Calcium in PDB 7dae: Epb in Complex with Tubulin
Protein crystallography data
The structure of Epb in Complex with Tubulin, PDB code: 7dae
was solved by
C.Wu,
Y.Wang,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
49.71 /
2.39
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
104.792,
157.21,
181.53,
90,
90,
90
|
R / Rfree (%)
|
17.4 /
22.2
|
Other elements in 7dae:
The structure of Epb in Complex with Tubulin also contains other interesting chemical elements:
Calcium Binding Sites:
The binding sites of Calcium atom in the Epb in Complex with Tubulin
(pdb code 7dae). This binding sites where shown within
5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the
Epb in Complex with Tubulin, PDB code: 7dae:
Jump to Calcium binding site number:
1;
2;
3;
4;
Calcium binding site 1 out
of 4 in 7dae
Go back to
Calcium Binding Sites List in 7dae
Calcium binding site 1 out
of 4 in the Epb in Complex with Tubulin
 Mono view
 Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 1 of Epb in Complex with Tubulin within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca503
b:47.6
occ:1.00
|
O
|
A:THR41
|
2.3
|
55.5
|
1.0
|
OD2
|
A:ASP39
|
2.3
|
48.6
|
1.0
|
OD1
|
A:ASP39
|
2.4
|
46.0
|
1.0
|
O
|
A:GLY44
|
2.4
|
44.5
|
1.0
|
O
|
A:HOH617
|
2.6
|
47.0
|
1.0
|
OE1
|
A:GLU55
|
2.6
|
42.9
|
1.0
|
OE2
|
A:GLU55
|
2.6
|
43.4
|
1.0
|
OG1
|
A:THR41
|
2.7
|
50.9
|
1.0
|
CG
|
A:ASP39
|
2.7
|
47.9
|
1.0
|
CD
|
A:GLU55
|
2.9
|
54.4
|
1.0
|
C
|
A:THR41
|
3.3
|
53.3
|
1.0
|
CB
|
A:THR41
|
3.6
|
49.4
|
1.0
|
C
|
A:GLY44
|
3.6
|
54.1
|
1.0
|
CA
|
A:THR41
|
3.9
|
52.9
|
1.0
|
N
|
A:THR41
|
4.1
|
56.2
|
1.0
|
CB
|
A:ASP39
|
4.2
|
41.4
|
1.0
|
O
|
A:HOH616
|
4.3
|
40.9
|
1.0
|
CA
|
A:GLY45
|
4.4
|
58.8
|
1.0
|
N
|
A:GLY45
|
4.4
|
49.2
|
1.0
|
CZ
|
A:PHE49
|
4.4
|
40.7
|
1.0
|
N
|
A:GLY44
|
4.4
|
51.0
|
1.0
|
CG
|
A:GLU55
|
4.5
|
49.0
|
1.0
|
OD2
|
A:ASP47
|
4.5
|
59.3
|
1.0
|
N
|
A:ILE42
|
4.5
|
51.8
|
1.0
|
NE2
|
A:HIS61
|
4.6
|
56.6
|
1.0
|
CA
|
A:GLY44
|
4.6
|
58.2
|
1.0
|
OD1
|
A:ASN50
|
4.8
|
49.7
|
1.0
|
ND2
|
A:ASN50
|
4.8
|
49.5
|
1.0
|
CA
|
A:ILE42
|
4.9
|
53.5
|
1.0
|
CE1
|
A:PHE49
|
4.9
|
47.6
|
1.0
|
CG2
|
A:THR41
|
5.0
|
44.7
|
1.0
|
|
Calcium binding site 2 out
of 4 in 7dae
Go back to
Calcium Binding Sites List in 7dae
Calcium binding site 2 out
of 4 in the Epb in Complex with Tubulin
 Mono view
 Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 2 of Epb in Complex with Tubulin within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca503
b:83.7
occ:1.00
|
O
|
B:HOH637
|
2.4
|
48.8
|
1.0
|
O
|
B:HOH602
|
2.7
|
60.6
|
1.0
|
OE2
|
B:GLU111
|
2.7
|
66.3
|
1.0
|
OE1
|
B:GLU111
|
3.0
|
70.1
|
1.0
|
CD
|
B:GLU111
|
3.2
|
62.4
|
1.0
|
CG
|
B:GLU111
|
4.7
|
37.0
|
1.0
|
|
Calcium binding site 3 out
of 4 in 7dae
Go back to
Calcium Binding Sites List in 7dae
Calcium binding site 3 out
of 4 in the Epb in Complex with Tubulin
 Mono view
 Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 3 of Epb in Complex with Tubulin within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Ca503
b:39.5
occ:1.00
|
O
|
C:THR41
|
2.4
|
43.3
|
1.0
|
OE1
|
C:GLU55
|
2.4
|
33.9
|
1.0
|
OD2
|
C:ASP39
|
2.5
|
42.2
|
1.0
|
OD1
|
C:ASP39
|
2.5
|
40.6
|
1.0
|
O
|
C:HOH602
|
2.5
|
34.9
|
1.0
|
O
|
C:GLY44
|
2.5
|
43.2
|
1.0
|
OG1
|
C:THR41
|
2.6
|
39.3
|
1.0
|
OE2
|
C:GLU55
|
2.6
|
40.2
|
1.0
|
CG
|
C:ASP39
|
2.8
|
41.1
|
1.0
|
CD
|
C:GLU55
|
2.9
|
38.4
|
1.0
|
C
|
C:THR41
|
3.4
|
37.6
|
1.0
|
C
|
C:GLY44
|
3.6
|
46.6
|
1.0
|
CB
|
C:THR41
|
3.6
|
45.9
|
1.0
|
CA
|
C:THR41
|
3.9
|
38.7
|
1.0
|
N
|
C:THR41
|
4.1
|
37.5
|
1.0
|
CA
|
C:GLY45
|
4.2
|
43.2
|
1.0
|
N
|
C:GLY45
|
4.3
|
46.0
|
1.0
|
OD2
|
C:ASP47
|
4.3
|
52.3
|
1.0
|
CB
|
C:ASP39
|
4.3
|
38.7
|
1.0
|
O
|
C:HOH624
|
4.4
|
32.1
|
1.0
|
CG
|
C:GLU55
|
4.4
|
32.2
|
1.0
|
N
|
C:GLY44
|
4.5
|
38.2
|
1.0
|
CA
|
C:GLY44
|
4.6
|
39.6
|
1.0
|
N
|
C:ILE42
|
4.6
|
39.0
|
1.0
|
OD1
|
C:ASN50
|
4.7
|
34.1
|
1.0
|
CZ
|
C:PHE49
|
4.7
|
34.1
|
1.0
|
NE2
|
C:HIS61
|
4.7
|
42.1
|
1.0
|
O
|
C:HOH744
|
4.9
|
40.6
|
1.0
|
CE1
|
C:PHE49
|
4.9
|
36.4
|
1.0
|
CG2
|
C:THR41
|
4.9
|
34.5
|
1.0
|
|
Calcium binding site 4 out
of 4 in 7dae
Go back to
Calcium Binding Sites List in 7dae
Calcium binding site 4 out
of 4 in the Epb in Complex with Tubulin
 Mono view
 Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 4 of Epb in Complex with Tubulin within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Ca201
b:77.8
occ:1.00
|
O
|
A:HOH694
|
2.9
|
54.4
|
1.0
|
O
|
A:HOH719
|
3.0
|
44.0
|
1.0
|
OD2
|
E:ASP44
|
3.4
|
59.8
|
1.0
|
O
|
A:HOH624
|
3.6
|
53.5
|
1.0
|
OG
|
A:SER158
|
4.1
|
37.2
|
1.0
|
O
|
A:GLU196
|
4.4
|
37.8
|
1.0
|
O
|
A:GLY162
|
4.5
|
50.0
|
1.0
|
CG
|
E:ASP44
|
4.5
|
58.6
|
1.0
|
OD1
|
A:ASP199
|
4.7
|
36.2
|
1.0
|
OD1
|
E:ASP44
|
4.8
|
61.9
|
1.0
|
CB
|
A:SER158
|
4.8
|
25.9
|
1.0
|
O
|
A:HIS197
|
4.9
|
31.6
|
1.0
|
O
|
A:HOH728
|
5.0
|
56.5
|
1.0
|
CA
|
A:HIS197
|
5.0
|
34.2
|
1.0
|
|
Reference:
Q.Xiao,
T.Xue,
W.Shuai,
C.Wu,
Z.Zhang,
T.Zhang,
S.Zeng,
B.Sun,
Y.Wang.
High-Resolution X-Ray Structure of Three Microtubule-Stabilizing Agents in Complex with Tubulin Provide A Rationale For Drug Design. Biochem.Biophys.Res.Commun. V. 534 330 2021.
ISSN: ESSN 1090-2104
PubMed: 33272565
DOI: 10.1016/J.BBRC.2020.11.082
Page generated: Thu Jul 18 23:59:48 2024
|