Magnesium in PDB 5ng1: Tubulin-Mtc-Zampanolide Complex
Protein crystallography data
The structure of Tubulin-Mtc-Zampanolide Complex, PDB code: 5ng1
was solved by
J.J.Field,
B.Pera,
J.Estevez Gallego,
E.Calvo,
J.Rodriguez-Salarichs,
G.Saez-Calvo,
D.Zuwerra,
M.Jordi,
A.E.Prota,
G.Menchon,
J.H.Miller,
K.-H.Altmann,
J.F.Diaz,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
47.69 /
2.20
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
104.237,
157.418,
178.858,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
17.3 /
22
|
Other elements in 5ng1:
The structure of Tubulin-Mtc-Zampanolide Complex also contains other interesting chemical elements:
Magnesium Binding Sites:
The binding sites of Magnesium atom in the Tubulin-Mtc-Zampanolide Complex
(pdb code 5ng1). 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-Mtc-Zampanolide Complex, PDB code: 5ng1:
Jump to Magnesium binding site number:
1;
2;
3;
4;
5;
Magnesium binding site 1 out
of 5 in 5ng1
Go back to
Magnesium Binding Sites List in 5ng1
Magnesium binding site 1 out
of 5 in the Tubulin-Mtc-Zampanolide Complex
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 1 of Tubulin-Mtc-Zampanolide Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg502
b:36.5
occ:1.00
|
O1G
|
A:GTP501
|
2.0
|
37.3
|
1.0
|
O
|
A:HOH622
|
2.0
|
39.7
|
1.0
|
O
|
A:HOH631
|
2.0
|
38.6
|
1.0
|
O
|
A:HOH615
|
2.0
|
35.7
|
1.0
|
O
|
A:HOH634
|
2.1
|
39.5
|
1.0
|
O1B
|
A:GTP501
|
2.2
|
31.7
|
1.0
|
PG
|
A:GTP501
|
3.1
|
45.4
|
1.0
|
PB
|
A:GTP501
|
3.2
|
36.9
|
1.0
|
O2G
|
A:GTP501
|
3.4
|
42.1
|
1.0
|
O3B
|
A:GTP501
|
3.5
|
49.5
|
1.0
|
O3A
|
A:GTP501
|
3.8
|
40.0
|
1.0
|
NZ
|
B:LYS254
|
3.9
|
52.6
|
1.0
|
OD1
|
A:ASP69
|
4.0
|
44.0
|
1.0
|
OE1
|
A:GLU71
|
4.0
|
65.0
|
1.0
|
OD2
|
A:ASP98
|
4.1
|
50.8
|
1.0
|
OD2
|
A:ASP69
|
4.1
|
41.9
|
1.0
|
CB
|
A:GLN11
|
4.1
|
39.2
|
1.0
|
N
|
A:GLN11
|
4.3
|
36.3
|
1.0
|
O3G
|
A:GTP501
|
4.4
|
35.7
|
1.0
|
CB
|
A:ASP98
|
4.4
|
37.1
|
1.0
|
CG
|
A:ASP69
|
4.4
|
48.3
|
1.0
|
CG
|
A:ASP98
|
4.5
|
49.7
|
1.0
|
O2B
|
A:GTP501
|
4.5
|
45.4
|
1.0
|
ND2
|
B:ASN249
|
4.6
|
0.1
|
1.0
|
O1A
|
A:GTP501
|
4.7
|
38.3
|
1.0
|
CA
|
A:GLN11
|
4.8
|
42.8
|
1.0
|
PA
|
A:GTP501
|
4.8
|
39.5
|
1.0
|
OG1
|
A:THR145
|
4.8
|
39.2
|
1.0
|
CE
|
B:LYS254
|
5.0
|
39.0
|
1.0
|
|
Magnesium binding site 2 out
of 5 in 5ng1
Go back to
Magnesium Binding Sites List in 5ng1
Magnesium binding site 2 out
of 5 in the Tubulin-Mtc-Zampanolide Complex
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 2 of Tubulin-Mtc-Zampanolide Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg502
b:35.9
occ:1.00
|
O1A
|
B:GDP501
|
2.3
|
36.3
|
1.0
|
OE1
|
B:GLN11
|
2.3
|
43.8
|
1.0
|
O
|
C:HOH657
|
2.3
|
44.0
|
1.0
|
O
|
B:HOH664
|
2.3
|
42.2
|
1.0
|
O
|
B:HOH651
|
2.4
|
65.5
|
1.0
|
O
|
B:HOH603
|
2.6
|
47.5
|
1.0
|
PA
|
B:GDP501
|
3.5
|
35.9
|
1.0
|
CD
|
B:GLN11
|
3.5
|
44.9
|
1.0
|
O3A
|
B:GDP501
|
3.7
|
40.1
|
1.0
|
OD2
|
B:ASP179
|
3.9
|
52.5
|
1.0
|
CB
|
B:GLN11
|
4.2
|
32.0
|
1.0
|
OD1
|
B:ASN101
|
4.2
|
46.3
|
1.0
|
CG
|
B:GLN11
|
4.3
|
39.6
|
1.0
|
O5'
|
B:GDP501
|
4.3
|
37.8
|
1.0
|
C5'
|
B:GDP501
|
4.4
|
39.0
|
1.0
|
O
|
C:HOH652
|
4.4
|
46.6
|
1.0
|
OE1
|
C:GLU254
|
4.4
|
56.7
|
1.0
|
NE2
|
B:GLN11
|
4.5
|
45.5
|
1.0
|
O2A
|
B:GDP501
|
4.6
|
36.8
|
1.0
|
O1B
|
B:GDP501
|
4.6
|
31.5
|
1.0
|
C8
|
B:GDP501
|
4.8
|
36.1
|
1.0
|
PB
|
B:GDP501
|
4.8
|
35.5
|
1.0
|
ND2
|
B:ASN101
|
4.8
|
34.4
|
1.0
|
CG
|
B:ASP179
|
4.9
|
50.0
|
1.0
|
CG
|
B:ASN101
|
4.9
|
44.0
|
1.0
|
|
Magnesium binding site 3 out
of 5 in 5ng1
Go back to
Magnesium Binding Sites List in 5ng1
Magnesium binding site 3 out
of 5 in the Tubulin-Mtc-Zampanolide Complex
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 3 of Tubulin-Mtc-Zampanolide Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mg502
b:35.0
occ:1.00
|
O1G
|
C:GTP501
|
2.0
|
33.0
|
1.0
|
O
|
C:HOH717
|
2.0
|
32.2
|
1.0
|
O
|
C:HOH625
|
2.0
|
32.0
|
1.0
|
O
|
C:HOH610
|
2.1
|
34.8
|
1.0
|
O1B
|
C:GTP501
|
2.1
|
30.6
|
1.0
|
O
|
C:HOH607
|
2.2
|
37.0
|
1.0
|
PG
|
C:GTP501
|
3.1
|
36.5
|
1.0
|
PB
|
C:GTP501
|
3.2
|
30.0
|
1.0
|
O3B
|
C:GTP501
|
3.6
|
39.9
|
1.0
|
O2G
|
C:GTP501
|
3.6
|
34.5
|
1.0
|
O3A
|
C:GTP501
|
3.7
|
34.0
|
1.0
|
NZ
|
D:LYS254
|
3.8
|
47.3
|
1.0
|
OE1
|
C:GLU71
|
3.9
|
64.3
|
1.0
|
CB
|
C:GLN11
|
4.1
|
28.5
|
1.0
|
OD1
|
C:ASP69
|
4.1
|
47.2
|
1.0
|
OD2
|
C:ASP98
|
4.2
|
55.0
|
1.0
|
OD2
|
C:ASP69
|
4.3
|
33.7
|
1.0
|
CG
|
C:GLU71
|
4.3
|
47.9
|
1.0
|
N
|
C:GLN11
|
4.4
|
31.7
|
1.0
|
O1A
|
C:GTP501
|
4.4
|
35.6
|
1.0
|
O3G
|
C:GTP501
|
4.4
|
33.5
|
1.0
|
O2B
|
C:GTP501
|
4.5
|
34.3
|
1.0
|
CB
|
C:ASP98
|
4.5
|
38.5
|
1.0
|
OE1
|
C:GLN11
|
4.6
|
50.3
|
1.0
|
CD
|
C:GLU71
|
4.6
|
57.0
|
1.0
|
ND2
|
D:ASN249
|
4.6
|
78.5
|
1.0
|
CG
|
C:ASP69
|
4.6
|
36.0
|
1.0
|
PA
|
C:GTP501
|
4.7
|
35.4
|
1.0
|
CG
|
C:ASP98
|
4.7
|
46.5
|
1.0
|
CA
|
C:GLN11
|
4.8
|
34.2
|
1.0
|
CE
|
D:LYS254
|
5.0
|
45.3
|
1.0
|
|
Magnesium binding site 4 out
of 5 in 5ng1
Go back to
Magnesium Binding Sites List in 5ng1
Magnesium binding site 4 out
of 5 in the Tubulin-Mtc-Zampanolide Complex
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 4 of Tubulin-Mtc-Zampanolide Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Mg502
b:55.0
occ:1.00
|
O
|
D:HOH606
|
2.1
|
57.6
|
1.0
|
OE1
|
D:GLN11
|
2.2
|
72.4
|
1.0
|
O
|
D:HOH676
|
2.5
|
65.4
|
1.0
|
O1A
|
D:GDP501
|
2.5
|
64.0
|
1.0
|
CD
|
D:GLN11
|
3.4
|
66.9
|
1.0
|
PA
|
D:GDP501
|
3.6
|
56.4
|
1.0
|
O3A
|
D:GDP501
|
3.7
|
56.5
|
1.0
|
CB
|
D:GLN11
|
4.0
|
60.5
|
1.0
|
O
|
D:HOH683
|
4.1
|
59.7
|
1.0
|
CG
|
D:GLN11
|
4.2
|
63.7
|
1.0
|
OD1
|
D:ASN101
|
4.3
|
68.6
|
1.0
|
NE2
|
D:GLN11
|
4.4
|
67.2
|
1.0
|
C5'
|
D:GDP501
|
4.4
|
51.8
|
1.0
|
O5'
|
D:GDP501
|
4.4
|
56.3
|
1.0
|
O1B
|
D:GDP501
|
4.6
|
44.5
|
1.0
|
O2A
|
D:GDP501
|
4.7
|
55.1
|
1.0
|
PB
|
D:GDP501
|
4.8
|
55.4
|
1.0
|
C8
|
D:GDP501
|
4.9
|
47.9
|
1.0
|
|
Magnesium binding site 5 out
of 5 in 5ng1
Go back to
Magnesium Binding Sites List in 5ng1
Magnesium binding site 5 out
of 5 in the Tubulin-Mtc-Zampanolide Complex
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 5 of Tubulin-Mtc-Zampanolide Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Mg702
b:61.2
occ:1.00
|
O1G
|
F:ACP701
|
2.2
|
94.9
|
1.0
|
O1B
|
F:ACP701
|
2.3
|
0.8
|
1.0
|
OE2
|
F:GLU331
|
2.4
|
81.4
|
1.0
|
ND2
|
F:ASN333
|
2.4
|
95.3
|
1.0
|
OE1
|
F:GLU331
|
3.0
|
82.8
|
1.0
|
CD
|
F:GLU331
|
3.1
|
73.8
|
1.0
|
NZ
|
F:LYS74
|
3.2
|
89.1
|
1.0
|
CG
|
F:ASN333
|
3.6
|
87.0
|
1.0
|
PG
|
F:ACP701
|
3.6
|
0.7
|
1.0
|
PB
|
F:ACP701
|
3.7
|
0.5
|
1.0
|
OD1
|
F:ASN333
|
4.1
|
92.8
|
1.0
|
O2B
|
F:ACP701
|
4.1
|
0.8
|
1.0
|
CE
|
F:LYS74
|
4.2
|
83.7
|
1.0
|
C3B
|
F:ACP701
|
4.2
|
0.3
|
1.0
|
O2G
|
F:ACP701
|
4.3
|
86.8
|
1.0
|
CG
|
F:GLU331
|
4.6
|
61.0
|
1.0
|
O3G
|
F:ACP701
|
4.7
|
0.7
|
1.0
|
CB
|
F:ASN333
|
4.8
|
70.4
|
1.0
|
O3A
|
F:ACP701
|
5.0
|
0.5
|
1.0
|
|
Reference:
J.J.Field,
B.Pera,
J.E.Gallego,
E.Calvo,
J.Rodriguez-Salarichs,
G.Saez-Calvo,
D.Zuwerra,
M.Jordi,
J.M.Andreu,
A.E.Prota,
G.Menchon,
J.H.Miller,
K.H.Altmann,
J.F.Diaz.
Zampanolide Binding to Tubulin Indicates Cross-Talk of Taxane Site with Colchicine and Nucleotide Sites. J. Nat. Prod. V. 81 494 2018.
ISSN: ESSN 1520-6025
PubMed: 29023132
DOI: 10.1021/ACS.JNATPROD.7B00704
Page generated: Sun Sep 29 23:15:56 2024
|