Magnesium 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:
Magnesium Binding Sites:
The binding sites of Magnesium atom in the Epb in Complex with Tubulin
(pdb code 7dae). This binding sites where shown within
5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the
Epb in Complex with Tubulin, PDB code: 7dae:
Jump to Magnesium binding site number:
1;
2;
3;
4;
Magnesium binding site 1 out
of 4 in 7dae
Go back to
Magnesium Binding Sites List in 7dae
Magnesium binding site 1 out
of 4 in the Epb in Complex with Tubulin
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 1 of Epb in Complex with Tubulin within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg502
b:26.9
occ:1.00
|
O
|
A:HOH692
|
2.1
|
25.1
|
1.0
|
O
|
A:HOH646
|
2.1
|
28.6
|
1.0
|
O1G
|
A:GTP501
|
2.1
|
25.9
|
1.0
|
O
|
A:HOH679
|
2.1
|
29.5
|
1.0
|
O
|
A:HOH619
|
2.1
|
25.3
|
1.0
|
O1B
|
A:GTP501
|
2.1
|
24.0
|
1.0
|
PG
|
A:GTP501
|
3.2
|
30.7
|
1.0
|
PB
|
A:GTP501
|
3.2
|
25.0
|
1.0
|
O3B
|
A:GTP501
|
3.6
|
35.0
|
1.0
|
O2G
|
A:GTP501
|
3.7
|
26.9
|
1.0
|
O3A
|
A:GTP501
|
3.8
|
32.8
|
1.0
|
NZ
|
B:LYS252
|
3.9
|
34.3
|
1.0
|
CB
|
A:GLN11
|
4.1
|
26.5
|
1.0
|
OE1
|
A:GLU71
|
4.2
|
45.1
|
1.0
|
OD1
|
A:ASP69
|
4.2
|
29.3
|
1.0
|
OD2
|
A:ASP69
|
4.3
|
28.2
|
1.0
|
CG
|
A:GLU71
|
4.3
|
47.2
|
1.0
|
OD2
|
A:ASP98
|
4.3
|
34.5
|
1.0
|
N
|
A:GLN11
|
4.4
|
25.1
|
1.0
|
O1A
|
A:GTP501
|
4.5
|
24.9
|
1.0
|
O3G
|
A:GTP501
|
4.5
|
27.3
|
1.0
|
O2B
|
A:GTP501
|
4.5
|
33.2
|
1.0
|
CB
|
A:ASP98
|
4.6
|
31.2
|
1.0
|
CG
|
A:ASP69
|
4.7
|
27.5
|
1.0
|
PA
|
A:GTP501
|
4.7
|
25.6
|
1.0
|
CD
|
A:GLU71
|
4.7
|
44.9
|
1.0
|
CG
|
A:ASP98
|
4.8
|
32.3
|
1.0
|
NE2
|
A:GLN11
|
4.8
|
29.1
|
1.0
|
CA
|
A:GLN11
|
4.8
|
26.8
|
1.0
|
|
Magnesium binding site 2 out
of 4 in 7dae
Go back to
Magnesium Binding Sites List in 7dae
Magnesium binding site 2 out
of 4 in the Epb in Complex with Tubulin
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 2 of Epb in Complex with Tubulin within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg502
b:27.4
occ:1.00
|
OE1
|
B:GLN11
|
2.2
|
42.3
|
1.0
|
O1A
|
B:GDP501
|
2.3
|
27.8
|
1.0
|
O
|
C:HOH737
|
2.3
|
35.4
|
1.0
|
O
|
B:HOH618
|
3.0
|
44.3
|
1.0
|
CD
|
B:GLN11
|
3.4
|
52.1
|
1.0
|
OD2
|
B:ASP177
|
3.4
|
55.6
|
1.0
|
PA
|
B:GDP501
|
3.4
|
25.4
|
1.0
|
O3A
|
B:GDP501
|
3.6
|
28.5
|
1.0
|
OD1
|
B:ASN99
|
4.1
|
32.4
|
1.0
|
O5'
|
B:GDP501
|
4.2
|
21.6
|
1.0
|
C5'
|
B:GDP501
|
4.2
|
25.1
|
1.0
|
CB
|
B:GLN11
|
4.3
|
19.6
|
1.0
|
CG
|
B:GLN11
|
4.3
|
33.3
|
1.0
|
NE2
|
B:GLN11
|
4.3
|
39.4
|
1.0
|
O
|
C:HOH705
|
4.5
|
43.0
|
1.0
|
CG
|
B:ASP177
|
4.5
|
36.7
|
1.0
|
O1B
|
B:GDP501
|
4.6
|
25.5
|
1.0
|
O2A
|
B:GDP501
|
4.6
|
26.8
|
1.0
|
OE1
|
C:GLU254
|
4.7
|
38.7
|
1.0
|
PB
|
B:GDP501
|
4.8
|
26.5
|
1.0
|
C8
|
B:GDP501
|
4.8
|
27.9
|
1.0
|
ND2
|
B:ASN99
|
4.9
|
22.4
|
1.0
|
CG
|
B:ASN99
|
4.9
|
29.4
|
1.0
|
|
Magnesium binding site 3 out
of 4 in 7dae
Go back to
Magnesium Binding Sites List in 7dae
Magnesium binding site 3 out
of 4 in the Epb in Complex with Tubulin
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 3 of Epb in Complex with Tubulin within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg506
b:63.6
occ:1.00
|
O
|
B:HOH704
|
2.4
|
62.6
|
1.0
|
O
|
B:HOH634
|
2.8
|
50.4
|
1.0
|
OD2
|
B:ASP118
|
3.9
|
47.1
|
1.0
|
OD1
|
B:ASP118
|
4.0
|
42.6
|
1.0
|
O
|
B:HOH658
|
4.0
|
43.4
|
1.0
|
CG
|
B:ASP118
|
4.4
|
43.8
|
1.0
|
CB
|
B:ASP114
|
4.6
|
36.4
|
1.0
|
OD2
|
B:ASP114
|
4.9
|
58.4
|
1.0
|
|
Magnesium binding site 4 out
of 4 in 7dae
Go back to
Magnesium Binding Sites List in 7dae
Magnesium binding site 4 out
of 4 in the Epb in Complex with Tubulin
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 4 of Epb in Complex with Tubulin within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mg502
b:25.2
occ:1.00
|
O
|
C:HOH688
|
2.1
|
27.6
|
1.0
|
O1B
|
C:GTP501
|
2.1
|
17.2
|
1.0
|
O
|
C:HOH627
|
2.1
|
26.6
|
1.0
|
O1G
|
C:GTP501
|
2.1
|
20.7
|
1.0
|
O
|
C:HOH654
|
2.3
|
23.9
|
1.0
|
PB
|
C:GTP501
|
3.3
|
22.3
|
1.0
|
PG
|
C:GTP501
|
3.3
|
27.1
|
1.0
|
O3B
|
C:GTP501
|
3.7
|
28.7
|
1.0
|
OD1
|
C:ASP69
|
3.8
|
27.2
|
1.0
|
O2G
|
C:GTP501
|
3.8
|
24.8
|
1.0
|
OE1
|
C:GLU71
|
3.8
|
49.0
|
1.0
|
O3A
|
C:GTP501
|
3.8
|
24.8
|
1.0
|
OD2
|
C:ASP69
|
3.9
|
26.9
|
1.0
|
NZ
|
D:LYS252
|
4.1
|
25.3
|
1.0
|
CG
|
C:GLU71
|
4.1
|
27.9
|
1.0
|
CB
|
C:GLN11
|
4.2
|
17.0
|
1.0
|
CG
|
C:ASP69
|
4.3
|
28.0
|
1.0
|
N
|
C:GLN11
|
4.3
|
22.4
|
1.0
|
O
|
C:HOH608
|
4.4
|
55.2
|
1.0
|
OD2
|
C:ASP98
|
4.4
|
36.2
|
1.0
|
CD
|
C:GLU71
|
4.5
|
39.8
|
1.0
|
CB
|
C:ASP98
|
4.5
|
27.9
|
1.0
|
O2B
|
C:GTP501
|
4.6
|
22.9
|
1.0
|
O3G
|
C:GTP501
|
4.6
|
21.4
|
1.0
|
O1A
|
C:GTP501
|
4.7
|
27.6
|
1.0
|
O
|
C:HOH637
|
4.7
|
34.2
|
1.0
|
CA
|
C:GLN11
|
4.8
|
25.0
|
1.0
|
OE1
|
C:GLN11
|
4.8
|
37.8
|
1.0
|
CG
|
C:ASP98
|
4.9
|
32.4
|
1.0
|
PA
|
C:GTP501
|
4.9
|
25.6
|
1.0
|
OG1
|
C:THR145
|
5.0
|
25.7
|
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: Wed Oct 2 15:44:03 2024
|