Magnesium in PDB 8bde: Tubulin-Baccatin III Complex
Protein crystallography data
The structure of Tubulin-Baccatin III Complex, PDB code: 8bde
was solved by
A.E.Prota,
D.Lucena-Agell,
Y.Ma,
J.Estevez-Gallego,
S.Li,
K.Bargsten,
K.H.Altmann,
N.Gaillard,
S.Kamimura,
T.Muehlethaler,
F.Gago,
M.A.Oliva,
M.O.Steinmetz,
W.S.Fang,
J.F.Diaz,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
49.20 /
1.90
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
104.1,
157.15,
179.15,
90,
90,
90
|
R / Rfree (%)
|
19.2 /
21.8
|
Other elements in 8bde:
The structure of Tubulin-Baccatin III Complex also contains other interesting chemical elements:
Magnesium Binding Sites:
The binding sites of Magnesium atom in the Tubulin-Baccatin III Complex
(pdb code 8bde). This binding sites where shown within
5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the
Tubulin-Baccatin III Complex, PDB code: 8bde:
Jump to Magnesium binding site number:
1;
2;
3;
4;
5;
Magnesium binding site 1 out
of 5 in 8bde
Go back to
Magnesium Binding Sites List in 8bde
Magnesium binding site 1 out
of 5 in the Tubulin-Baccatin III Complex
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 1 of Tubulin-Baccatin III Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg502
b:36.0
occ:1.00
|
O
|
A:HOH664
|
2.0
|
34.8
|
1.0
|
O2G
|
A:GTP501
|
2.0
|
30.6
|
1.0
|
O
|
A:HOH708
|
2.1
|
37.2
|
1.0
|
O
|
A:HOH656
|
2.1
|
36.7
|
1.0
|
O1B
|
A:GTP501
|
2.1
|
30.0
|
1.0
|
O
|
A:HOH685
|
2.2
|
34.8
|
1.0
|
PG
|
A:GTP501
|
3.1
|
33.5
|
1.0
|
PB
|
A:GTP501
|
3.2
|
34.1
|
1.0
|
O3G
|
A:GTP501
|
3.6
|
36.1
|
1.0
|
O3B
|
A:GTP501
|
3.6
|
40.5
|
1.0
|
O3A
|
A:GTP501
|
3.7
|
35.2
|
1.0
|
NZ
|
B:LYS254
|
3.7
|
36.2
|
1.0
|
OE2
|
A:GLU71
|
4.0
|
65.5
|
1.0
|
OD1
|
A:ASP69
|
4.1
|
41.6
|
1.0
|
CB
|
A:GLN11
|
4.2
|
34.5
|
1.0
|
OD2
|
A:ASP69
|
4.3
|
40.1
|
1.0
|
CG
|
A:GLU71
|
4.3
|
55.0
|
1.0
|
OD2
|
A:ASP98
|
4.4
|
40.1
|
1.0
|
CB
|
A:ASP98
|
4.4
|
35.5
|
1.0
|
N
|
A:GLN11
|
4.4
|
39.9
|
1.0
|
O1G
|
A:GTP501
|
4.4
|
36.7
|
1.0
|
O1A
|
A:GTP501
|
4.5
|
34.5
|
1.0
|
O2B
|
A:GTP501
|
4.5
|
35.1
|
1.0
|
NE2
|
A:GLN11
|
4.5
|
43.9
|
1.0
|
CG
|
A:ASP69
|
4.6
|
43.0
|
1.0
|
PA
|
A:GTP501
|
4.7
|
35.1
|
1.0
|
CD
|
A:GLU71
|
4.7
|
61.1
|
1.0
|
CG
|
A:ASP98
|
4.7
|
42.3
|
1.0
|
CE
|
B:LYS254
|
4.8
|
35.1
|
1.0
|
CA
|
A:GLN11
|
4.9
|
34.0
|
1.0
|
|
Magnesium binding site 2 out
of 5 in 8bde
Go back to
Magnesium Binding Sites List in 8bde
Magnesium binding site 2 out
of 5 in the Tubulin-Baccatin III Complex
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 2 of Tubulin-Baccatin III Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg502
b:29.8
occ:1.00
|
O1A
|
B:GDP501
|
2.3
|
33.5
|
1.0
|
OE1
|
B:GLN11
|
2.3
|
40.9
|
1.0
|
O
|
B:HOH625
|
2.3
|
43.0
|
1.0
|
O
|
C:HOH674
|
2.4
|
47.6
|
1.0
|
O
|
B:HOH693
|
2.5
|
42.3
|
1.0
|
O
|
B:HOH613
|
2.5
|
43.3
|
1.0
|
O
|
B:HOH728
|
2.7
|
67.6
|
1.0
|
CD
|
B:GLN11
|
3.5
|
45.0
|
1.0
|
PA
|
B:GDP501
|
3.6
|
33.5
|
1.0
|
OD2
|
B:ASP179
|
3.8
|
41.7
|
1.0
|
O3A
|
B:GDP501
|
3.9
|
34.8
|
1.0
|
CB
|
B:GLN11
|
4.1
|
32.8
|
1.0
|
CG
|
B:GLN11
|
4.2
|
38.9
|
1.0
|
OD1
|
B:ASN101
|
4.3
|
38.8
|
1.0
|
C5'
|
B:GDP501
|
4.4
|
33.8
|
1.0
|
O5'
|
B:GDP501
|
4.4
|
33.5
|
1.0
|
NE2
|
B:GLN11
|
4.5
|
46.5
|
1.0
|
OE1
|
C:GLU254
|
4.5
|
46.1
|
1.0
|
O1B
|
B:GDP501
|
4.6
|
29.4
|
1.0
|
O
|
C:HOH656
|
4.6
|
49.6
|
1.0
|
O2A
|
B:GDP501
|
4.7
|
33.3
|
1.0
|
C8
|
B:GDP501
|
4.8
|
36.1
|
1.0
|
CG
|
B:ASP179
|
4.9
|
40.1
|
1.0
|
PB
|
B:GDP501
|
4.9
|
30.4
|
1.0
|
O
|
B:HOH710
|
4.9
|
56.1
|
1.0
|
|
Magnesium binding site 3 out
of 5 in 8bde
Go back to
Magnesium Binding Sites List in 8bde
Magnesium binding site 3 out
of 5 in the Tubulin-Baccatin III Complex
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 3 of Tubulin-Baccatin III Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mg502
b:32.3
occ:1.00
|
O
|
C:HOH694
|
2.0
|
32.3
|
1.0
|
O1B
|
C:GTP501
|
2.0
|
33.7
|
1.0
|
O1G
|
C:GTP501
|
2.0
|
32.3
|
1.0
|
O
|
C:HOH769
|
2.1
|
33.8
|
1.0
|
O
|
C:HOH692
|
2.1
|
31.3
|
1.0
|
O
|
C:HOH684
|
2.1
|
31.0
|
1.0
|
PB
|
C:GTP501
|
3.2
|
31.7
|
1.0
|
PG
|
C:GTP501
|
3.2
|
33.0
|
1.0
|
O3B
|
C:GTP501
|
3.5
|
36.6
|
1.0
|
O2G
|
C:GTP501
|
3.6
|
33.5
|
1.0
|
O3A
|
C:GTP501
|
3.7
|
33.2
|
1.0
|
OE1
|
C:GLU71
|
3.9
|
52.3
|
1.0
|
NZ
|
D:LYS254
|
3.9
|
33.6
|
1.0
|
OD1
|
C:ASP69
|
4.0
|
35.4
|
1.0
|
CB
|
C:GLN11
|
4.2
|
29.9
|
1.0
|
CG
|
C:GLU71
|
4.2
|
40.9
|
1.0
|
OD2
|
C:ASP69
|
4.2
|
35.2
|
1.0
|
OD2
|
C:ASP98
|
4.3
|
39.7
|
1.0
|
N
|
C:GLN11
|
4.4
|
30.7
|
1.0
|
CB
|
C:ASP98
|
4.4
|
39.7
|
1.0
|
O2B
|
C:GTP501
|
4.4
|
32.9
|
1.0
|
O3G
|
C:GTP501
|
4.5
|
29.8
|
1.0
|
CD
|
C:GLU71
|
4.6
|
46.5
|
1.0
|
CG
|
C:ASP69
|
4.6
|
35.4
|
1.0
|
O1A
|
C:GTP501
|
4.6
|
30.4
|
1.0
|
CG
|
C:ASP98
|
4.7
|
38.5
|
1.0
|
PA
|
C:GTP501
|
4.8
|
31.1
|
1.0
|
OE1
|
C:GLN11
|
4.8
|
42.0
|
1.0
|
CA
|
C:GLN11
|
4.9
|
29.9
|
1.0
|
|
Magnesium binding site 4 out
of 5 in 8bde
Go back to
Magnesium Binding Sites List in 8bde
Magnesium binding site 4 out
of 5 in the Tubulin-Baccatin III Complex
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 4 of Tubulin-Baccatin III Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Mg502
b:82.6
occ:1.00
|
O
|
D:HOH670
|
2.0
|
75.6
|
1.0
|
OE1
|
D:GLN11
|
2.1
|
85.6
|
1.0
|
O1A
|
D:GDP501
|
2.4
|
58.4
|
1.0
|
O
|
D:HOH688
|
2.7
|
64.4
|
1.0
|
O
|
D:HOH606
|
2.8
|
71.4
|
1.0
|
CD
|
D:GLN11
|
3.4
|
67.5
|
1.0
|
PA
|
D:GDP501
|
3.7
|
55.6
|
1.0
|
O
|
D:HOH707
|
3.9
|
63.1
|
1.0
|
O3A
|
D:GDP501
|
4.0
|
52.4
|
1.0
|
NE2
|
D:GLN11
|
4.2
|
62.2
|
1.0
|
OD1
|
D:ASN101
|
4.3
|
75.6
|
1.0
|
C5'
|
D:GDP501
|
4.3
|
59.3
|
1.0
|
CB
|
D:GLN11
|
4.3
|
51.7
|
1.0
|
CG
|
D:GLN11
|
4.3
|
61.2
|
1.0
|
O5'
|
D:GDP501
|
4.5
|
58.5
|
1.0
|
O2A
|
D:GDP501
|
4.8
|
54.6
|
1.0
|
O1B
|
D:GDP501
|
4.8
|
45.5
|
1.0
|
|
Magnesium binding site 5 out
of 5 in 8bde
Go back to
Magnesium Binding Sites List in 8bde
Magnesium binding site 5 out
of 5 in the Tubulin-Baccatin III Complex
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 5 of Tubulin-Baccatin III Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Mg401
b:82.3
occ:1.00
|
O
|
F:HOH514
|
2.1
|
85.5
|
1.0
|
OE1
|
F:GLU331
|
2.3
|
105.5
|
1.0
|
O2B
|
F:ACP402
|
2.4
|
125.7
|
1.0
|
OD1
|
F:ASN333
|
2.5
|
97.4
|
1.0
|
O1G
|
F:ACP402
|
2.6
|
134.7
|
1.0
|
CD
|
F:GLU331
|
3.0
|
98.4
|
1.0
|
OE2
|
F:GLU331
|
3.0
|
104.0
|
1.0
|
O3G
|
F:ACP402
|
3.3
|
135.0
|
1.0
|
PG
|
F:ACP402
|
3.4
|
134.8
|
1.0
|
PB
|
F:ACP402
|
3.7
|
123.9
|
1.0
|
CG
|
F:ASN333
|
3.7
|
86.9
|
1.0
|
NZ
|
F:LYS74
|
4.1
|
95.8
|
1.0
|
O1B
|
F:ACP402
|
4.1
|
123.7
|
1.0
|
C3B
|
F:ACP402
|
4.2
|
129.8
|
1.0
|
ND2
|
F:ASN333
|
4.2
|
83.2
|
1.0
|
CG
|
F:GLU331
|
4.4
|
82.0
|
1.0
|
O2G
|
F:ACP402
|
4.8
|
133.2
|
1.0
|
CE
|
F:LYS74
|
4.9
|
90.9
|
1.0
|
CB
|
F:ASN333
|
4.9
|
73.3
|
1.0
|
O3A
|
F:ACP402
|
5.0
|
118.1
|
1.0
|
|
Reference:
A.E.Prota,
D.Lucena-Agell,
Y.Ma,
J.Estevez-Gallego,
S.Li,
K.Bargsten,
F.Josa-Prado,
K.H.Altmann,
N.Gaillard,
S.Kamimura,
T.Muhlethaler,
F.Gago,
M.A.Oliva,
M.O.Steinmetz,
W.S.Fang,
J.F.Diaz.
Structural Insight Into the Stabilization of Microtubules By Taxanes. Elife V. 12 2023.
ISSN: ESSN 2050-084X
PubMed: 36876916
DOI: 10.7554/ELIFE.84791
Page generated: Thu Oct 3 19:17:55 2024
|