Magnesium in PDB 6ses: Tubulin-B2 Complex
Protein crystallography data
The structure of Tubulin-B2 Complex, PDB code: 6ses
was solved by
B.Guo,
A.Rodriguez-Gabin,
A.E.Prota,
T.Muehlethaler,
N.Zhang,
K.Ye,
M.O.Steinmetz,
S.Band Horwitz,
A.B.Smith Iii,
H.M.Mcdaid,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
49.40 /
2.00
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
104.050,
157.170,
178.420,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
n/a /
n/a
|
Magnesium Binding Sites:
The binding sites of Magnesium atom in the Tubulin-B2 Complex
(pdb code 6ses). 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-B2 Complex, PDB code: 6ses:
Jump to Magnesium binding site number:
1;
2;
3;
4;
5;
Magnesium binding site 1 out
of 5 in 6ses
Go back to
Magnesium Binding Sites List in 6ses
Magnesium binding site 1 out
of 5 in the Tubulin-B2 Complex
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 1 of Tubulin-B2 Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg502
b:37.5
occ:1.00
|
O
|
A:HOH614
|
1.9
|
37.5
|
1.0
|
O
|
A:HOH668
|
2.1
|
34.4
|
1.0
|
O
|
A:HOH630
|
2.2
|
37.6
|
1.0
|
O3G
|
A:GTP501
|
2.2
|
31.6
|
1.0
|
O
|
A:HOH612
|
2.2
|
35.9
|
1.0
|
O1B
|
A:GTP501
|
2.2
|
33.1
|
1.0
|
OE1
|
A:GLU71
|
3.3
|
64.8
|
1.0
|
PG
|
A:GTP501
|
3.4
|
39.6
|
1.0
|
PB
|
A:GTP501
|
3.4
|
33.6
|
1.0
|
O3B
|
A:GTP501
|
3.8
|
39.7
|
1.0
|
O3A
|
A:GTP501
|
3.8
|
39.0
|
1.0
|
O1G
|
A:GTP501
|
3.8
|
36.8
|
1.0
|
CB
|
A:GLN11
|
3.9
|
38.6
|
1.0
|
OD1
|
A:ASP69
|
3.9
|
46.9
|
1.0
|
OD2
|
A:ASP69
|
4.0
|
46.2
|
1.0
|
NZ
|
B:LYS254
|
4.0
|
47.6
|
1.0
|
N
|
A:GLN11
|
4.2
|
37.5
|
1.0
|
OD2
|
A:ASP98
|
4.4
|
45.8
|
1.0
|
CG
|
A:ASP69
|
4.4
|
48.4
|
1.0
|
OE1
|
A:GLN11
|
4.4
|
55.9
|
1.0
|
O1A
|
A:GTP501
|
4.5
|
37.4
|
1.0
|
CD
|
A:GLU71
|
4.5
|
76.8
|
1.0
|
CB
|
A:ASP98
|
4.6
|
38.9
|
1.0
|
CA
|
A:GLN11
|
4.6
|
38.6
|
1.0
|
O2G
|
A:GTP501
|
4.7
|
29.6
|
1.0
|
O2B
|
A:GTP501
|
4.7
|
36.5
|
1.0
|
PA
|
A:GTP501
|
4.8
|
39.1
|
1.0
|
CG
|
A:ASP98
|
4.9
|
42.9
|
1.0
|
CB
|
A:GLU71
|
4.9
|
66.8
|
1.0
|
|
Magnesium binding site 2 out
of 5 in 6ses
Go back to
Magnesium Binding Sites List in 6ses
Magnesium binding site 2 out
of 5 in the Tubulin-B2 Complex
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 2 of Tubulin-B2 Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg502
b:32.5
occ:1.00
|
O
|
B:HOH650
|
2.1
|
41.1
|
1.0
|
O1A
|
B:GDP501
|
2.2
|
39.4
|
1.0
|
OE1
|
B:GLN11
|
2.3
|
48.9
|
1.0
|
O
|
B:HOH709
|
2.3
|
44.9
|
1.0
|
O
|
C:HOH662
|
2.4
|
52.7
|
1.0
|
O
|
B:HOH603
|
2.6
|
48.0
|
1.0
|
O
|
B:HOH693
|
2.8
|
76.1
|
1.0
|
CD
|
B:GLN11
|
3.5
|
44.1
|
1.0
|
PA
|
B:GDP501
|
3.6
|
37.4
|
1.0
|
OD2
|
B:ASP179
|
3.9
|
64.5
|
1.0
|
O3A
|
B:GDP501
|
4.0
|
38.3
|
1.0
|
CB
|
B:GLN11
|
4.2
|
36.6
|
1.0
|
OD1
|
B:ASN101
|
4.3
|
41.5
|
1.0
|
CG
|
B:GLN11
|
4.3
|
38.3
|
1.0
|
OE1
|
C:GLU254
|
4.4
|
50.0
|
1.0
|
C5'
|
B:GDP501
|
4.4
|
42.4
|
1.0
|
O5'
|
B:GDP501
|
4.4
|
33.0
|
1.0
|
NE2
|
B:GLN11
|
4.5
|
45.7
|
1.0
|
O
|
B:HOH737
|
4.6
|
70.8
|
1.0
|
O1B
|
B:GDP501
|
4.6
|
26.6
|
1.0
|
O2A
|
B:GDP501
|
4.6
|
35.7
|
1.0
|
C8
|
B:GDP501
|
4.8
|
41.2
|
1.0
|
PB
|
B:GDP501
|
4.9
|
37.1
|
1.0
|
CG
|
B:ASP179
|
4.9
|
62.6
|
1.0
|
ND2
|
B:ASN101
|
5.0
|
42.3
|
1.0
|
|
Magnesium binding site 3 out
of 5 in 6ses
Go back to
Magnesium Binding Sites List in 6ses
Magnesium binding site 3 out
of 5 in the Tubulin-B2 Complex
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 3 of Tubulin-B2 Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mg502
b:32.8
occ:1.00
|
O1G
|
C:GTP501
|
2.2
|
33.4
|
1.0
|
O
|
C:HOH679
|
2.2
|
31.8
|
1.0
|
O
|
C:HOH667
|
2.2
|
31.0
|
1.0
|
O
|
C:HOH779
|
2.2
|
30.5
|
1.0
|
O
|
C:HOH723
|
2.2
|
36.0
|
1.0
|
O1B
|
C:GTP501
|
2.3
|
33.4
|
1.0
|
PG
|
C:GTP501
|
3.2
|
38.3
|
1.0
|
PB
|
C:GTP501
|
3.3
|
39.3
|
1.0
|
O2G
|
C:GTP501
|
3.5
|
31.9
|
1.0
|
O3B
|
C:GTP501
|
3.5
|
39.9
|
1.0
|
NZ
|
D:LYS254
|
3.9
|
42.5
|
1.0
|
O3A
|
C:GTP501
|
3.9
|
38.8
|
1.0
|
CG
|
C:GLU71
|
4.0
|
47.2
|
1.0
|
OD1
|
C:ASP69
|
4.0
|
41.0
|
1.0
|
OE2
|
C:GLU71
|
4.1
|
60.6
|
1.0
|
OD2
|
C:ASP69
|
4.3
|
43.7
|
1.0
|
OD2
|
C:ASP98
|
4.3
|
45.3
|
1.0
|
CB
|
C:GLN11
|
4.3
|
27.1
|
1.0
|
O
|
C:HOH714
|
4.4
|
65.4
|
1.0
|
CB
|
C:ASP98
|
4.4
|
38.4
|
1.0
|
O3G
|
C:GTP501
|
4.5
|
33.0
|
1.0
|
N
|
C:GLN11
|
4.5
|
32.2
|
1.0
|
CD
|
C:GLU71
|
4.6
|
58.5
|
1.0
|
O2B
|
C:GTP501
|
4.6
|
37.2
|
1.0
|
CG
|
C:ASP69
|
4.6
|
37.5
|
1.0
|
O1A
|
C:GTP501
|
4.7
|
42.7
|
1.0
|
CG
|
C:ASP98
|
4.7
|
41.2
|
1.0
|
PA
|
C:GTP501
|
4.8
|
44.3
|
1.0
|
OE1
|
C:GLN11
|
5.0
|
47.8
|
1.0
|
|
Magnesium binding site 4 out
of 5 in 6ses
Go back to
Magnesium Binding Sites List in 6ses
Magnesium binding site 4 out
of 5 in the Tubulin-B2 Complex
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 4 of Tubulin-B2 Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Mg502
b:57.0
occ:1.00
|
O1A
|
D:GDP501
|
2.1
|
69.8
|
1.0
|
OE1
|
D:GLN11
|
2.4
|
59.1
|
1.0
|
O
|
D:HOH736
|
2.5
|
52.0
|
1.0
|
O
|
D:HOH684
|
2.7
|
49.3
|
1.0
|
O
|
D:HOH618
|
3.0
|
77.0
|
1.0
|
PA
|
D:GDP501
|
3.5
|
54.0
|
1.0
|
CD
|
D:GLN11
|
3.6
|
68.1
|
1.0
|
O
|
D:HOH770
|
3.7
|
52.6
|
1.0
|
C5'
|
D:GDP501
|
4.1
|
55.1
|
1.0
|
OD1
|
D:ASN101
|
4.1
|
76.2
|
1.0
|
O3A
|
D:GDP501
|
4.3
|
55.6
|
1.0
|
O5'
|
D:GDP501
|
4.3
|
59.4
|
1.0
|
NE2
|
D:GLN11
|
4.5
|
60.6
|
1.0
|
O2A
|
D:GDP501
|
4.5
|
49.6
|
1.0
|
CB
|
D:GLN11
|
4.5
|
54.5
|
1.0
|
CG
|
D:GLN11
|
4.6
|
63.8
|
1.0
|
O1B
|
D:GDP501
|
4.8
|
48.5
|
1.0
|
C8
|
D:GDP501
|
4.9
|
40.0
|
1.0
|
|
Magnesium binding site 5 out
of 5 in 6ses
Go back to
Magnesium Binding Sites List in 6ses
Magnesium binding site 5 out
of 5 in the Tubulin-B2 Complex
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 5 of Tubulin-B2 Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Mg402
b:76.0
occ:1.00
|
O1G
|
F:ACP401
|
2.4
|
0.5
|
1.0
|
OE1
|
F:GLU331
|
2.4
|
1.0
|
1.0
|
ND2
|
F:ASN333
|
2.6
|
0.6
|
1.0
|
O1B
|
F:ACP401
|
2.7
|
0.2
|
1.0
|
CD
|
F:GLU331
|
3.2
|
99.5
|
1.0
|
OE2
|
F:GLU331
|
3.3
|
0.6
|
1.0
|
PG
|
F:ACP401
|
3.6
|
1.0
|
1.0
|
O3G
|
F:ACP401
|
3.8
|
0.8
|
1.0
|
CG
|
F:ASN333
|
3.8
|
94.2
|
1.0
|
PB
|
F:ACP401
|
3.9
|
0.7
|
1.0
|
NZ
|
F:LYS74
|
4.3
|
0.3
|
1.0
|
OD1
|
F:ASN333
|
4.4
|
94.2
|
1.0
|
C3B
|
F:ACP401
|
4.4
|
0.3
|
1.0
|
CG
|
F:GLU331
|
4.5
|
81.3
|
1.0
|
O2B
|
F:ACP401
|
4.5
|
0.9
|
1.0
|
O
|
F:HOH566
|
4.6
|
77.1
|
1.0
|
O2G
|
F:ACP401
|
4.8
|
0.4
|
1.0
|
CB
|
F:ASN333
|
5.0
|
74.5
|
1.0
|
|
Reference:
B.Guo,
A.Rodriguez-Gabin,
A.E.Prota,
T.Muhlethaler,
N.Zhang,
K.Ye,
M.O.Steinmetz,
S.B.Horwitz,
A.B.Smith 3Rd,
H.M.Mcdaid.
Structural Refinement of the Tubulin Ligand (+)-Discodermolide to Attenuate Chemotherapy-Mediated Senescence. Mol.Pharmacol. V. 98 156 2020.
ISSN: ESSN 1521-0111
PubMed: 32591477
DOI: 10.1124/MOL.119.117457
Page generated: Tue Oct 1 17:53:57 2024
|