Calcium in PDB 1px2: Crystal Structure of Rat Synapsin I C Domain Complexed to Ca.Atp (Form 1)
Protein crystallography data
The structure of Crystal Structure of Rat Synapsin I C Domain Complexed to Ca.Atp (Form 1), PDB code: 1px2
was solved by
C.A.Brautigam,
Y.Chelliah,
J.Deisenhofer,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
20.00 /
2.23
|
Space group
|
P 65 2 2
|
Cell size a, b, c (Å), α, β, γ (°)
|
96.000,
96.000,
305.800,
90.00,
90.00,
120.00
|
R / Rfree (%)
|
20.3 /
24
|
Calcium Binding Sites:
The binding sites of Calcium atom in the Crystal Structure of Rat Synapsin I C Domain Complexed to Ca.Atp (Form 1)
(pdb code 1px2). This binding sites where shown within
5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the
Crystal Structure of Rat Synapsin I C Domain Complexed to Ca.Atp (Form 1), PDB code: 1px2:
Jump to Calcium binding site number:
1;
2;
Calcium binding site 1 out
of 2 in 1px2
Go back to
Calcium Binding Sites List in 1px2
Calcium binding site 1 out
of 2 in the Crystal Structure of Rat Synapsin I C Domain Complexed to Ca.Atp (Form 1)
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 Rat Synapsin I C Domain Complexed to Ca.Atp (Form 1) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca817
b:72.8
occ:1.00
|
OE2
|
A:GLU386
|
2.4
|
48.9
|
1.0
|
O3G
|
A:ATP800
|
2.4
|
52.8
|
0.4
|
O2A
|
A:ATP800
|
2.4
|
37.2
|
0.6
|
O2A
|
A:ATP800
|
2.5
|
48.8
|
0.4
|
O1G
|
A:ATP800
|
2.6
|
52.3
|
0.4
|
O1G
|
A:ATP800
|
2.6
|
33.2
|
0.6
|
PG
|
A:ATP800
|
2.7
|
53.1
|
0.4
|
O3B
|
A:ATP800
|
2.9
|
51.7
|
0.4
|
O
|
A:HOH832
|
3.2
|
45.5
|
1.0
|
O2B
|
A:ATP800
|
3.3
|
34.9
|
0.6
|
CD
|
A:GLU386
|
3.3
|
47.5
|
1.0
|
OE1
|
A:GLU386
|
3.4
|
48.9
|
1.0
|
O1B
|
A:ATP800
|
3.5
|
51.1
|
0.4
|
OE2
|
A:GLU373
|
3.6
|
62.9
|
1.0
|
PB
|
A:ATP800
|
3.8
|
50.4
|
0.4
|
PA
|
A:ATP800
|
3.8
|
36.1
|
0.6
|
PG
|
A:ATP800
|
3.8
|
31.7
|
0.6
|
PA
|
A:ATP800
|
3.8
|
48.2
|
0.4
|
O3B
|
A:ATP800
|
3.8
|
33.5
|
0.6
|
PB
|
A:ATP800
|
4.0
|
34.4
|
0.6
|
CD
|
A:GLU373
|
4.1
|
58.5
|
1.0
|
O3A
|
A:ATP800
|
4.1
|
49.9
|
0.4
|
O2G
|
A:ATP800
|
4.1
|
52.8
|
0.4
|
O3A
|
A:ATP800
|
4.1
|
35.3
|
0.6
|
O
|
A:HOH866
|
4.4
|
37.9
|
1.0
|
OE1
|
A:GLU373
|
4.5
|
62.6
|
1.0
|
O3G
|
A:ATP800
|
4.6
|
25.8
|
0.6
|
CG
|
A:GLU386
|
4.7
|
44.6
|
1.0
|
C5'
|
A:ATP800
|
4.7
|
38.8
|
0.6
|
C5'
|
A:ATP800
|
4.7
|
45.8
|
0.4
|
O3'
|
A:ATP800
|
4.7
|
40.9
|
0.6
|
CG
|
A:GLU373
|
4.7
|
54.2
|
1.0
|
O5'
|
A:ATP800
|
4.8
|
47.8
|
0.4
|
O5'
|
A:ATP800
|
4.8
|
38.5
|
0.6
|
O1A
|
A:ATP800
|
4.8
|
34.9
|
0.6
|
O1A
|
A:ATP800
|
4.9
|
47.7
|
0.4
|
CG1
|
A:VAL388
|
4.9
|
38.6
|
1.0
|
|
Calcium binding site 2 out
of 2 in 1px2
Go back to
Calcium Binding Sites List in 1px2
Calcium binding site 2 out
of 2 in the Crystal Structure of Rat Synapsin I C Domain Complexed to Ca.Atp (Form 1)
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 Rat Synapsin I C Domain Complexed to Ca.Atp (Form 1) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca817
b:48.4
occ:1.00
|
OE2
|
B:GLU373
|
2.2
|
40.5
|
0.5
|
O3G
|
B:ATP800
|
2.3
|
48.4
|
0.5
|
O2A
|
B:ATP800
|
2.4
|
45.1
|
0.5
|
O2A
|
B:ATP800
|
2.5
|
30.4
|
0.6
|
O2B
|
B:ATP800
|
2.6
|
28.6
|
0.6
|
OE2
|
B:GLU386
|
2.7
|
32.8
|
1.0
|
PG
|
B:ATP800
|
2.9
|
48.4
|
0.5
|
O3G
|
B:ATP800
|
2.9
|
23.2
|
0.6
|
O
|
B:HOH883
|
3.0
|
54.0
|
1.0
|
O3B
|
B:ATP800
|
3.0
|
47.5
|
0.5
|
CD
|
B:GLU373
|
3.0
|
39.0
|
0.5
|
O1B
|
B:ATP800
|
3.1
|
46.8
|
0.5
|
O1G
|
B:ATP800
|
3.1
|
48.3
|
0.5
|
OE1
|
B:GLU373
|
3.1
|
39.2
|
0.5
|
O
|
B:HOH916
|
3.3
|
53.8
|
1.0
|
O3B
|
B:ATP800
|
3.3
|
26.7
|
0.6
|
PB
|
B:ATP800
|
3.4
|
26.8
|
0.6
|
PB
|
B:ATP800
|
3.5
|
46.2
|
0.5
|
PA
|
B:ATP800
|
3.7
|
28.5
|
0.6
|
PA
|
B:ATP800
|
3.7
|
44.4
|
0.5
|
CD
|
B:GLU386
|
3.7
|
35.2
|
1.0
|
PG
|
B:ATP800
|
3.7
|
26.6
|
0.6
|
O3A
|
B:ATP800
|
3.8
|
28.1
|
0.6
|
O3A
|
B:ATP800
|
3.9
|
45.0
|
0.5
|
OE1
|
B:GLU386
|
4.1
|
37.2
|
1.0
|
O2G
|
B:ATP800
|
4.1
|
22.8
|
0.6
|
O2G
|
B:ATP800
|
4.2
|
47.8
|
0.5
|
O
|
B:HOH881
|
4.4
|
44.3
|
1.0
|
CG
|
B:GLU373
|
4.5
|
38.1
|
0.5
|
O1A
|
B:ATP800
|
4.6
|
28.0
|
0.6
|
CD
|
B:GLU373
|
4.6
|
49.9
|
0.5
|
OE1
|
B:GLU373
|
4.7
|
51.6
|
0.5
|
O5'
|
B:ATP800
|
4.7
|
43.8
|
0.5
|
C5'
|
B:ATP800
|
4.7
|
43.0
|
0.5
|
O1A
|
B:ATP800
|
4.7
|
44.0
|
0.5
|
CG
|
B:GLU373
|
4.8
|
47.5
|
0.5
|
O3'
|
B:ATP800
|
4.8
|
32.3
|
0.6
|
O5'
|
B:ATP800
|
4.8
|
29.6
|
0.6
|
O1B
|
B:ATP800
|
4.9
|
27.4
|
0.6
|
OE2
|
B:GLU373
|
4.9
|
51.3
|
0.5
|
C5'
|
B:ATP800
|
4.9
|
30.5
|
0.6
|
CG1
|
B:VAL388
|
5.0
|
30.6
|
1.0
|
O2B
|
B:ATP800
|
5.0
|
45.7
|
0.5
|
|
Reference:
C.A.Brautigam,
Y.Chelliah,
J.Deisenhofer.
Tetramerization and Atp Binding By A Protein Comprising the A, B, and C Domains of Rat Synapsin I. J.Biol.Chem. V. 279 11948 2004.
ISSN: ISSN 0021-9258
PubMed: 14688264
DOI: 10.1074/JBC.M312015200
Page generated: Thu Jul 11 13:55:09 2024
|