Magnesium in PDB 5njh: Triazolopyrimidines Stabilize Microtubules By Binding to the Vinca Inhibitor Site of Tubulin
Protein crystallography data
The structure of Triazolopyrimidines Stabilize Microtubules By Binding to the Vinca Inhibitor Site of Tubulin, PDB code: 5njh
was solved by
A.Sharma,
G.S.Calvo,
A.E.Prota,
J.F.Diaz,
M.O.Steinmetz,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
48.09 /
2.39
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
103.430,
158.353,
173.458,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
21.8 /
23.7
|
Other elements in 5njh:
The structure of Triazolopyrimidines Stabilize Microtubules By Binding to the Vinca Inhibitor Site of Tubulin also contains other interesting chemical elements:
Magnesium Binding Sites:
The binding sites of Magnesium atom in the Triazolopyrimidines Stabilize Microtubules By Binding to the Vinca Inhibitor Site of Tubulin
(pdb code 5njh). This binding sites where shown within
5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the
Triazolopyrimidines Stabilize Microtubules By Binding to the Vinca Inhibitor Site of Tubulin, PDB code: 5njh:
Jump to Magnesium binding site number:
1;
2;
3;
4;
5;
Magnesium binding site 1 out
of 5 in 5njh
Go back to
Magnesium Binding Sites List in 5njh
Magnesium binding site 1 out
of 5 in the Triazolopyrimidines Stabilize Microtubules By Binding to the Vinca Inhibitor Site of Tubulin
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 1 of Triazolopyrimidines Stabilize Microtubules By Binding to the Vinca Inhibitor Site of Tubulin within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg502
b:45.3
occ:1.00
|
O1B
|
A:GTP501
|
1.9
|
41.1
|
1.0
|
O1G
|
A:GTP501
|
2.0
|
38.3
|
1.0
|
O
|
A:HOH622
|
2.0
|
47.4
|
1.0
|
O
|
A:HOH635
|
2.1
|
43.1
|
1.0
|
O
|
A:HOH616
|
2.1
|
47.4
|
1.0
|
O
|
A:HOH636
|
2.2
|
43.4
|
1.0
|
PB
|
A:GTP501
|
3.1
|
41.4
|
1.0
|
PG
|
A:GTP501
|
3.1
|
46.0
|
1.0
|
O3B
|
A:GTP501
|
3.4
|
55.1
|
1.0
|
O3G
|
A:GTP501
|
3.5
|
43.2
|
1.0
|
O3A
|
A:GTP501
|
3.7
|
44.1
|
1.0
|
NZ
|
B:LYS254
|
3.8
|
46.4
|
1.0
|
CB
|
A:GLN11
|
4.0
|
42.1
|
1.0
|
OD1
|
A:ASP69
|
4.0
|
47.5
|
1.0
|
OE1
|
A:GLU71
|
4.1
|
62.6
|
1.0
|
OD2
|
A:ASP69
|
4.3
|
51.3
|
1.0
|
N
|
A:GLN11
|
4.3
|
39.5
|
1.0
|
OE1
|
A:GLN11
|
4.4
|
46.1
|
1.0
|
O2B
|
A:GTP501
|
4.4
|
45.2
|
1.0
|
OD2
|
A:ASP98
|
4.4
|
52.9
|
1.0
|
O2G
|
A:GTP501
|
4.4
|
41.4
|
1.0
|
CG
|
A:GLU71
|
4.4
|
59.0
|
1.0
|
O1A
|
A:GTP501
|
4.4
|
49.2
|
1.0
|
CB
|
A:ASP98
|
4.5
|
49.9
|
1.0
|
NE2
|
B:GLN247
|
4.6
|
0.2
|
1.0
|
CG
|
A:ASP69
|
4.6
|
49.1
|
1.0
|
PA
|
A:GTP501
|
4.6
|
46.7
|
1.0
|
CG
|
A:ASP98
|
4.8
|
51.1
|
1.0
|
CD
|
A:GLU71
|
4.8
|
62.0
|
1.0
|
CA
|
A:GLN11
|
4.8
|
41.6
|
1.0
|
|
Magnesium binding site 2 out
of 5 in 5njh
Go back to
Magnesium Binding Sites List in 5njh
Magnesium binding site 2 out
of 5 in the Triazolopyrimidines Stabilize Microtubules By Binding to the Vinca Inhibitor Site of Tubulin
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 2 of Triazolopyrimidines Stabilize Microtubules By Binding to the Vinca Inhibitor Site of Tubulin within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg502
b:73.7
occ:1.00
|
O
|
C:HOH603
|
3.2
|
47.9
|
1.0
|
NE2
|
B:GLN11
|
3.3
|
51.3
|
1.0
|
OE2
|
B:GLU71
|
3.6
|
74.5
|
1.0
|
O1B
|
B:GDP501
|
3.7
|
42.8
|
1.0
|
O1A
|
B:GDP501
|
3.8
|
51.5
|
1.0
|
O3A
|
B:GDP501
|
4.2
|
50.4
|
1.0
|
O
|
B:HOH635
|
4.2
|
50.0
|
1.0
|
CB
|
B:GLN11
|
4.3
|
48.2
|
1.0
|
CD
|
B:GLN11
|
4.3
|
50.4
|
1.0
|
O
|
B:HOH620
|
4.3
|
50.7
|
1.0
|
PB
|
B:GDP501
|
4.4
|
40.4
|
1.0
|
CD
|
B:GLU71
|
4.5
|
75.4
|
1.0
|
PA
|
B:GDP501
|
4.6
|
59.1
|
1.0
|
O3B
|
B:GDP501
|
4.7
|
56.0
|
1.0
|
OE1
|
C:GLU254
|
4.8
|
48.5
|
1.0
|
ND2
|
B:ASN101
|
4.8
|
43.0
|
1.0
|
OE1
|
B:GLU71
|
4.9
|
76.8
|
1.0
|
CG
|
B:GLN11
|
4.9
|
48.6
|
1.0
|
OE2
|
C:GLU254
|
5.0
|
48.4
|
1.0
|
|
Magnesium binding site 3 out
of 5 in 5njh
Go back to
Magnesium Binding Sites List in 5njh
Magnesium binding site 3 out
of 5 in the Triazolopyrimidines Stabilize Microtubules By Binding to the Vinca Inhibitor Site of Tubulin
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 3 of Triazolopyrimidines Stabilize Microtubules By Binding to the Vinca Inhibitor Site of Tubulin within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mg502
b:44.6
occ:1.00
|
O
|
C:HOH644
|
2.0
|
47.8
|
1.0
|
O
|
C:HOH614
|
2.0
|
43.4
|
1.0
|
O1B
|
C:GTP501
|
2.0
|
38.7
|
1.0
|
O1G
|
C:GTP501
|
2.1
|
44.7
|
1.0
|
O
|
C:HOH628
|
2.1
|
43.6
|
1.0
|
O
|
C:HOH646
|
2.3
|
47.0
|
1.0
|
PB
|
C:GTP501
|
3.2
|
42.8
|
1.0
|
PG
|
C:GTP501
|
3.2
|
41.8
|
1.0
|
O3B
|
C:GTP501
|
3.5
|
61.4
|
1.0
|
NZ
|
D:LYS254
|
3.8
|
53.3
|
1.0
|
O2G
|
C:GTP501
|
3.8
|
42.6
|
1.0
|
O3A
|
C:GTP501
|
3.9
|
56.5
|
1.0
|
OE1
|
C:GLU71
|
4.0
|
56.3
|
1.0
|
OD1
|
C:ASP69
|
4.1
|
41.6
|
1.0
|
CB
|
C:GLN11
|
4.2
|
45.8
|
1.0
|
CG
|
C:GLU71
|
4.2
|
55.3
|
1.0
|
OD2
|
C:ASP69
|
4.3
|
42.1
|
1.0
|
O2B
|
C:GTP501
|
4.4
|
46.3
|
1.0
|
O3G
|
C:GTP501
|
4.5
|
47.4
|
1.0
|
OE1
|
C:GLN11
|
4.5
|
48.4
|
1.0
|
N
|
C:GLN11
|
4.5
|
44.3
|
1.0
|
CB
|
C:ASP98
|
4.6
|
52.7
|
1.0
|
OD2
|
C:ASP98
|
4.6
|
54.3
|
1.0
|
O1A
|
C:GTP501
|
4.6
|
55.3
|
1.0
|
CG
|
C:ASP69
|
4.6
|
42.1
|
1.0
|
CD
|
C:GLU71
|
4.6
|
56.5
|
1.0
|
PA
|
C:GTP501
|
4.7
|
59.5
|
1.0
|
OG1
|
C:THR145
|
4.8
|
38.3
|
1.0
|
CE
|
D:LYS254
|
4.9
|
50.6
|
1.0
|
CG
|
C:ASP98
|
4.9
|
53.6
|
1.0
|
CA
|
C:GLN11
|
4.9
|
45.1
|
1.0
|
O2A
|
C:GTP501
|
5.0
|
58.7
|
1.0
|
|
Magnesium binding site 4 out
of 5 in 5njh
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Magnesium Binding Sites List in 5njh
Magnesium binding site 4 out
of 5 in the Triazolopyrimidines Stabilize Microtubules By Binding to the Vinca Inhibitor Site of Tubulin
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 4 of Triazolopyrimidines Stabilize Microtubules By Binding to the Vinca Inhibitor Site of Tubulin within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Mg502
b:54.4
occ:1.00
|
OE1
|
D:GLN11
|
2.1
|
63.7
|
1.0
|
O
|
D:HOH620
|
2.3
|
61.2
|
1.0
|
O1A
|
D:GDP501
|
2.3
|
57.9
|
1.0
|
O
|
D:HOH638
|
2.4
|
57.7
|
1.0
|
O
|
D:HOH652
|
3.2
|
66.1
|
1.0
|
CD
|
D:GLN11
|
3.4
|
62.5
|
1.0
|
PA
|
D:GDP501
|
3.7
|
56.7
|
1.0
|
O3A
|
D:GDP501
|
4.0
|
59.8
|
1.0
|
NE2
|
D:GLN11
|
4.2
|
64.3
|
1.0
|
CB
|
D:GLN11
|
4.2
|
56.5
|
1.0
|
CG
|
D:GLN11
|
4.3
|
58.9
|
1.0
|
C5'
|
D:GDP501
|
4.3
|
56.2
|
1.0
|
O
|
D:HOH636
|
4.4
|
64.6
|
1.0
|
O5'
|
D:GDP501
|
4.5
|
51.2
|
1.0
|
OD1
|
D:ASN101
|
4.7
|
70.4
|
1.0
|
O2A
|
D:GDP501
|
4.7
|
50.6
|
1.0
|
O1B
|
D:GDP501
|
4.9
|
53.0
|
1.0
|
C8
|
D:GDP501
|
5.0
|
55.4
|
1.0
|
|
Magnesium binding site 5 out
of 5 in 5njh
Go back to
Magnesium Binding Sites List in 5njh
Magnesium binding site 5 out
of 5 in the Triazolopyrimidines Stabilize Microtubules By Binding to the Vinca Inhibitor Site of Tubulin
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 5 of Triazolopyrimidines Stabilize Microtubules By Binding to the Vinca Inhibitor Site of Tubulin within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Mg401
b:0.6
occ:1.00
|
O1B
|
F:ACP402
|
2.4
|
0.1
|
1.0
|
O1G
|
F:ACP402
|
2.5
|
0.9
|
1.0
|
OE1
|
F:GLU331
|
2.5
|
77.0
|
1.0
|
NZ
|
F:LYS74
|
2.8
|
75.2
|
1.0
|
O
|
F:HOH505
|
3.1
|
97.1
|
1.0
|
O2B
|
F:ACP402
|
3.3
|
0.2
|
1.0
|
PB
|
F:ACP402
|
3.3
|
0.6
|
1.0
|
CD
|
F:GLU331
|
3.4
|
76.0
|
1.0
|
PG
|
F:ACP402
|
3.7
|
0.7
|
1.0
|
OE2
|
F:GLU331
|
3.7
|
76.7
|
1.0
|
C3B
|
F:ACP402
|
4.0
|
0.7
|
1.0
|
CE
|
F:LYS74
|
4.1
|
74.5
|
1.0
|
OD1
|
F:ASN333
|
4.4
|
82.3
|
1.0
|
O3G
|
F:ACP402
|
4.6
|
0.3
|
1.0
|
ND2
|
F:ASN333
|
4.6
|
83.0
|
1.0
|
O3A
|
F:ACP402
|
4.7
|
0.2
|
1.0
|
CG
|
F:GLU331
|
4.8
|
74.9
|
1.0
|
O2G
|
F:ACP402
|
4.8
|
0.6
|
1.0
|
CG
|
F:ASN333
|
4.9
|
82.1
|
1.0
|
|
Reference:
G.Saez-Calvo,
A.Sharma,
F.A.Balaguer,
I.Barasoain,
J.Rodriguez-Salarichs,
N.Olieric,
H.Munoz-Hernandez,
M.A.Berbis,
S.Wendeborn,
M.A.Penalva,
R.Matesanz,
A.Canales,
A.E.Prota,
J.Jimenez-Barbero,
J.M.Andreu,
C.Lamberth,
M.O.Steinmetz,
J.F.Diaz.
Triazolopyrimidines Are Microtubule-Stabilizing Agents That Bind the Vinca Inhibitor Site of Tubulin. Cell Chem Biol V. 24 737 2017.
ISSN: ESSN 2451-9456
PubMed: 28579361
DOI: 10.1016/J.CHEMBIOL.2017.05.016
Page generated: Sun Sep 29 23:18:53 2024
|