Calcium in PDB 5m7g: Tubulin-MTD147 Complex
Protein crystallography data
The structure of Tubulin-MTD147 Complex, PDB code: 5m7g
was solved by
T.Bohnacker,
A.E.Prota,
M.O.Steinmetz,
M.P.Wymann,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
46.72 /
2.25
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
104.083,
156.864,
179.684,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
17.2 /
21.7
|
Other elements in 5m7g:
The structure of Tubulin-MTD147 Complex also contains other interesting chemical elements:
Calcium Binding Sites:
The binding sites of Calcium atom in the Tubulin-MTD147 Complex
(pdb code 5m7g). This binding sites where shown within
5.0 Angstroms radius around Calcium atom.
In total 5 binding sites of Calcium where determined in the
Tubulin-MTD147 Complex, PDB code: 5m7g:
Jump to Calcium binding site number:
1;
2;
3;
4;
5;
Calcium binding site 1 out
of 5 in 5m7g
Go back to
Calcium Binding Sites List in 5m7g
Calcium binding site 1 out
of 5 in the Tubulin-MTD147 Complex
 Mono view
 Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 1 of Tubulin-MTD147 Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca503
b:81.3
occ:1.00
|
O
|
A:GLY44
|
2.4
|
0.7
|
1.0
|
O
|
A:HOH622
|
2.4
|
68.2
|
1.0
|
OD2
|
A:ASP39
|
2.4
|
78.2
|
1.0
|
OE1
|
A:GLU55
|
2.5
|
85.2
|
1.0
|
OD1
|
A:ASP39
|
2.5
|
83.2
|
1.0
|
O
|
A:THR41
|
2.6
|
90.1
|
1.0
|
OG1
|
A:THR41
|
2.7
|
77.4
|
1.0
|
OE2
|
A:GLU55
|
2.8
|
73.8
|
1.0
|
CG
|
A:ASP39
|
2.8
|
80.2
|
1.0
|
CD
|
A:GLU55
|
2.9
|
81.4
|
1.0
|
C
|
A:GLY44
|
3.3
|
95.3
|
1.0
|
CB
|
A:THR41
|
3.6
|
84.0
|
1.0
|
C
|
A:THR41
|
3.6
|
94.0
|
1.0
|
CA
|
A:THR41
|
4.0
|
90.7
|
1.0
|
N
|
A:GLY45
|
4.1
|
87.9
|
1.0
|
CA
|
A:GLY45
|
4.1
|
87.0
|
1.0
|
N
|
A:GLY44
|
4.3
|
93.0
|
1.0
|
CA
|
A:GLY44
|
4.3
|
93.8
|
1.0
|
CB
|
A:ASP39
|
4.3
|
71.7
|
1.0
|
N
|
A:THR41
|
4.4
|
89.7
|
1.0
|
CG
|
A:GLU55
|
4.4
|
82.3
|
1.0
|
OD1
|
A:ASN50
|
4.4
|
76.8
|
1.0
|
CZ
|
A:PHE49
|
4.5
|
67.9
|
1.0
|
O
|
A:HOH675
|
4.6
|
80.7
|
1.0
|
N
|
A:ILE42
|
4.7
|
94.9
|
1.0
|
OD2
|
A:ASP47
|
4.8
|
79.2
|
1.0
|
NE2
|
A:HIS61
|
4.9
|
83.7
|
1.0
|
CG2
|
A:THR41
|
4.9
|
83.8
|
1.0
|
ND2
|
A:ASN50
|
4.9
|
76.7
|
1.0
|
|
Calcium binding site 2 out
of 5 in 5m7g
Go back to
Calcium Binding Sites List in 5m7g
Calcium binding site 2 out
of 5 in the Tubulin-MTD147 Complex
 Mono view
 Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 2 of Tubulin-MTD147 Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca504
b:0.3
occ:1.00
|
O
|
A:HOH643
|
2.7
|
77.2
|
1.0
|
O
|
A:HOH662
|
2.9
|
73.8
|
1.0
|
O
|
A:HOH651
|
3.1
|
69.7
|
1.0
|
OD2
|
E:ASP44
|
3.6
|
0.5
|
1.0
|
O
|
A:HOH672
|
4.0
|
67.3
|
1.0
|
OG
|
A:SER158
|
4.1
|
61.2
|
1.0
|
O
|
A:GLU196
|
4.3
|
62.1
|
1.0
|
NZ
|
A:LYS166
|
4.4
|
50.4
|
1.0
|
O
|
A:GLY162
|
4.5
|
77.2
|
1.0
|
O
|
A:HOH607
|
4.6
|
65.3
|
1.0
|
CB
|
A:SER158
|
4.7
|
56.5
|
1.0
|
CG
|
E:ASP44
|
4.7
|
0.8
|
1.0
|
CA
|
A:HIS197
|
4.8
|
50.8
|
1.0
|
OD1
|
A:ASP199
|
4.9
|
66.6
|
1.0
|
O
|
A:HIS197
|
4.9
|
58.1
|
1.0
|
|
Calcium binding site 3 out
of 5 in 5m7g
Go back to
Calcium Binding Sites List in 5m7g
Calcium binding site 3 out
of 5 in the Tubulin-MTD147 Complex
 Mono view
 Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 3 of Tubulin-MTD147 Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca504
b:83.6
occ:1.00
|
O
|
B:HOH652
|
2.4
|
76.3
|
1.0
|
OE2
|
B:GLU113
|
2.6
|
84.0
|
1.0
|
CD
|
B:GLU113
|
3.4
|
82.2
|
1.0
|
OE1
|
B:GLU113
|
3.4
|
87.1
|
1.0
|
OE1
|
B:GLU110
|
4.6
|
52.4
|
1.0
|
CG
|
B:GLU113
|
4.9
|
62.7
|
1.0
|
|
Calcium binding site 4 out
of 5 in 5m7g
Go back to
Calcium Binding Sites List in 5m7g
Calcium binding site 4 out
of 5 in the Tubulin-MTD147 Complex
 Mono view
 Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 4 of Tubulin-MTD147 Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Ca503
b:68.0
occ:1.00
|
O
|
C:HOH605
|
2.4
|
59.2
|
1.0
|
O
|
C:GLY44
|
2.4
|
71.1
|
1.0
|
O
|
C:THR41
|
2.5
|
74.2
|
1.0
|
OE1
|
C:GLU55
|
2.5
|
61.7
|
1.0
|
OE2
|
C:GLU55
|
2.5
|
63.2
|
1.0
|
OD2
|
C:ASP39
|
2.5
|
69.5
|
1.0
|
OD1
|
C:ASP39
|
2.6
|
68.5
|
1.0
|
OG1
|
C:THR41
|
2.6
|
73.0
|
1.0
|
CD
|
C:GLU55
|
2.8
|
62.4
|
1.0
|
CG
|
C:ASP39
|
2.9
|
70.4
|
1.0
|
C
|
C:THR41
|
3.4
|
77.2
|
1.0
|
C
|
C:GLY44
|
3.4
|
73.6
|
1.0
|
CB
|
C:THR41
|
3.5
|
67.4
|
1.0
|
CA
|
C:THR41
|
3.9
|
73.3
|
1.0
|
OD2
|
C:ASP47
|
4.2
|
75.6
|
1.0
|
N
|
C:THR41
|
4.2
|
75.7
|
1.0
|
N
|
C:GLY45
|
4.3
|
75.9
|
1.0
|
CG
|
C:GLU55
|
4.3
|
59.5
|
1.0
|
CA
|
C:GLY45
|
4.3
|
77.3
|
1.0
|
O
|
C:HOH613
|
4.3
|
59.7
|
1.0
|
CA
|
C:GLY44
|
4.4
|
76.1
|
1.0
|
N
|
C:GLY44
|
4.4
|
75.5
|
1.0
|
CB
|
C:ASP39
|
4.4
|
70.6
|
1.0
|
OD1
|
C:ASN50
|
4.4
|
50.4
|
1.0
|
CZ
|
C:PHE49
|
4.5
|
63.4
|
1.0
|
N
|
C:ILE42
|
4.6
|
77.9
|
1.0
|
NE2
|
C:HIS61
|
4.7
|
47.3
|
1.0
|
CE1
|
C:PHE49
|
4.8
|
59.3
|
1.0
|
CG2
|
C:THR41
|
4.9
|
53.0
|
1.0
|
ND2
|
C:ASN50
|
4.9
|
44.9
|
1.0
|
|
Calcium binding site 5 out
of 5 in 5m7g
Go back to
Calcium Binding Sites List in 5m7g
Calcium binding site 5 out
of 5 in the Tubulin-MTD147 Complex
 Mono view
 Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 5 of Tubulin-MTD147 Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Ca504
b:0.3
occ:1.00
|
O
|
C:HOH767
|
2.4
|
96.0
|
1.0
|
O
|
C:HOH763
|
2.8
|
81.2
|
1.0
|
OE2
|
C:GLU220
|
4.2
|
0.9
|
1.0
|
CG
|
C:GLU220
|
4.6
|
92.5
|
1.0
|
CD
|
C:GLU220
|
4.8
|
0.8
|
1.0
|
O
|
C:ASP218
|
4.8
|
67.8
|
1.0
|
|
Reference:
T.Bohnacker,
A.E.Prota,
F.Beaufils,
J.E.Burke,
A.Melone,
A.J.Inglis,
D.Rageot,
A.M.Sele,
V.Cmiljanovic,
N.Cmiljanovic,
K.Bargsten,
A.Aher,
A.Akhmanova,
J.F.Diaz,
D.Fabbro,
M.Zvelebil,
R.L.Williams,
M.O.Steinmetz,
M.P.Wymann.
Deconvolution of Buparlisib'S Mechanism of Action Defines Specific PI3K and Tubulin Inhibitors For Therapeutic Intervention. Nat Commun V. 8 14683 2017.
ISSN: ESSN 2041-1723
PubMed: 28276440
DOI: 10.1038/NCOMMS14683
Page generated: Mon Jul 15 07:57:33 2024
|