Magnesium in PDB 8b7c: Tubulin-Maytansinoid-12 Complex
Protein crystallography data
The structure of Tubulin-Maytansinoid-12 Complex, PDB code: 8b7c
was solved by
Z.Boiarska,
H.Perez-Pena,
A.-C.Abel,
P.Marzullo,
B.Alvarez-Bernad,
F.Bonato,
B.Santini,
D.Horvath,
D.Lucena-Agell,
F.Vasile,
M.Sironi,
J.F.Diaz,
M.O.Steinmetz,
A.E.Prota,
S.Pieraccini,
D.Passarella,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
49.57 /
1.90
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
104.866,
157.939,
180.57,
90,
90,
90
|
R / Rfree (%)
|
18.3 /
21.2
|
Other elements in 8b7c:
The structure of Tubulin-Maytansinoid-12 Complex also contains other interesting chemical elements:
Magnesium Binding Sites:
The binding sites of Magnesium atom in the Tubulin-Maytansinoid-12 Complex
(pdb code 8b7c). 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-Maytansinoid-12 Complex, PDB code: 8b7c:
Jump to Magnesium binding site number:
1;
2;
3;
4;
5;
Magnesium binding site 1 out
of 5 in 8b7c
Go back to
Magnesium Binding Sites List in 8b7c
Magnesium binding site 1 out
of 5 in the Tubulin-Maytansinoid-12 Complex
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 1 of Tubulin-Maytansinoid-12 Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg502
b:34.0
occ:1.00
|
O
|
A:HOH640
|
2.0
|
31.7
|
1.0
|
O
|
A:HOH729
|
2.1
|
31.1
|
1.0
|
O1G
|
A:GTP501
|
2.1
|
29.5
|
1.0
|
O
|
A:HOH614
|
2.1
|
35.8
|
1.0
|
O
|
A:HOH645
|
2.1
|
32.9
|
1.0
|
O1B
|
A:GTP501
|
2.1
|
27.9
|
1.0
|
PG
|
A:GTP501
|
3.2
|
34.4
|
1.0
|
PB
|
A:GTP501
|
3.3
|
31.5
|
1.0
|
O3B
|
A:GTP501
|
3.6
|
38.6
|
1.0
|
O2G
|
A:GTP501
|
3.7
|
33.5
|
1.0
|
OE1
|
A:GLU71
|
3.7
|
68.5
|
1.0
|
O3A
|
A:GTP501
|
3.8
|
36.9
|
1.0
|
NZ
|
B:LYS254
|
3.8
|
39.0
|
1.0
|
OD1
|
A:ASP69
|
4.0
|
37.2
|
1.0
|
CB
|
A:GLN11
|
4.2
|
30.9
|
1.0
|
OD2
|
A:ASP69
|
4.2
|
40.4
|
1.0
|
OD2
|
A:ASP98
|
4.3
|
41.3
|
1.0
|
CB
|
A:ASP98
|
4.4
|
35.6
|
1.0
|
N
|
A:GLN11
|
4.4
|
29.9
|
1.0
|
O
|
A:HOH710
|
4.4
|
54.0
|
1.0
|
O3G
|
A:GTP501
|
4.5
|
31.2
|
1.0
|
O2B
|
A:GTP501
|
4.6
|
35.9
|
1.0
|
CG
|
A:ASP69
|
4.6
|
41.8
|
1.0
|
O1A
|
A:GTP501
|
4.6
|
31.2
|
1.0
|
CG
|
A:ASP98
|
4.7
|
41.0
|
1.0
|
PA
|
A:GTP501
|
4.8
|
33.1
|
1.0
|
CA
|
A:GLN11
|
4.9
|
32.1
|
1.0
|
OE1
|
A:GLN11
|
4.9
|
43.8
|
1.0
|
CD
|
A:GLU71
|
4.9
|
76.8
|
1.0
|
CE
|
B:LYS254
|
4.9
|
37.5
|
1.0
|
CB
|
A:GLU71
|
5.0
|
70.1
|
1.0
|
|
Magnesium binding site 2 out
of 5 in 8b7c
Go back to
Magnesium Binding Sites List in 8b7c
Magnesium binding site 2 out
of 5 in the Tubulin-Maytansinoid-12 Complex
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 2 of Tubulin-Maytansinoid-12 Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg502
b:26.5
occ:1.00
|
O
|
B:HOH699
|
2.0
|
35.2
|
1.0
|
O
|
B:HOH730
|
2.1
|
54.4
|
1.0
|
OE1
|
B:GLN11
|
2.2
|
42.8
|
1.0
|
O1A
|
B:GDP501
|
2.3
|
31.9
|
1.0
|
O
|
C:HOH662
|
2.3
|
49.0
|
1.0
|
O
|
B:HOH622
|
2.4
|
41.5
|
1.0
|
CD
|
B:GLN11
|
3.4
|
48.4
|
1.0
|
O
|
B:HOH820
|
3.5
|
68.1
|
1.0
|
PA
|
B:GDP501
|
3.6
|
31.9
|
1.0
|
OD2
|
B:ASP179
|
3.9
|
39.2
|
1.0
|
O3A
|
B:GDP501
|
3.9
|
33.8
|
1.0
|
O
|
B:HOH614
|
4.1
|
84.7
|
1.0
|
CB
|
B:GLN11
|
4.1
|
33.2
|
1.0
|
CG
|
B:GLN11
|
4.2
|
40.7
|
1.0
|
O
|
B:HOH799
|
4.3
|
67.7
|
1.0
|
C5'
|
B:GDP501
|
4.3
|
32.3
|
1.0
|
NE2
|
B:GLN11
|
4.4
|
52.2
|
1.0
|
O5'
|
B:GDP501
|
4.4
|
33.0
|
1.0
|
OD1
|
B:ASN101
|
4.4
|
36.6
|
1.0
|
O
|
C:HOH637
|
4.5
|
55.9
|
1.0
|
OE1
|
C:GLU254
|
4.6
|
39.3
|
1.0
|
O1B
|
B:GDP501
|
4.7
|
27.1
|
1.0
|
O2A
|
B:GDP501
|
4.7
|
30.8
|
1.0
|
CG
|
B:ASP179
|
4.8
|
40.9
|
1.0
|
O
|
B:HOH768
|
4.8
|
69.1
|
1.0
|
C8
|
B:GDP501
|
4.8
|
39.2
|
1.0
|
PB
|
B:GDP501
|
4.9
|
31.8
|
1.0
|
|
Magnesium binding site 3 out
of 5 in 8b7c
Go back to
Magnesium Binding Sites List in 8b7c
Magnesium binding site 3 out
of 5 in the Tubulin-Maytansinoid-12 Complex
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 3 of Tubulin-Maytansinoid-12 Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mg502
b:29.7
occ:1.00
|
O
|
C:HOH760
|
2.0
|
28.3
|
1.0
|
O
|
C:HOH636
|
2.0
|
29.3
|
1.0
|
O1G
|
C:GTP501
|
2.0
|
27.5
|
1.0
|
O
|
C:HOH668
|
2.1
|
28.6
|
1.0
|
O1B
|
C:GTP501
|
2.1
|
28.9
|
1.0
|
O
|
C:HOH724
|
2.2
|
30.3
|
1.0
|
PG
|
C:GTP501
|
3.2
|
32.0
|
1.0
|
PB
|
C:GTP501
|
3.3
|
30.1
|
1.0
|
O3B
|
C:GTP501
|
3.6
|
33.0
|
1.0
|
O2G
|
C:GTP501
|
3.7
|
32.9
|
1.0
|
O3A
|
C:GTP501
|
3.8
|
33.6
|
1.0
|
OE2
|
C:GLU71
|
3.9
|
48.3
|
1.0
|
NZ
|
D:LYS254
|
3.9
|
34.0
|
1.0
|
OD1
|
C:ASP69
|
4.1
|
32.4
|
1.0
|
CG
|
C:GLU71
|
4.1
|
42.8
|
1.0
|
OD2
|
C:ASP69
|
4.1
|
33.2
|
1.0
|
CB
|
C:GLN11
|
4.2
|
27.6
|
1.0
|
OD2
|
C:ASP98
|
4.3
|
43.9
|
1.0
|
CB
|
C:ASP98
|
4.4
|
33.0
|
1.0
|
N
|
C:GLN11
|
4.4
|
25.9
|
1.0
|
CD
|
C:GLU71
|
4.5
|
48.2
|
1.0
|
O3G
|
C:GTP501
|
4.5
|
29.9
|
1.0
|
O2B
|
C:GTP501
|
4.5
|
31.4
|
1.0
|
CG
|
C:ASP69
|
4.5
|
32.7
|
1.0
|
O1A
|
C:GTP501
|
4.6
|
30.4
|
1.0
|
O
|
C:HOH634
|
4.6
|
45.5
|
1.0
|
CG
|
C:ASP98
|
4.7
|
38.1
|
1.0
|
PA
|
C:GTP501
|
4.8
|
30.6
|
1.0
|
NE2
|
C:GLN11
|
4.9
|
34.9
|
1.0
|
CA
|
C:GLN11
|
4.9
|
27.6
|
1.0
|
|
Magnesium binding site 4 out
of 5 in 8b7c
Go back to
Magnesium Binding Sites List in 8b7c
Magnesium binding site 4 out
of 5 in the Tubulin-Maytansinoid-12 Complex
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 4 of Tubulin-Maytansinoid-12 Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Mg502
b:61.2
occ:1.00
|
O
|
D:HOH618
|
2.0
|
54.3
|
1.0
|
O1A
|
D:GDP501
|
2.2
|
68.1
|
1.0
|
OE1
|
D:GLN11
|
2.2
|
77.6
|
1.0
|
O
|
D:HOH645
|
3.1
|
50.8
|
1.0
|
CD
|
D:GLN11
|
3.3
|
75.0
|
1.0
|
PA
|
D:GDP501
|
3.7
|
58.3
|
1.0
|
NE2
|
D:GLN11
|
4.2
|
72.6
|
1.0
|
CB
|
D:GLN11
|
4.2
|
55.2
|
1.0
|
CG
|
D:GLN11
|
4.2
|
66.9
|
1.0
|
C5'
|
D:GDP501
|
4.3
|
56.8
|
1.0
|
O
|
D:HOH718
|
4.4
|
62.4
|
1.0
|
O3A
|
D:GDP501
|
4.5
|
51.3
|
1.0
|
O5'
|
D:GDP501
|
4.5
|
58.0
|
1.0
|
O2A
|
D:GDP501
|
4.5
|
58.1
|
1.0
|
O1B
|
D:GDP501
|
4.7
|
44.8
|
1.0
|
C8
|
D:GDP501
|
4.9
|
44.2
|
1.0
|
|
Magnesium binding site 5 out
of 5 in 8b7c
Go back to
Magnesium Binding Sites List in 8b7c
Magnesium binding site 5 out
of 5 in the Tubulin-Maytansinoid-12 Complex
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 5 of Tubulin-Maytansinoid-12 Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Mg402
b:69.4
occ:1.00
|
OE2
|
F:GLU331
|
2.0
|
101.7
|
1.0
|
O3G
|
F:ACP401
|
2.1
|
80.0
|
1.0
|
O1B
|
F:ACP401
|
2.5
|
99.7
|
1.0
|
ND2
|
F:ASN333
|
3.0
|
100.1
|
1.0
|
CD
|
F:GLU331
|
3.2
|
90.7
|
1.0
|
PG
|
F:ACP401
|
3.3
|
98.4
|
1.0
|
PB
|
F:ACP401
|
3.7
|
93.9
|
1.0
|
C3B
|
F:ACP401
|
3.7
|
96.2
|
1.0
|
NZ
|
F:LYS74
|
3.7
|
79.9
|
1.0
|
O2G
|
F:ACP401
|
3.8
|
94.6
|
1.0
|
CG
|
F:ASN333
|
4.0
|
91.9
|
1.0
|
CG
|
F:GLU331
|
4.0
|
78.8
|
1.0
|
OE1
|
F:GLU331
|
4.1
|
97.2
|
1.0
|
OD1
|
F:ASN333
|
4.2
|
99.9
|
1.0
|
O2B
|
F:ACP401
|
4.5
|
99.8
|
1.0
|
O1G
|
F:ACP401
|
4.7
|
93.9
|
1.0
|
O3A
|
F:ACP401
|
4.9
|
90.3
|
1.0
|
|
Reference:
Z.Boiarska,
H.Perez-Pena,
A.C.Abel,
P.Marzullo,
B.Alvarez-Bernad,
F.Bonato,
B.Santini,
D.Horvath,
D.Lucena-Agell,
F.Vasile,
M.Sironi,
J.F.Diaz,
A.E.Prota,
S.Pieraccini,
D.Passarella.
Maytansinol Functionalization: Towards Useful Probes For Studying Microtubule Dynamics. Chemistry V. 29 03431 2023.
ISSN: ISSN 0947-6539
PubMed: 36468686
DOI: 10.1002/CHEM.202203431
Page generated: Thu Dec 28 08:07:25 2023
|