Calcium in PDB 3n5a: Synaptotagmin-7, C2B-Domain, Calcium Bound
Protein crystallography data
The structure of Synaptotagmin-7, C2B-Domain, Calcium Bound, PDB code: 3n5a
was solved by
D.R.Tomchick,
J.Rizo,
T.K.Craig,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
|
Resolution Low / High (Å)
|
23.51 /
1.44
|
|
Space group
|
P 21 21 21
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
35.598,
44.892,
87.383,
90.00,
90.00,
90.00
|
|
R / Rfree (%)
|
16 /
18.1
|
Calcium Binding Sites:
The binding sites of Calcium atom in the Synaptotagmin-7, C2B-Domain, Calcium Bound
(pdb code 3n5a). This binding sites where shown within
5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the
Synaptotagmin-7, C2B-Domain, Calcium Bound, PDB code: 3n5a:
Jump to Calcium binding site number:
1;
2;
3;
4;
Calcium binding site 1 out
of 4 in 3n5a
Go back to
Calcium Binding Sites List in 3n5a
Calcium binding site 1 out
of 4 in the Synaptotagmin-7, C2B-Domain, Calcium Bound
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 1 of Synaptotagmin-7, C2B-Domain, Calcium Bound within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca101
b:8.8
occ:1.00
|
OD1
|
A:ASP359
|
2.3
|
10.7
|
1.0
|
|
O
|
A:LYS358
|
2.3
|
8.8
|
1.0
|
|
O
|
A:HOH120
|
2.4
|
13.9
|
1.0
|
|
OD2
|
A:ASP303
|
2.4
|
9.3
|
1.0
|
|
OD1
|
A:ASP357
|
2.4
|
8.1
|
1.0
|
|
OD2
|
A:ASP297
|
2.4
|
11.6
|
1.0
|
|
OD1
|
A:ASP297
|
2.7
|
9.2
|
1.0
|
|
CG
|
A:ASP297
|
2.9
|
9.9
|
1.0
|
|
CG
|
A:ASP357
|
3.2
|
8.0
|
1.0
|
|
HA
|
A:ASP359
|
3.2
|
9.4
|
1.0
|
|
OD2
|
A:ASP357
|
3.3
|
9.0
|
1.0
|
|
C
|
A:LYS358
|
3.4
|
8.9
|
1.0
|
|
HB2
|
A:ASP303
|
3.4
|
9.7
|
1.0
|
|
CG
|
A:ASP303
|
3.5
|
7.9
|
1.0
|
|
CG
|
A:ASP359
|
3.6
|
10.4
|
1.0
|
|
H
|
A:ASP303
|
3.6
|
8.9
|
1.0
|
|
CA
|
A:CA102
|
3.8
|
10.1
|
1.0
|
|
CA
|
A:ASP359
|
3.9
|
7.9
|
1.0
|
|
CB
|
A:ASP303
|
3.9
|
8.1
|
1.0
|
|
N
|
A:ASP359
|
4.1
|
9.0
|
1.0
|
|
HA
|
A:SER302
|
4.1
|
8.3
|
1.0
|
|
N
|
A:ASP303
|
4.1
|
7.5
|
1.0
|
|
O
|
A:HOH18
|
4.3
|
14.0
|
1.0
|
|
CB
|
A:ASP359
|
4.3
|
9.0
|
1.0
|
|
O
|
A:HOH176
|
4.3
|
27.6
|
1.0
|
|
N
|
A:LYS358
|
4.4
|
8.1
|
1.0
|
|
CB
|
A:ASP297
|
4.4
|
9.8
|
1.0
|
|
O
|
A:HOH137
|
4.4
|
39.5
|
1.0
|
|
C
|
A:ASP357
|
4.4
|
8.1
|
1.0
|
|
O
|
A:HOH138
|
4.5
|
23.8
|
1.0
|
|
OD2
|
A:ASP359
|
4.5
|
12.3
|
1.0
|
|
OD1
|
A:ASP303
|
4.5
|
9.8
|
1.0
|
|
CA
|
A:LYS358
|
4.5
|
7.7
|
1.0
|
|
O
|
A:HOH48
|
4.5
|
35.6
|
1.0
|
|
O
|
A:ASP357
|
4.6
|
8.8
|
1.0
|
|
CB
|
A:ASP357
|
4.6
|
7.7
|
1.0
|
|
H
|
A:LYS358
|
4.6
|
9.7
|
1.0
|
|
CA
|
A:ASP303
|
4.7
|
7.5
|
1.0
|
|
HB3
|
A:ASP297
|
4.7
|
11.8
|
1.0
|
|
HB3
|
A:ASP303
|
4.7
|
9.7
|
1.0
|
|
HB2
|
A:ASP297
|
4.8
|
11.8
|
1.0
|
|
HB3
|
A:ASP359
|
4.8
|
10.7
|
1.0
|
|
C
|
A:SER302
|
4.8
|
7.3
|
1.0
|
|
H
|
A:ASP359
|
4.9
|
10.7
|
1.0
|
|
CA
|
A:SER302
|
4.9
|
6.9
|
1.0
|
|
HB3
|
A:LYS358
|
4.9
|
11.3
|
1.0
|
|
CA
|
A:ASP357
|
5.0
|
8.6
|
1.0
|
|
Calcium binding site 2 out
of 4 in 3n5a
Go back to
Calcium Binding Sites List in 3n5a
Calcium binding site 2 out
of 4 in the Synaptotagmin-7, C2B-Domain, Calcium Bound
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 2 of Synaptotagmin-7, C2B-Domain, Calcium Bound within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca102
b:10.1
occ:1.00
|
OD2
|
A:ASP357
|
2.3
|
9.0
|
1.0
|
|
O
|
A:HOH34
|
2.3
|
15.8
|
1.0
|
|
O
|
A:MET296
|
2.3
|
10.1
|
0.5
|
|
OD2
|
A:ASP365
|
2.3
|
10.8
|
1.0
|
|
OD1
|
A:ASP297
|
2.4
|
9.2
|
1.0
|
|
OD2
|
A:ASP359
|
2.5
|
12.3
|
1.0
|
|
OD1
|
A:ASP359
|
2.5
|
10.7
|
1.0
|
|
O
|
A:MET296
|
2.6
|
10.5
|
0.5
|
|
CG
|
A:ASP359
|
2.8
|
10.4
|
1.0
|
|
C
|
A:MET296
|
3.3
|
8.3
|
0.5
|
|
CG
|
A:ASP365
|
3.4
|
12.4
|
1.0
|
|
C
|
A:MET296
|
3.4
|
11.4
|
0.5
|
|
CG
|
A:ASP357
|
3.5
|
8.0
|
1.0
|
|
HB3
|
A:MET296
|
3.5
|
12.0
|
0.5
|
|
CG
|
A:ASP297
|
3.6
|
9.9
|
1.0
|
|
HA
|
A:ASP297
|
3.6
|
11.4
|
1.0
|
|
HB2
|
A:MET296
|
3.8
|
12.0
|
0.5
|
|
CA
|
A:CA101
|
3.8
|
8.8
|
1.0
|
|
HB2
|
A:ASP365
|
3.8
|
11.8
|
1.0
|
|
HB3
|
A:MET296
|
3.8
|
10.1
|
0.5
|
|
HB2
|
A:MET296
|
3.9
|
10.1
|
0.5
|
|
CB
|
A:MET296
|
4.0
|
10.0
|
0.5
|
|
N
|
A:ASP297
|
4.1
|
8.9
|
1.0
|
|
O
|
A:HOH144
|
4.1
|
27.3
|
1.0
|
|
OD1
|
A:ASP357
|
4.1
|
8.1
|
1.0
|
|
O
|
A:HOH99
|
4.2
|
22.8
|
1.0
|
|
OD1
|
A:ASP365
|
4.2
|
14.5
|
1.0
|
|
CA
|
A:CA103
|
4.2
|
16.2
|
1.0
|
|
CA
|
A:ASP297
|
4.2
|
9.5
|
1.0
|
|
CB
|
A:ASP365
|
4.2
|
9.9
|
1.0
|
|
CB
|
A:MET296
|
4.2
|
8.4
|
0.5
|
|
O
|
A:HOH48
|
4.3
|
35.6
|
1.0
|
|
CA
|
A:MET296
|
4.3
|
6.5
|
0.5
|
|
CB
|
A:ASP359
|
4.3
|
9.0
|
1.0
|
|
OD2
|
A:ASP297
|
4.3
|
11.6
|
1.0
|
|
HB3
|
A:ASP357
|
4.3
|
9.1
|
1.0
|
|
CA
|
A:MET296
|
4.4
|
8.4
|
0.5
|
|
CB
|
A:ASP297
|
4.5
|
9.8
|
1.0
|
|
H
|
A:ASP365
|
4.5
|
11.8
|
1.0
|
|
CB
|
A:ASP357
|
4.6
|
7.7
|
1.0
|
|
HB3
|
A:ASP359
|
4.6
|
10.7
|
1.0
|
|
H
|
A:ASP297
|
4.8
|
10.6
|
0.5
|
|
HB2
|
A:ASP359
|
4.8
|
10.7
|
1.0
|
|
HB3
|
A:ASP365
|
4.8
|
11.8
|
1.0
|
|
H
|
A:ASP297
|
4.8
|
10.6
|
0.5
|
|
HA
|
A:MET296
|
4.8
|
7.7
|
0.5
|
|
O
|
A:ASP357
|
4.8
|
8.8
|
1.0
|
|
O
|
A:HOH118
|
4.9
|
31.4
|
1.0
|
|
O
|
A:HOH100
|
4.9
|
20.8
|
1.0
|
|
HB3
|
A:ASP297
|
5.0
|
11.8
|
1.0
|
|
O
|
A:HOH120
|
5.0
|
13.9
|
1.0
|
|
HA
|
A:ASP359
|
5.0
|
9.4
|
1.0
|
|
Calcium binding site 3 out
of 4 in 3n5a
Go back to
Calcium Binding Sites List in 3n5a
Calcium binding site 3 out
of 4 in the Synaptotagmin-7, C2B-Domain, Calcium Bound
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 3 of Synaptotagmin-7, C2B-Domain, Calcium Bound within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca103
b:16.2
occ:1.00
|
O
|
A:ARG363
|
2.3
|
7.9
|
0.6
|
|
OD2
|
A:ASP359
|
2.4
|
12.3
|
1.0
|
|
OG
|
A:SER362
|
2.4
|
11.2
|
1.0
|
|
OD1
|
A:ASP365
|
2.4
|
14.5
|
1.0
|
|
O
|
A:ARG363
|
2.5
|
11.5
|
0.4
|
|
O
|
A:HOH99
|
2.6
|
22.8
|
1.0
|
|
CG
|
A:ASP365
|
3.2
|
12.4
|
1.0
|
|
HB2
|
A:SER362
|
3.4
|
12.7
|
1.0
|
|
OD2
|
A:ASP365
|
3.4
|
10.8
|
1.0
|
|
CG
|
A:ASP359
|
3.5
|
10.4
|
1.0
|
|
CB
|
A:SER362
|
3.5
|
10.6
|
1.0
|
|
C
|
A:ARG363
|
3.5
|
8.6
|
0.6
|
|
C
|
A:ARG363
|
3.6
|
10.2
|
0.4
|
|
HB2
|
A:ASP359
|
3.6
|
10.7
|
1.0
|
|
O
|
A:HOH34
|
3.9
|
15.8
|
1.0
|
|
O
|
A:HOH168
|
3.9
|
39.2
|
1.0
|
|
CB
|
A:ASP359
|
4.0
|
9.0
|
1.0
|
|
O
|
A:HOH145
|
4.0
|
30.2
|
1.0
|
|
HB3
|
A:ASP359
|
4.0
|
10.7
|
1.0
|
|
N
|
A:ARG363
|
4.1
|
9.8
|
0.4
|
|
HA
|
A:ASN364
|
4.1
|
10.5
|
1.0
|
|
C
|
A:SER362
|
4.1
|
8.1
|
1.0
|
|
N
|
A:ARG363
|
4.1
|
8.4
|
0.6
|
|
CA
|
A:CA102
|
4.2
|
10.1
|
1.0
|
|
HB3
|
A:SER362
|
4.2
|
12.7
|
1.0
|
|
N
|
A:ASP365
|
4.2
|
9.9
|
1.0
|
|
H
|
A:ASP365
|
4.3
|
11.8
|
1.0
|
|
O
|
A:HOH118
|
4.3
|
31.4
|
1.0
|
|
H
|
A:ARG363
|
4.3
|
11.7
|
0.4
|
|
C
|
A:ASN364
|
4.3
|
9.7
|
1.0
|
|
H
|
A:ARG363
|
4.4
|
10.0
|
0.6
|
|
O
|
A:HOH150
|
4.4
|
34.5
|
1.0
|
|
CA
|
A:ARG363
|
4.4
|
8.4
|
0.6
|
|
HB2
|
A:ARG363
|
4.4
|
13.4
|
0.6
|
|
CA
|
A:SER362
|
4.4
|
8.2
|
1.0
|
|
CA
|
A:ARG363
|
4.4
|
8.4
|
0.4
|
|
CB
|
A:ASP365
|
4.5
|
9.9
|
1.0
|
|
N
|
A:ASN364
|
4.5
|
10.3
|
1.0
|
|
O
|
A:SER362
|
4.5
|
9.3
|
1.0
|
|
CA
|
A:ASN364
|
4.5
|
8.8
|
1.0
|
|
HA
|
A:ASP365
|
4.6
|
12.0
|
1.0
|
|
OD1
|
A:ASP359
|
4.6
|
10.7
|
1.0
|
|
HB3
|
A:ARG363
|
4.6
|
12.8
|
0.4
|
|
CA
|
A:ASP365
|
4.7
|
10.0
|
1.0
|
|
O
|
A:ASN364
|
4.8
|
11.2
|
1.0
|
|
HB2
|
A:ASP365
|
4.9
|
11.8
|
1.0
|
|
CB
|
A:ARG363
|
5.0
|
11.2
|
0.6
|
|
Calcium binding site 4 out
of 4 in 3n5a
Go back to
Calcium Binding Sites List in 3n5a
Calcium binding site 4 out
of 4 in the Synaptotagmin-7, C2B-Domain, Calcium Bound
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 4 of Synaptotagmin-7, C2B-Domain, Calcium Bound within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca104
b:12.9
occ:1.00
|
O
|
A:ASP359
|
2.6
|
12.5
|
1.0
|
|
OD1
|
A:ASN364
|
2.6
|
9.6
|
1.0
|
|
O
|
A:SER362
|
2.7
|
9.3
|
1.0
|
|
O
|
A:HOH64
|
2.9
|
16.5
|
1.0
|
|
H
|
A:ASN364
|
3.4
|
12.3
|
0.5
|
|
HA
|
A:ARG363
|
3.5
|
10.1
|
0.4
|
|
H
|
A:ASN364
|
3.5
|
12.3
|
0.5
|
|
HA
|
A:ARG363
|
3.5
|
10.0
|
0.6
|
|
H
|
A:ASP359
|
3.6
|
10.7
|
1.0
|
|
CG
|
A:ASN364
|
3.6
|
8.9
|
1.0
|
|
C
|
A:ASP359
|
3.8
|
9.2
|
1.0
|
|
N
|
A:ASN364
|
3.8
|
10.3
|
1.0
|
|
C
|
A:SER362
|
3.8
|
8.1
|
1.0
|
|
O
|
A:HOH406
|
3.9
|
32.1
|
1.0
|
|
HB2
|
A:ASP359
|
3.9
|
10.7
|
1.0
|
|
HD21
|
A:ASN364
|
4.1
|
13.9
|
1.0
|
|
C
|
A:ARG363
|
4.1
|
8.6
|
0.6
|
|
O
|
A:HOH81
|
4.1
|
32.1
|
1.0
|
|
CA
|
A:ARG363
|
4.1
|
8.4
|
0.4
|
|
CA
|
A:ARG363
|
4.2
|
8.4
|
0.6
|
|
H
|
A:SER362
|
4.2
|
11.2
|
1.0
|
|
ND2
|
A:ASN364
|
4.2
|
11.6
|
1.0
|
|
C
|
A:ARG363
|
4.2
|
10.2
|
0.4
|
|
N
|
A:ASP359
|
4.3
|
9.0
|
1.0
|
|
HA
|
A:ASN364
|
4.4
|
10.5
|
1.0
|
|
N
|
A:ARG363
|
4.4
|
8.4
|
0.6
|
|
N
|
A:ARG363
|
4.4
|
9.8
|
0.4
|
|
CA
|
A:ASP359
|
4.5
|
7.9
|
1.0
|
|
CA
|
A:ASN364
|
4.5
|
8.8
|
1.0
|
|
HA
|
A:LYS360
|
4.5
|
13.0
|
1.0
|
|
CB
|
A:ASP359
|
4.6
|
9.0
|
1.0
|
|
CB
|
A:ASN364
|
4.6
|
8.2
|
1.0
|
|
N
|
A:LYS360
|
4.8
|
9.6
|
1.0
|
|
O
|
A:HOH93
|
4.8
|
25.6
|
1.0
|
|
HG3
|
A:LYS358
|
4.8
|
15.1
|
1.0
|
|
N
|
A:SER362
|
4.8
|
9.4
|
1.0
|
|
O
|
A:ARG363
|
4.9
|
7.9
|
0.6
|
|
HB3
|
A:ASP359
|
4.9
|
10.7
|
1.0
|
|
C
|
A:LYS360
|
4.9
|
10.0
|
1.0
|
|
O
|
A:LYS360
|
4.9
|
11.2
|
1.0
|
|
HB2
|
A:ASN364
|
5.0
|
9.8
|
1.0
|
|
CA
|
A:LYS360
|
5.0
|
10.8
|
1.0
|
|
CA
|
A:SER362
|
5.0
|
8.2
|
1.0
|
|
Reference:
M.Xue,
T.K.Craig,
O.H.Shin,
L.Li,
C.A.Brautigam,
D.R.Tomchick,
T.C.Sudhof,
C.Rosenmund,
J.Rizo.
Structural and Mutational Analysis of Functional Differentiation Between Synaptotagmins-1 and -7. Plos One V. 5 12544 2010.
ISSN: ESSN 1932-6203
PubMed: 20824061
DOI: 10.1371/JOURNAL.PONE.0012544
Page generated: Sat Jul 13 14:52:51 2024
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