|
H
|
A:THR164
|
4.1
|
28.0
|
1.0
|
|
HG21
|
A:THR164
|
4.2
|
31.8
|
1.0
|
|
OD2
|
A:ASP156
|
4.3
|
32.2
|
1.0
|
|
N
|
A:ASP160
|
4.3
|
30.1
|
1.0
|
|
CA
|
A:ASP156
|
4.4
|
29.7
|
1.0
|
|
N
|
A:ARG162
|
4.4
|
30.2
|
1.0
|
|
CG
|
A:GLU167
|
4.4
|
29.0
|
1.0
|
|
CA
|
A:LEU163
|
4.4
|
23.1
|
1.0
|
|
H
|
A:LYS157
|
4.4
|
34.5
|
1.0
|
|
N
|
A:ASN158
|
4.4
|
34.9
|
1.0
|
|
N
|
A:LEU163
|
4.4
|
23.2
|
1.0
|
|
HG2
|
A:ARG162
|
4.4
|
41.6
|
1.0
|
|
H
|
A:HIS159
|
4.4
|
42.7
|
1.0
|
|
CB
|
A:ASP156
|
4.5
|
30.1
|
1.0
|
|
CA
|
A:ARG162
|
4.5
|
24.6
|
1.0
|
|
CB
|
A:ASP160
|
4.6
|
32.4
|
1.0
|
|
C
|
A:ASP156
|
4.6
|
35.9
|
1.0
|
|
N
|
A:LYS157
|
4.6
|
28.7
|
1.0
|
|
CG
|
A:ARG162
|
4.6
|
34.7
|
1.0
|
|
N
|
A:HIS159
|
4.7
|
35.6
|
1.0
|
|
O
|
A:HOH2132
|
4.7
|
41.5
|
1.0
|
|
H
|
A:ASP161
|
4.7
|
37.7
|
1.0
|
|
CB
|
A:ASN158
|
4.7
|
35.8
|
1.0
|
|
HB2
|
A:ASP156
|
4.7
|
36.1
|
1.0
|
|
HG3
|
A:GLU167
|
4.8
|
34.8
|
1.0
|
|
HG2
|
A:GLU167
|
4.8
|
34.8
|
1.0
|
|
N
|
A:THR164
|
4.8
|
23.3
|
1.0
|
|
HB3
|
A:ASP160
|
4.8
|
38.8
|
1.0
|
|
HD21
|
A:ASN158
|
4.8
|
46.9
|
1.0
|
|
C
|
A:ASN158
|
4.8
|
38.8
|
1.0
|
|
CA
|
A:ASN158
|
4.9
|
37.4
|
1.0
|
|
CA
|
A:ASP160
|
4.9
|
33.8
|
1.0
|
|
CD2
|
A:LEU163
|
4.9
|
26.9
|
1.0
|
|
HB2
|
A:GLU167
|
5.0
|
31.1
|
1.0
|
|
HD23
|
A:LEU163
|
5.0
|
32.3
|
1.0
|
|
N
|
A:ASP161
|
5.0
|
31.4
|
1.0
|
|
Calcium binding site 3 out
of 3 in 5aan
Go back to
Calcium Binding Sites List in 5aan
Calcium binding site 3 out
of 3 in the Crystal Structure of Drosophila Ncs-1 Bound to Penothiazine FD44
 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 Drosophila Ncs-1 Bound to Penothiazine FD44 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca1188
b:23.4
occ:1.00
|
O
|
A:TYR115
|
2.3
|
26.0
|
1.0
|
|
O
|
A:HOH2109
|
2.3
|
31.4
|
1.0
|
|
OD1
|
A:ASP109
|
2.3
|
23.2
|
1.0
|
|
OD1
|
A:ASP113
|
2.4
|
24.8
|
1.0
|
|
OD1
|
A:ASP111
|
2.4
|
28.2
|
1.0
|
|
OE1
|
A:GLU120
|
2.4
|
24.3
|
1.0
|
|
OE2
|
A:GLU120
|
2.5
|
27.8
|
1.0
|
|
CD
|
A:GLU120
|
2.8
|
24.2
|
1.0
|
|
CG
|
A:ASP113
|
3.3
|
27.8
|
1.0
|
|
H
|
A:ASP113
|
3.3
|
28.4
|
1.0
|
|
CG
|
A:ASP111
|
3.3
|
31.9
|
1.0
|
|
HA
|
A:ASP109
|
3.4
|
28.2
|
1.0
|
|
CG
|
A:ASP109
|
3.4
|
23.3
|
1.0
|
|
C
|
A:TYR115
|
3.5
|
21.0
|
1.0
|
|
H
|
A:ASP111
|
3.5
|
33.2
|
1.0
|
|
H
|
A:TYR115
|
3.5
|
23.5
|
1.0
|
|
HA
|
A:ILE116
|
3.7
|
22.4
|
1.0
|
|
OD2
|
A:ASP111
|
3.7
|
38.2
|
1.0
|
|
OD2
|
A:ASP113
|
3.8
|
31.7
|
1.0
|
|
HG21
|
A:THR117
|
3.9
|
43.1
|
1.0
|
|
HB2
|
A:TYR115
|
4.0
|
24.2
|
1.0
|
|
H
|
A:THR117
|
4.1
|
30.6
|
1.0
|
|
CA
|
A:ASP109
|
4.1
|
23.5
|
1.0
|
|
N
|
A:ASP113
|
4.1
|
23.7
|
1.0
|
|
N
|
A:TYR115
|
4.2
|
19.6
|
1.0
|
|
CB
|
A:ASP109
|
4.2
|
19.0
|
1.0
|
|
CG
|
A:GLU120
|
4.3
|
24.8
|
1.0
|
|
N
|
A:ASP111
|
4.3
|
27.7
|
1.0
|
|
OD2
|
A:ASP109
|
4.3
|
23.5
|
1.0
|
|
CA
|
A:TYR115
|
4.3
|
21.0
|
1.0
|
|
H
|
A:ASN112
|
4.3
|
29.1
|
0.5
|
|
CB
|
A:ASP113
|
4.3
|
27.4
|
1.0
|
|
H
|
A:ASN112
|
4.3
|
29.1
|
0.5
|
|
C
|
A:ASP109
|
4.4
|
27.6
|
1.0
|
|
H
|
A:VAL110
|
4.4
|
29.6
|
1.0
|
|
HB3
|
A:ASP113
|
4.4
|
32.8
|
1.0
|
|
N
|
A:ILE116
|
4.4
|
22.1
|
1.0
|
|
HB2
|
A:ASP109
|
4.4
|
22.8
|
1.0
|
|
CA
|
A:ILE116
|
4.4
|
18.7
|
1.0
|
|
N
|
A:VAL110
|
4.5
|
24.7
|
1.0
|
|
HG3
|
A:GLU120
|
4.6
|
29.7
|
1.0
|
|
H
|
A:GLY114
|
4.6
|
25.7
|
1.0
|
|
CB
|
A:ASP111
|
4.6
|
26.4
|
1.0
|
|
N
|
A:ASN112
|
4.6
|
24.2
|
1.0
|
|
CB
|
A:TYR115
|
4.6
|
20.2
|
1.0
|
|
N
|
A:THR117
|
4.7
|
25.5
|
1.0
|
|
CA
|
A:ASP113
|
4.7
|
25.6
|
1.0
|
|
HG2
|
A:GLU120
|
4.7
|
29.7
|
1.0
|
|
CA
|
A:ASP111
|
4.7
|
26.4
|
1.0
|
|
C
|
A:ASP111
|
4.8
|
28.5
|
1.0
|
|
CG2
|
A:THR117
|
4.8
|
35.9
|
1.0
|
|
N
|
A:GLY114
|
4.9
|
21.4
|
1.0
|
|
O
|
A:ASP109
|
4.9
|
23.0
|
1.0
|
|
HB3
|
A:ASP111
|
4.9
|
31.7
|
1.0
|
|
HB3
|
A:TYR115
|
5.0
|
24.2
|
1.0
|
|
C
|
A:ILE116
|
5.0
|
21.8
|
1.0
|
|
O
|
A:HOH2119
|
5.0
|
38.0
|
1.0
|
|
C
|
A:ASP113
|
5.0
|
23.1
|
1.0
|
|
Reference:
A.Mansilla,
A.Chaves-Sanjuan,
N.E.Campillo,
O.Semelidou,
L.Martinez-Gonzalez,
L.Infantes,
J.M.Gonzalez-Rubio,
C.Gil,
S.Conde,
E.M.Skoulakis,
A.Ferrus,
A.Martinez,
M.J.Sanchez-Barrena.
Interference of the Complex Between Ncs-1 and RIC8A with Phenothiazines Regulates Synaptic Function and Is An Approach For Fragile X Syndrome. Proc. Natl. Acad. Sci. V. 114 E999 2017U.S.A..
ISSN: ESSN 1091-6490
PubMed: 28119500
DOI: 10.1073/PNAS.1611089114
Page generated: Sun Jul 14 16:28:49 2024
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