Magnesium in PDB 7z7d: Tubulin-Todalam-Vinblastine-Complex
Protein crystallography data
The structure of Tubulin-Todalam-Vinblastine-Complex, PDB code: 7z7d
was solved by
T.Muehlethaler,
L.Milanos,
J.A.Ortega,
T.B.Blum,
D.Gioia,
B.Roy,
A.E.Prota,
A.Cavalli,
M.O.Steinmetz,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
45.60 /
2.00
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
105.286,
157.296,
182.526,
90,
90,
90
|
R / Rfree (%)
|
20.4 /
23.6
|
Other elements in 7z7d:
The structure of Tubulin-Todalam-Vinblastine-Complex also contains other interesting chemical elements:
Magnesium Binding Sites:
The binding sites of Magnesium atom in the Tubulin-Todalam-Vinblastine-Complex
(pdb code 7z7d). 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-Todalam-Vinblastine-Complex, PDB code: 7z7d:
Jump to Magnesium binding site number:
1;
2;
3;
4;
5;
Magnesium binding site 1 out
of 5 in 7z7d
Go back to
Magnesium Binding Sites List in 7z7d
Magnesium binding site 1 out
of 5 in the Tubulin-Todalam-Vinblastine-Complex
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 1 of Tubulin-Todalam-Vinblastine-Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg502
b:35.0
occ:1.00
|
O1G
|
A:GTP501
|
1.9
|
28.1
|
1.0
|
O
|
A:HOH678
|
2.0
|
31.6
|
1.0
|
O
|
A:HOH712
|
2.1
|
31.8
|
1.0
|
O
|
A:HOH614
|
2.1
|
33.9
|
1.0
|
O1B
|
A:GTP501
|
2.1
|
28.3
|
1.0
|
O
|
A:HOH682
|
2.2
|
37.2
|
1.0
|
PG
|
A:GTP501
|
3.1
|
34.5
|
1.0
|
PB
|
A:GTP501
|
3.2
|
34.4
|
1.0
|
O3B
|
A:GTP501
|
3.5
|
43.6
|
1.0
|
O3A
|
A:GTP501
|
3.6
|
42.2
|
1.0
|
O2G
|
A:GTP501
|
3.7
|
35.8
|
1.0
|
OE1
|
A:GLU71
|
3.7
|
60.2
|
1.0
|
NZ
|
B:LYS254
|
3.8
|
33.6
|
1.0
|
CB
|
A:GLN11
|
4.2
|
35.0
|
1.0
|
OD1
|
A:ASP69
|
4.2
|
38.2
|
1.0
|
O3G
|
A:GTP501
|
4.4
|
33.2
|
1.0
|
CB
|
A:ASP98
|
4.4
|
43.0
|
1.0
|
OD2
|
A:ASP69
|
4.4
|
39.3
|
1.0
|
OD2
|
A:ASP98
|
4.5
|
39.1
|
1.0
|
N
|
A:GLN11
|
4.5
|
31.2
|
1.0
|
O2B
|
A:GTP501
|
4.5
|
39.1
|
1.0
|
O1A
|
A:GTP501
|
4.6
|
33.7
|
1.0
|
OE1
|
A:GLN11
|
4.7
|
42.0
|
1.0
|
PA
|
A:GTP501
|
4.7
|
37.2
|
1.0
|
CG
|
A:ASP98
|
4.7
|
34.2
|
1.0
|
CG
|
A:ASP69
|
4.8
|
39.4
|
1.0
|
CD
|
A:GLU71
|
4.9
|
51.8
|
1.0
|
CE
|
B:LYS254
|
4.9
|
39.4
|
1.0
|
CA
|
A:GLN11
|
4.9
|
42.2
|
1.0
|
|
Magnesium binding site 2 out
of 5 in 7z7d
Go back to
Magnesium Binding Sites List in 7z7d
Magnesium binding site 2 out
of 5 in the Tubulin-Todalam-Vinblastine-Complex
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 2 of Tubulin-Todalam-Vinblastine-Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg502
b:37.9
occ:1.00
|
OE1
|
B:GLN11
|
2.2
|
50.6
|
1.0
|
O
|
B:HOH609
|
2.2
|
50.7
|
1.0
|
O1A
|
B:GDP501
|
2.3
|
26.9
|
1.0
|
O
|
B:HOH774
|
2.5
|
52.8
|
1.0
|
O
|
B:HOH706
|
2.9
|
32.1
|
1.0
|
O
|
B:HOH756
|
2.9
|
51.5
|
1.0
|
O
|
C:HOH701
|
2.9
|
60.9
|
1.0
|
CD
|
B:GLN11
|
3.4
|
56.1
|
1.0
|
O
|
B:HOH779
|
3.4
|
52.7
|
1.0
|
PA
|
B:GDP501
|
3.6
|
29.3
|
1.0
|
O3A
|
B:GDP501
|
3.9
|
29.8
|
1.0
|
CB
|
B:GLN11
|
4.1
|
30.7
|
1.0
|
O
|
B:HOH777
|
4.2
|
57.2
|
1.0
|
CG
|
B:GLN11
|
4.2
|
42.1
|
1.0
|
OE2
|
C:GLU254
|
4.3
|
49.9
|
1.0
|
NE2
|
B:GLN11
|
4.3
|
46.4
|
1.0
|
C5'
|
B:GDP501
|
4.4
|
30.1
|
1.0
|
O5'
|
B:GDP501
|
4.5
|
30.8
|
1.0
|
OD1
|
B:ASN101
|
4.5
|
40.9
|
1.0
|
O1B
|
B:GDP501
|
4.7
|
27.5
|
1.0
|
O2A
|
B:GDP501
|
4.7
|
28.8
|
1.0
|
PB
|
B:GDP501
|
4.9
|
28.9
|
1.0
|
C8
|
B:GDP501
|
4.9
|
30.8
|
1.0
|
O
|
B:HOH793
|
5.0
|
57.6
|
1.0
|
|
Magnesium binding site 3 out
of 5 in 7z7d
Go back to
Magnesium Binding Sites List in 7z7d
Magnesium binding site 3 out
of 5 in the Tubulin-Todalam-Vinblastine-Complex
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 3 of Tubulin-Todalam-Vinblastine-Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mg502
b:27.8
occ:1.00
|
O1G
|
C:GTP501
|
2.0
|
29.4
|
1.0
|
O
|
C:HOH686
|
2.0
|
30.6
|
1.0
|
O
|
C:HOH750
|
2.0
|
26.4
|
1.0
|
O1B
|
C:GTP501
|
2.1
|
25.6
|
1.0
|
O
|
C:HOH691
|
2.1
|
29.6
|
1.0
|
O
|
C:HOH720
|
2.2
|
31.1
|
1.0
|
PG
|
C:GTP501
|
3.1
|
32.7
|
1.0
|
PB
|
C:GTP501
|
3.2
|
29.2
|
1.0
|
O3B
|
C:GTP501
|
3.6
|
32.0
|
1.0
|
O2G
|
C:GTP501
|
3.6
|
30.7
|
1.0
|
O3A
|
C:GTP501
|
3.8
|
31.7
|
1.0
|
NZ
|
D:LYS254
|
3.9
|
32.1
|
1.0
|
OE2
|
C:GLU71
|
4.0
|
50.0
|
1.0
|
OD1
|
C:ASP69
|
4.1
|
30.7
|
1.0
|
OD2
|
C:ASP98
|
4.3
|
38.0
|
1.0
|
CB
|
C:GLN11
|
4.3
|
30.5
|
1.0
|
OD2
|
C:ASP69
|
4.3
|
31.0
|
1.0
|
CG
|
C:GLU71
|
4.3
|
34.9
|
1.0
|
O3G
|
C:GTP501
|
4.4
|
28.5
|
1.0
|
CB
|
C:ASP98
|
4.5
|
34.4
|
1.0
|
N
|
C:GLN11
|
4.5
|
32.1
|
1.0
|
O2B
|
C:GTP501
|
4.5
|
31.2
|
1.0
|
O1A
|
C:GTP501
|
4.6
|
30.7
|
1.0
|
O
|
C:HOH615
|
4.6
|
45.0
|
1.0
|
CD
|
C:GLU71
|
4.6
|
53.4
|
1.0
|
CG
|
C:ASP69
|
4.7
|
36.0
|
1.0
|
CG
|
C:ASP98
|
4.7
|
36.9
|
1.0
|
PA
|
C:GTP501
|
4.8
|
30.9
|
1.0
|
OE1
|
C:GLN11
|
5.0
|
40.0
|
1.0
|
CE
|
D:LYS254
|
5.0
|
33.6
|
1.0
|
CA
|
C:GLN11
|
5.0
|
30.9
|
1.0
|
|
Magnesium binding site 4 out
of 5 in 7z7d
Go back to
Magnesium Binding Sites List in 7z7d
Magnesium binding site 4 out
of 5 in the Tubulin-Todalam-Vinblastine-Complex
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 4 of Tubulin-Todalam-Vinblastine-Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Mg502
b:61.5
occ:1.00
|
O1A
|
D:GDP501
|
2.0
|
93.6
|
1.0
|
OE1
|
D:GLN11
|
2.8
|
64.3
|
1.0
|
O
|
D:HOH677
|
3.5
|
65.8
|
1.0
|
PA
|
D:GDP501
|
3.5
|
62.4
|
1.0
|
OD1
|
D:ASN101
|
3.7
|
67.5
|
1.0
|
CD
|
D:GLN11
|
4.0
|
68.6
|
1.0
|
C5'
|
D:GDP501
|
4.1
|
64.7
|
1.0
|
O5'
|
D:GDP501
|
4.3
|
55.7
|
1.0
|
O2A
|
D:GDP501
|
4.3
|
50.3
|
1.0
|
O3A
|
D:GDP501
|
4.5
|
73.1
|
1.0
|
ND2
|
D:ASN101
|
4.5
|
68.5
|
1.0
|
CG
|
D:ASN101
|
4.5
|
68.0
|
1.0
|
O1B
|
D:GDP501
|
4.7
|
42.0
|
1.0
|
CB
|
D:GLN11
|
4.8
|
61.8
|
1.0
|
NE2
|
D:GLN11
|
4.9
|
59.7
|
1.0
|
|
Magnesium binding site 5 out
of 5 in 7z7d
Go back to
Magnesium Binding Sites List in 7z7d
Magnesium binding site 5 out
of 5 in the Tubulin-Todalam-Vinblastine-Complex
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 5 of Tubulin-Todalam-Vinblastine-Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Mg402
b:70.3
occ:1.00
|
O
|
F:HOH503
|
2.2
|
70.3
|
1.0
|
O3G
|
F:ACP401
|
2.3
|
89.7
|
1.0
|
OE2
|
F:GLU331
|
2.4
|
94.9
|
1.0
|
ND2
|
F:ASN333
|
2.8
|
83.3
|
1.0
|
O1B
|
F:ACP401
|
2.9
|
91.8
|
1.0
|
CD
|
F:GLU331
|
3.3
|
82.2
|
1.0
|
OE1
|
F:GLU331
|
3.5
|
78.8
|
1.0
|
PG
|
F:ACP401
|
3.6
|
106.3
|
1.0
|
PB
|
F:ACP401
|
3.8
|
89.4
|
1.0
|
O2B
|
F:ACP401
|
3.8
|
112.7
|
1.0
|
CG
|
F:ASN333
|
3.9
|
73.8
|
1.0
|
O2G
|
F:ACP401
|
3.9
|
88.7
|
1.0
|
C3B
|
F:ACP401
|
4.3
|
93.2
|
1.0
|
OD1
|
F:ASN333
|
4.3
|
79.3
|
1.0
|
NZ
|
F:LYS74
|
4.3
|
78.7
|
1.0
|
CG
|
F:GLU331
|
4.7
|
68.2
|
1.0
|
O1G
|
F:ACP401
|
4.8
|
80.0
|
1.0
|
|
Reference:
T.Muhlethaler,
L.Milanos,
J.A.Ortega,
T.B.Blum,
D.Gioia,
B.Roy,
A.E.Prota,
A.Cavalli,
M.O.Steinmetz.
Rational Design of A Novel Tubulin Inhibitor with A Unique Mechanism of Action. Angew.Chem.Int.Ed.Engl. V. 61 04052 2022.
ISSN: ESSN 1521-3773
PubMed: 35404502
DOI: 10.1002/ANIE.202204052
Page generated: Thu Oct 3 16:17:02 2024
|