Magnesium in PDB 6eg5: The Structure of Sb-1-202-Tubulin Complex
Protein crystallography data
The structure of The Structure of Sb-1-202-Tubulin Complex, PDB code: 6eg5
was solved by
A.K.Banerjee,
Y.Wang,
H.Chen,
D.Miller,
W.Li,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
50.00 /
2.45
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
105.541,
158.033,
181.870,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
19.6 /
23.6
|
Other elements in 6eg5:
The structure of The Structure of Sb-1-202-Tubulin Complex also contains other interesting chemical elements:
Magnesium Binding Sites:
The binding sites of Magnesium atom in the The Structure of Sb-1-202-Tubulin Complex
(pdb code 6eg5). This binding sites where shown within
5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the
The Structure of Sb-1-202-Tubulin Complex, PDB code: 6eg5:
Jump to Magnesium binding site number:
1;
2;
3;
4;
5;
6;
Magnesium binding site 1 out
of 6 in 6eg5
Go back to
Magnesium Binding Sites List in 6eg5
Magnesium binding site 1 out
of 6 in the The Structure of Sb-1-202-Tubulin Complex
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 1 of The Structure of Sb-1-202-Tubulin Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg502
b:28.5
occ:1.00
|
O1G
|
A:GTP501
|
1.9
|
20.8
|
1.0
|
O
|
A:HOH677
|
2.0
|
31.6
|
1.0
|
O
|
A:HOH668
|
2.1
|
20.1
|
1.0
|
O1B
|
A:GTP501
|
2.1
|
19.7
|
1.0
|
O
|
A:HOH625
|
2.1
|
23.9
|
1.0
|
O
|
A:HOH713
|
2.2
|
23.8
|
1.0
|
PG
|
A:GTP501
|
3.1
|
22.7
|
1.0
|
PB
|
A:GTP501
|
3.2
|
20.7
|
1.0
|
O3B
|
A:GTP501
|
3.4
|
22.9
|
1.0
|
O2G
|
A:GTP501
|
3.6
|
22.6
|
1.0
|
O3A
|
A:GTP501
|
3.8
|
22.4
|
1.0
|
NZ
|
B:LYS252
|
4.0
|
39.0
|
1.0
|
OD1
|
A:ASP69
|
4.2
|
27.8
|
1.0
|
OD2
|
A:ASP98
|
4.2
|
32.7
|
1.0
|
CB
|
A:GLN11
|
4.3
|
25.6
|
1.0
|
O
|
B:HOH611
|
4.3
|
34.2
|
1.0
|
OD2
|
A:ASP69
|
4.3
|
29.8
|
1.0
|
CG
|
A:GLU71
|
4.4
|
48.1
|
1.0
|
N
|
A:GLN11
|
4.4
|
26.8
|
1.0
|
O3G
|
A:GTP501
|
4.4
|
20.9
|
1.0
|
CB
|
A:ASP98
|
4.4
|
33.3
|
1.0
|
OE2
|
A:GLU71
|
4.5
|
49.7
|
1.0
|
O1A
|
A:GTP501
|
4.5
|
21.7
|
1.0
|
O2B
|
A:GTP501
|
4.5
|
23.5
|
1.0
|
CD
|
A:GLU71
|
4.6
|
51.6
|
1.0
|
CG
|
A:ASP98
|
4.6
|
33.7
|
1.0
|
CG
|
A:ASP69
|
4.7
|
29.6
|
1.0
|
PA
|
A:GTP501
|
4.8
|
22.1
|
1.0
|
OE1
|
A:GLN11
|
4.8
|
26.6
|
1.0
|
CA
|
A:GLN11
|
4.9
|
26.4
|
1.0
|
|
Magnesium binding site 2 out
of 6 in 6eg5
Go back to
Magnesium Binding Sites List in 6eg5
Magnesium binding site 2 out
of 6 in the The Structure of Sb-1-202-Tubulin Complex
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 2 of The Structure of Sb-1-202-Tubulin Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg502
b:27.0
occ:1.00
|
O
|
B:HOH671
|
1.9
|
36.6
|
1.0
|
OE1
|
B:GLN11
|
2.1
|
36.8
|
1.0
|
O1A
|
B:GDP501
|
2.3
|
20.2
|
1.0
|
O
|
C:HOH784
|
2.3
|
31.7
|
1.0
|
O
|
B:HOH623
|
2.6
|
37.6
|
1.0
|
O
|
B:HOH684
|
2.6
|
32.4
|
1.0
|
CD
|
B:GLN11
|
3.4
|
36.5
|
1.0
|
OD2
|
B:ASP177
|
3.5
|
38.2
|
1.0
|
PA
|
B:GDP501
|
3.6
|
19.4
|
1.0
|
O3A
|
B:GDP501
|
4.0
|
18.4
|
1.0
|
CB
|
B:GLN11
|
4.2
|
30.5
|
1.0
|
O
|
C:HOH646
|
4.2
|
41.4
|
1.0
|
CG
|
B:GLN11
|
4.3
|
33.9
|
1.0
|
C5'
|
B:GDP501
|
4.3
|
20.1
|
1.0
|
NE2
|
B:GLN11
|
4.3
|
37.1
|
1.0
|
OD1
|
B:ASN99
|
4.4
|
26.2
|
1.0
|
O5'
|
B:GDP501
|
4.4
|
18.3
|
1.0
|
CG
|
B:ASP177
|
4.5
|
35.4
|
1.0
|
O1B
|
B:GDP501
|
4.7
|
18.2
|
1.0
|
O2A
|
B:GDP501
|
4.8
|
18.7
|
1.0
|
OE1
|
C:GLU254
|
4.8
|
35.1
|
1.0
|
C8
|
B:GDP501
|
4.9
|
22.9
|
1.0
|
|
Magnesium binding site 3 out
of 6 in 6eg5
Go back to
Magnesium Binding Sites List in 6eg5
Magnesium binding site 3 out
of 6 in the The Structure of Sb-1-202-Tubulin Complex
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 3 of The Structure of Sb-1-202-Tubulin Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mg502
b:25.8
occ:1.00
|
O1G
|
C:GTP501
|
1.9
|
19.1
|
1.0
|
O
|
C:HOH662
|
1.9
|
20.5
|
1.0
|
O1B
|
C:GTP501
|
2.0
|
18.8
|
1.0
|
O
|
C:HOH660
|
2.0
|
12.9
|
1.0
|
O
|
C:HOH682
|
2.1
|
19.4
|
1.0
|
O
|
C:HOH731
|
2.1
|
18.2
|
1.0
|
PG
|
C:GTP501
|
3.1
|
20.2
|
1.0
|
PB
|
C:GTP501
|
3.1
|
18.2
|
1.0
|
O3B
|
C:GTP501
|
3.4
|
19.4
|
1.0
|
O2G
|
C:GTP501
|
3.7
|
20.1
|
1.0
|
O3A
|
C:GTP501
|
3.7
|
19.9
|
1.0
|
O
|
D:HOH705
|
3.7
|
25.8
|
1.0
|
OE1
|
C:GLU71
|
4.0
|
36.4
|
1.0
|
OD1
|
C:ASP69
|
4.2
|
20.7
|
1.0
|
OD2
|
C:ASP98
|
4.2
|
27.1
|
1.0
|
CB
|
C:GLN11
|
4.2
|
20.8
|
1.0
|
OD2
|
C:ASP69
|
4.3
|
21.6
|
1.0
|
O3G
|
C:GTP501
|
4.4
|
18.3
|
1.0
|
O1A
|
C:GTP501
|
4.4
|
20.5
|
1.0
|
N
|
C:GLN11
|
4.4
|
20.2
|
1.0
|
CB
|
C:ASP98
|
4.4
|
27.6
|
1.0
|
O2B
|
C:GTP501
|
4.4
|
18.6
|
1.0
|
NZ
|
D:LYS252
|
4.6
|
42.4
|
1.0
|
PA
|
C:GTP501
|
4.7
|
21.1
|
1.0
|
CG
|
C:ASP69
|
4.7
|
22.3
|
1.0
|
CG
|
C:ASP98
|
4.7
|
27.1
|
1.0
|
OE1
|
C:GLN11
|
4.8
|
24.1
|
1.0
|
CA
|
C:GLN11
|
4.9
|
20.5
|
1.0
|
OG1
|
C:THR145
|
5.0
|
20.7
|
1.0
|
|
Magnesium binding site 4 out
of 6 in 6eg5
Go back to
Magnesium Binding Sites List in 6eg5
Magnesium binding site 4 out
of 6 in the The Structure of Sb-1-202-Tubulin Complex
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 4 of The Structure of Sb-1-202-Tubulin Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Mg602
b:64.0
occ:1.00
|
O3B
|
D:GTP601
|
2.4
|
69.2
|
1.0
|
O1G
|
D:GTP601
|
2.5
|
79.4
|
1.0
|
OE1
|
D:GLU69
|
2.9
|
1.0
|
1.0
|
PG
|
D:GTP601
|
3.1
|
76.5
|
1.0
|
CB
|
D:GLN11
|
3.5
|
57.4
|
1.0
|
PB
|
D:GTP601
|
3.6
|
56.2
|
1.0
|
O1B
|
D:GTP601
|
3.8
|
51.4
|
1.0
|
CD
|
D:GLU69
|
3.8
|
96.3
|
1.0
|
O3A
|
D:GTP601
|
3.9
|
56.2
|
1.0
|
OE1
|
D:GLN11
|
3.9
|
67.1
|
1.0
|
O3G
|
D:GTP601
|
4.1
|
72.3
|
1.0
|
O2G
|
D:GTP601
|
4.2
|
71.2
|
1.0
|
CD
|
D:GLN11
|
4.2
|
64.5
|
1.0
|
N
|
D:GLN11
|
4.3
|
48.9
|
1.0
|
CG
|
D:GLU69
|
4.3
|
92.6
|
1.0
|
CA
|
D:GLN11
|
4.4
|
53.5
|
1.0
|
CG
|
D:GLN11
|
4.5
|
60.8
|
1.0
|
O1A
|
D:GTP601
|
4.5
|
47.8
|
1.0
|
OD2
|
D:ASP67
|
4.6
|
52.5
|
1.0
|
OG1
|
D:THR72
|
4.7
|
0.9
|
1.0
|
OD1
|
D:ASP67
|
4.8
|
49.5
|
1.0
|
OE2
|
D:GLU69
|
4.8
|
95.1
|
1.0
|
O2B
|
D:GTP601
|
4.8
|
56.3
|
1.0
|
PA
|
D:GTP601
|
4.9
|
50.2
|
1.0
|
NE2
|
D:GLN11
|
5.0
|
67.0
|
1.0
|
|
Magnesium binding site 5 out
of 6 in 6eg5
Go back to
Magnesium Binding Sites List in 6eg5
Magnesium binding site 5 out
of 6 in the The Structure of Sb-1-202-Tubulin Complex
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 5 of The Structure of Sb-1-202-Tubulin Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Mg701
b:72.3
occ:1.00
|
O3G
|
F:ACP703
|
2.1
|
0.8
|
1.0
|
OD2
|
F:ASP318
|
2.5
|
49.7
|
1.0
|
O3A
|
F:ACP703
|
3.0
|
0.4
|
1.0
|
OE1
|
F:GLU331
|
3.2
|
82.8
|
1.0
|
CG
|
F:ASP318
|
3.4
|
43.8
|
1.0
|
O2A
|
F:ACP703
|
3.4
|
92.9
|
1.0
|
C5'
|
F:ACP703
|
3.4
|
97.5
|
1.0
|
PG
|
F:ACP703
|
3.5
|
0.1
|
1.0
|
CB
|
F:ASP318
|
3.7
|
41.6
|
1.0
|
PA
|
F:ACP703
|
3.7
|
0.4
|
1.0
|
OD2
|
F:ASP200
|
4.1
|
72.0
|
1.0
|
O5'
|
F:ACP703
|
4.1
|
0.8
|
1.0
|
NH2
|
F:ARG222
|
4.2
|
0.9
|
1.0
|
PB
|
F:ACP703
|
4.2
|
0.7
|
1.0
|
O2G
|
F:ACP703
|
4.3
|
99.4
|
1.0
|
CB
|
F:GLU331
|
4.3
|
64.8
|
1.0
|
C3B
|
F:ACP703
|
4.3
|
0.7
|
1.0
|
CD
|
F:GLU331
|
4.4
|
80.5
|
1.0
|
OD1
|
F:ASP318
|
4.4
|
44.5
|
1.0
|
O1G
|
F:ACP703
|
4.5
|
0.5
|
1.0
|
CG2
|
F:ILE330
|
4.6
|
64.1
|
1.0
|
OD1
|
F:ASN242
|
4.6
|
0.3
|
1.0
|
C3'
|
F:ACP703
|
4.6
|
89.0
|
1.0
|
C4'
|
F:ACP703
|
4.6
|
90.8
|
1.0
|
OD1
|
F:ASN333
|
4.9
|
59.9
|
1.0
|
O3'
|
F:ACP703
|
5.0
|
92.8
|
1.0
|
O1B
|
F:ACP703
|
5.0
|
0.2
|
1.0
|
CG
|
F:GLU331
|
5.0
|
72.2
|
1.0
|
|
Magnesium binding site 6 out
of 6 in 6eg5
Go back to
Magnesium Binding Sites List in 6eg5
Magnesium binding site 6 out
of 6 in the The Structure of Sb-1-202-Tubulin Complex
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 6 of The Structure of Sb-1-202-Tubulin Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Mg702
b:76.0
occ:1.00
|
OE2
|
F:GLU331
|
2.5
|
93.5
|
1.0
|
O1B
|
F:ACP703
|
3.0
|
0.2
|
1.0
|
O2G
|
F:ACP703
|
3.1
|
99.4
|
1.0
|
ND2
|
F:ASN333
|
3.4
|
62.8
|
1.0
|
CD
|
F:GLU331
|
3.5
|
80.5
|
1.0
|
OE1
|
F:GLU331
|
3.8
|
82.8
|
1.0
|
O
|
F:SER152
|
3.9
|
0.8
|
1.0
|
PB
|
F:ACP703
|
4.4
|
0.7
|
1.0
|
CB
|
F:ALA155
|
4.5
|
0.6
|
1.0
|
PG
|
F:ACP703
|
4.5
|
0.1
|
1.0
|
CG
|
F:GLU331
|
4.7
|
72.2
|
1.0
|
CG
|
F:ASN333
|
4.7
|
57.5
|
1.0
|
CE
|
F:LYS74
|
4.8
|
84.1
|
1.0
|
C3B
|
F:ACP703
|
4.8
|
0.7
|
1.0
|
O
|
F:HOH853
|
4.9
|
40.9
|
1.0
|
|
Reference:
H.Chen,
Y.Wang,
W.Li.
The Structure of Sb-1-202/Sb-2-204-Tubulin Complex To Be Published.
Page generated: Mon Sep 30 23:57:00 2024
|