Calcium in PDB 1tjx: Crystallographic Identification of CA2+ Coordination Sites in Synaptotagmin I C2B Domain
Protein crystallography data
The structure of Crystallographic Identification of CA2+ Coordination Sites in Synaptotagmin I C2B Domain, PDB code: 1tjx
was solved by
Y.Cheng,
S.M.Sequeira,
L.Malinina,
V.Tereshko,
T.H.Sollner,
D.J.Patel,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
19.50 /
1.04
|
Space group
|
P 32 2 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
54.550,
54.550,
103.590,
90.00,
90.00,
120.00
|
R / Rfree (%)
|
16.6 /
18.4
|
Calcium Binding Sites:
The binding sites of Calcium atom in the Crystallographic Identification of CA2+ Coordination Sites in Synaptotagmin I C2B Domain
(pdb code 1tjx). This binding sites where shown within
5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the
Crystallographic Identification of CA2+ Coordination Sites in Synaptotagmin I C2B Domain, PDB code: 1tjx:
Jump to Calcium binding site number:
1;
2;
Calcium binding site 1 out
of 2 in 1tjx
Go back to
Calcium Binding Sites List in 1tjx
Calcium binding site 1 out
of 2 in the Crystallographic Identification of CA2+ Coordination Sites in Synaptotagmin I C2B Domain
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 1 of Crystallographic Identification of CA2+ Coordination Sites in Synaptotagmin I C2B Domain within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca1419
b:20.0
occ:1.00
|
H1
|
A:HOH36
|
1.4
|
27.8
|
0.0
|
H2
|
A:HOH37
|
1.9
|
27.8
|
0.0
|
H1
|
A:HOH107
|
2.2
|
20.2
|
0.0
|
O
|
A:HOH36
|
2.3
|
28.3
|
1.0
|
O
|
A:HOH107
|
2.4
|
19.9
|
1.0
|
OD1
|
A:ASP363
|
2.4
|
16.2
|
1.0
|
OD1
|
A:ASP303
|
2.4
|
20.5
|
1.0
|
O
|
A:HOH37
|
2.5
|
28.4
|
1.0
|
O
|
A:MET302
|
2.5
|
19.2
|
1.0
|
H1
|
A:HOH37
|
2.6
|
27.8
|
0.0
|
OD2
|
A:ASP365
|
2.6
|
21.5
|
1.0
|
H2
|
A:HOH36
|
2.7
|
27.8
|
0.0
|
OD1
|
A:ASP365
|
2.7
|
19.4
|
1.0
|
CG
|
A:ASP365
|
3.1
|
18.1
|
1.0
|
H2
|
A:HOH107
|
3.3
|
20.2
|
0.0
|
C
|
A:MET302
|
3.5
|
18.2
|
1.0
|
HA
|
A:ASP303
|
3.5
|
20.0
|
1.0
|
HB3
|
A:MET302
|
3.6
|
16.7
|
1.0
|
CG
|
A:ASP363
|
3.6
|
13.1
|
1.0
|
CG
|
A:ASP303
|
3.7
|
20.8
|
1.0
|
CA
|
A:CA1420
|
3.7
|
20.0
|
1.0
|
O
|
A:HOH121
|
3.8
|
17.1
|
1.0
|
H1
|
A:HOH121
|
3.9
|
17.3
|
0.0
|
CA
|
A:ASP303
|
4.2
|
19.8
|
1.0
|
HB2
|
A:MET302
|
4.2
|
16.7
|
1.0
|
H2
|
A:HOH109
|
4.2
|
23.4
|
0.0
|
N
|
A:ASP303
|
4.2
|
18.6
|
1.0
|
CB
|
A:MET302
|
4.2
|
16.4
|
1.0
|
HB3
|
A:ASP363
|
4.3
|
11.3
|
1.0
|
OD2
|
A:ASP363
|
4.3
|
16.1
|
1.0
|
OD2
|
A:ASP303
|
4.5
|
22.6
|
1.0
|
CB
|
A:ASP303
|
4.5
|
20.3
|
1.0
|
CA
|
A:MET302
|
4.5
|
16.8
|
1.0
|
CB
|
A:ASP363
|
4.6
|
12.2
|
1.0
|
CB
|
A:ASP365
|
4.6
|
15.4
|
1.0
|
H2
|
A:HOH121
|
4.7
|
17.3
|
0.0
|
O
|
A:HOH109
|
4.7
|
23.1
|
1.0
|
OD2
|
A:ASP371
|
4.8
|
27.6
|
1.0
|
HA
|
A:MET302
|
4.9
|
17.0
|
1.0
|
HB3
|
A:ASP303
|
4.9
|
20.1
|
1.0
|
HE3
|
A:MET302
|
4.9
|
13.3
|
0.5
|
HB2
|
A:ASP363
|
5.0
|
11.3
|
1.0
|
HB3
|
A:ASP365
|
5.0
|
15.0
|
1.0
|
HB2
|
A:ASP365
|
5.0
|
15.0
|
1.0
|
|
Calcium binding site 2 out
of 2 in 1tjx
Go back to
Calcium Binding Sites List in 1tjx
Calcium binding site 2 out
of 2 in the Crystallographic Identification of CA2+ Coordination Sites in Synaptotagmin I C2B Domain
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 2 of Crystallographic Identification of CA2+ Coordination Sites in Synaptotagmin I C2B Domain within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca1420
b:20.0
occ:1.00
|
H2
|
A:HOH109
|
1.8
|
23.4
|
0.0
|
O
|
A:TYR364
|
2.4
|
12.4
|
1.0
|
O
|
A:HOH109
|
2.4
|
23.1
|
1.0
|
OD2
|
A:ASP363
|
2.5
|
16.1
|
1.0
|
OD1
|
A:ASP365
|
2.5
|
19.4
|
1.0
|
OD1
|
A:ASP309
|
2.5
|
18.7
|
1.0
|
OD1
|
A:ASP303
|
2.5
|
20.5
|
1.0
|
OD2
|
A:ASP303
|
2.6
|
22.6
|
1.0
|
OD1
|
A:ASP363
|
2.7
|
16.2
|
1.0
|
H1
|
A:HOH109
|
2.7
|
23.4
|
0.0
|
CG
|
A:ASP363
|
2.9
|
13.1
|
1.0
|
CG
|
A:ASP303
|
2.9
|
20.8
|
1.0
|
HB2
|
A:ASP309
|
3.3
|
13.4
|
1.0
|
C
|
A:TYR364
|
3.5
|
12.0
|
1.0
|
CG
|
A:ASP309
|
3.5
|
15.3
|
1.0
|
CG
|
A:ASP365
|
3.6
|
18.1
|
1.0
|
HA
|
A:ASP365
|
3.7
|
13.9
|
1.0
|
H
|
A:ASP309
|
3.7
|
13.8
|
1.0
|
CA
|
A:CA1419
|
3.7
|
20.0
|
1.0
|
H1
|
A:HOH37
|
3.8
|
27.8
|
0.0
|
CB
|
A:ASP309
|
3.9
|
14.0
|
1.0
|
H2
|
A:HOH38
|
3.9
|
39.5
|
0.0
|
N
|
A:ASP309
|
4.2
|
14.3
|
1.0
|
N
|
A:ASP365
|
4.2
|
12.9
|
1.0
|
HA
|
A:SER308
|
4.3
|
14.8
|
1.0
|
CA
|
A:ASP365
|
4.3
|
14.4
|
1.0
|
OD2
|
A:ASP365
|
4.4
|
21.5
|
1.0
|
CB
|
A:ASP363
|
4.4
|
12.2
|
1.0
|
N
|
A:TYR364
|
4.4
|
10.5
|
1.0
|
H1
|
A:HOH107
|
4.4
|
20.2
|
0.0
|
CB
|
A:ASP303
|
4.5
|
20.3
|
1.0
|
H2
|
A:HOH110
|
4.5
|
27.8
|
0.0
|
O
|
A:HOH38
|
4.5
|
39.4
|
1.0
|
CB
|
A:ASP365
|
4.6
|
15.4
|
1.0
|
C
|
A:ASP363
|
4.6
|
10.3
|
1.0
|
H
|
A:TYR364
|
4.6
|
10.5
|
1.0
|
CA
|
A:TYR364
|
4.6
|
11.0
|
1.0
|
O
|
A:HOH37
|
4.6
|
28.4
|
1.0
|
H2
|
A:HOH37
|
4.6
|
27.8
|
0.0
|
HB3
|
A:ASP309
|
4.6
|
13.4
|
1.0
|
OD2
|
A:ASP309
|
4.7
|
17.4
|
1.0
|
CA
|
A:ASP309
|
4.7
|
12.7
|
1.0
|
H1
|
A:HOH121
|
4.7
|
17.3
|
0.0
|
O
|
A:HOH110
|
4.7
|
26.9
|
1.0
|
HB3
|
A:ASP303
|
4.7
|
20.1
|
1.0
|
HB3
|
A:ASP363
|
4.8
|
11.3
|
1.0
|
HB2
|
A:ASP363
|
4.9
|
11.3
|
1.0
|
C
|
A:SER308
|
4.9
|
13.8
|
1.0
|
HB2
|
A:ASP303
|
4.9
|
20.1
|
1.0
|
O
|
A:ASP363
|
4.9
|
11.4
|
1.0
|
HB2
|
A:MET302
|
4.9
|
16.7
|
1.0
|
HA
|
A:ASP363
|
4.9
|
10.6
|
1.0
|
HB3
|
A:TYR364
|
4.9
|
11.2
|
1.0
|
HD2
|
A:TYR364
|
4.9
|
15.2
|
1.0
|
CA
|
A:ASP363
|
4.9
|
10.5
|
1.0
|
H1
|
A:HOH36
|
5.0
|
27.8
|
0.0
|
|
Reference:
Y.Cheng,
S.M.Sequeira,
L.Malinina,
V.Tereshko,
T.H.Sollner,
D.J.Patel.
Crystallographic Identification of CA2+ and SR2+ Coordination Sites in Synaptotagmin I C2B Domain. Protein Sci. V. 13 2665 2004.
ISSN: ISSN 0961-8368
PubMed: 15340165
DOI: 10.1110/PS.04832604
Page generated: Thu Jul 11 23:03:38 2024
|