Magnesium in PDB 5xke: Crystal Structure of T2R-Ttl-Demecolcine Complex
Protein crystallography data
The structure of Crystal Structure of T2R-Ttl-Demecolcine Complex, PDB code: 5xke
was solved by
Y.Wang,
J.Yang,
T.Wang,
L.Chen,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
50.00 /
2.60
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
105.405,
158.023,
182.429,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
22.1 /
26.4
|
Other elements in 5xke:
The structure of Crystal Structure of T2R-Ttl-Demecolcine Complex also contains other interesting chemical elements:
Magnesium Binding Sites:
The binding sites of Magnesium atom in the Crystal Structure of T2R-Ttl-Demecolcine Complex
(pdb code 5xke). This binding sites where shown within
5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the
Crystal Structure of T2R-Ttl-Demecolcine Complex, PDB code: 5xke:
Jump to Magnesium binding site number:
1;
2;
3;
4;
Magnesium binding site 1 out
of 4 in 5xke
Go back to
Magnesium Binding Sites List in 5xke
Magnesium binding site 1 out
of 4 in the Crystal Structure of T2R-Ttl-Demecolcine Complex
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 1 of Crystal Structure of T2R-Ttl-Demecolcine Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg502
b:33.2
occ:1.00
|
O
|
A:HOH613
|
2.0
|
43.4
|
1.0
|
O2G
|
A:GTP501
|
2.0
|
36.8
|
1.0
|
O
|
A:HOH619
|
2.2
|
51.8
|
1.0
|
O
|
A:HOH641
|
2.2
|
38.2
|
1.0
|
O1B
|
A:GTP501
|
2.2
|
35.5
|
1.0
|
O
|
A:HOH615
|
2.3
|
40.0
|
1.0
|
PG
|
A:GTP501
|
3.2
|
36.7
|
1.0
|
PB
|
A:GTP501
|
3.3
|
36.2
|
1.0
|
O3B
|
A:GTP501
|
3.6
|
37.7
|
1.0
|
O1G
|
A:GTP501
|
3.7
|
37.5
|
1.0
|
NZ
|
B:LYS252
|
3.9
|
50.5
|
1.0
|
O3A
|
A:GTP501
|
3.9
|
36.0
|
1.0
|
OD1
|
A:ASP69
|
4.2
|
50.0
|
1.0
|
CB
|
A:GLN11
|
4.2
|
40.5
|
1.0
|
OE1
|
A:GLU71
|
4.2
|
62.8
|
1.0
|
OD2
|
A:ASP69
|
4.4
|
49.6
|
1.0
|
CB
|
A:ASP98
|
4.5
|
53.1
|
1.0
|
O3G
|
A:GTP501
|
4.5
|
36.5
|
1.0
|
N
|
A:GLN11
|
4.5
|
42.2
|
1.0
|
OE1
|
A:GLN11
|
4.6
|
40.5
|
1.0
|
O
|
A:HOH639
|
4.6
|
43.5
|
1.0
|
O1A
|
A:GTP501
|
4.7
|
35.3
|
1.0
|
O2B
|
A:GTP501
|
4.7
|
37.3
|
1.0
|
OD2
|
A:ASP98
|
4.7
|
54.7
|
1.0
|
CD
|
A:GLU71
|
4.7
|
61.7
|
1.0
|
CG
|
A:ASP69
|
4.8
|
50.6
|
1.0
|
CG
|
A:ASP98
|
4.8
|
54.5
|
1.0
|
PA
|
A:GTP501
|
4.9
|
35.0
|
1.0
|
OG1
|
A:THR145
|
4.9
|
38.3
|
1.0
|
CA
|
A:GLN11
|
5.0
|
40.5
|
1.0
|
CE
|
B:LYS252
|
5.0
|
48.2
|
1.0
|
OE2
|
A:GLU71
|
5.0
|
64.6
|
1.0
|
|
Magnesium binding site 2 out
of 4 in 5xke
Go back to
Magnesium Binding Sites List in 5xke
Magnesium binding site 2 out
of 4 in the Crystal Structure of T2R-Ttl-Demecolcine Complex
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 2 of Crystal Structure of T2R-Ttl-Demecolcine Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg502
b:28.6
occ:1.00
|
O
|
B:HOH622
|
2.0
|
48.2
|
1.0
|
O1A
|
B:GDP501
|
2.1
|
31.3
|
1.0
|
O
|
C:HOH622
|
2.2
|
39.4
|
1.0
|
OE1
|
B:GLN11
|
2.4
|
44.4
|
1.0
|
O
|
B:HOH617
|
2.6
|
40.9
|
1.0
|
O
|
B:HOH637
|
2.6
|
35.0
|
1.0
|
O
|
B:HOH644
|
3.0
|
52.8
|
1.0
|
CD
|
B:GLN11
|
3.4
|
45.3
|
1.0
|
PA
|
B:GDP501
|
3.5
|
30.4
|
1.0
|
O3A
|
B:GDP501
|
3.9
|
30.8
|
1.0
|
OD2
|
B:ASP177
|
4.0
|
49.6
|
1.0
|
CB
|
B:GLN11
|
4.0
|
41.4
|
1.0
|
CG
|
B:GLN11
|
4.2
|
44.1
|
1.0
|
C5'
|
B:GDP501
|
4.4
|
32.3
|
1.0
|
O1B
|
B:GDP501
|
4.4
|
31.5
|
1.0
|
O5'
|
B:GDP501
|
4.4
|
30.8
|
1.0
|
OE1
|
C:GLU254
|
4.4
|
51.4
|
1.0
|
NE2
|
B:GLN11
|
4.4
|
46.5
|
1.0
|
OD1
|
B:ASN99
|
4.4
|
35.3
|
1.0
|
O2A
|
B:GDP501
|
4.6
|
30.8
|
1.0
|
CG
|
B:ASP177
|
4.8
|
48.9
|
1.0
|
C8
|
B:GDP501
|
4.8
|
36.5
|
1.0
|
PB
|
B:GDP501
|
4.9
|
31.4
|
1.0
|
|
Magnesium binding site 3 out
of 4 in 5xke
Go back to
Magnesium Binding Sites List in 5xke
Magnesium binding site 3 out
of 4 in the Crystal Structure of T2R-Ttl-Demecolcine Complex
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 3 of Crystal Structure of T2R-Ttl-Demecolcine Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mg502
b:34.9
occ:1.00
|
O1G
|
C:GTP501
|
2.0
|
33.3
|
1.0
|
O1B
|
C:GTP501
|
2.0
|
32.2
|
1.0
|
O
|
C:HOH612
|
2.1
|
26.0
|
1.0
|
O
|
C:HOH619
|
2.1
|
23.1
|
1.0
|
O
|
C:HOH651
|
2.1
|
40.2
|
1.0
|
O
|
C:HOH636
|
2.3
|
30.4
|
1.0
|
PG
|
C:GTP501
|
3.1
|
33.2
|
1.0
|
PB
|
C:GTP501
|
3.1
|
32.4
|
1.0
|
O3B
|
C:GTP501
|
3.4
|
33.0
|
1.0
|
O2G
|
C:GTP501
|
3.6
|
33.8
|
1.0
|
O3A
|
C:GTP501
|
3.7
|
33.0
|
1.0
|
NZ
|
D:LYS252
|
3.9
|
50.7
|
1.0
|
OD1
|
C:ASP69
|
4.1
|
39.1
|
1.0
|
OD2
|
C:ASP69
|
4.3
|
39.1
|
1.0
|
CB
|
C:GLN11
|
4.3
|
35.3
|
1.0
|
O3G
|
C:GTP501
|
4.4
|
32.8
|
1.0
|
OE1
|
C:GLU71
|
4.4
|
52.1
|
1.0
|
OD2
|
C:ASP98
|
4.5
|
49.4
|
1.0
|
CB
|
C:ASP98
|
4.5
|
47.5
|
1.0
|
N
|
C:GLN11
|
4.5
|
33.7
|
1.0
|
O2B
|
C:GTP501
|
4.5
|
32.6
|
1.0
|
O1A
|
C:GTP501
|
4.6
|
33.5
|
1.0
|
CG
|
C:ASP69
|
4.6
|
39.2
|
1.0
|
NE2
|
C:GLN11
|
4.7
|
38.9
|
1.0
|
PA
|
C:GTP501
|
4.7
|
33.1
|
1.0
|
OG1
|
C:THR145
|
4.8
|
37.9
|
1.0
|
CG
|
C:ASP98
|
4.8
|
48.6
|
1.0
|
CB
|
C:GLU71
|
4.8
|
48.9
|
1.0
|
ND2
|
D:ASN247
|
5.0
|
97.9
|
1.0
|
|
Magnesium binding site 4 out
of 4 in 5xke
Go back to
Magnesium Binding Sites List in 5xke
Magnesium binding site 4 out
of 4 in the Crystal Structure of T2R-Ttl-Demecolcine Complex
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 4 of Crystal Structure of T2R-Ttl-Demecolcine Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Mg502
b:77.3
occ:1.00
|
O1B
|
D:GTP501
|
2.9
|
74.3
|
1.0
|
O2G
|
D:GTP501
|
3.0
|
77.5
|
1.0
|
O1G
|
D:GTP501
|
3.1
|
77.5
|
1.0
|
OE1
|
D:GLU69
|
3.5
|
0.1
|
1.0
|
NE2
|
D:GLN11
|
3.6
|
82.1
|
1.0
|
PG
|
D:GTP501
|
3.6
|
79.6
|
1.0
|
CB
|
D:GLN11
|
3.6
|
79.1
|
1.0
|
PB
|
D:GTP501
|
4.2
|
73.4
|
1.0
|
OG1
|
D:THR72
|
4.3
|
0.3
|
1.0
|
OD2
|
D:ASP67
|
4.3
|
75.0
|
1.0
|
CG
|
D:GLN11
|
4.3
|
81.0
|
1.0
|
CG2
|
D:THR72
|
4.3
|
0.7
|
1.0
|
O3B
|
D:GTP501
|
4.4
|
76.8
|
1.0
|
N
|
D:GLN11
|
4.4
|
74.8
|
1.0
|
CD
|
D:GLN11
|
4.4
|
81.2
|
1.0
|
CD
|
D:GLU69
|
4.4
|
0.1
|
1.0
|
CA
|
D:GLN11
|
4.5
|
77.2
|
1.0
|
O1A
|
D:GTP501
|
4.6
|
73.0
|
1.0
|
OD1
|
D:ASP67
|
4.6
|
71.6
|
1.0
|
O3A
|
D:GTP501
|
4.7
|
72.8
|
1.0
|
CB
|
D:GLU69
|
4.8
|
0.1
|
1.0
|
CG
|
D:ASP67
|
4.9
|
73.6
|
1.0
|
O3G
|
D:GTP501
|
4.9
|
79.2
|
1.0
|
CB
|
D:THR72
|
5.0
|
0.8
|
1.0
|
|
Reference:
W.Yan,
J.Yang.
Identification of A Powerful and Reversible Microtubule-Inhibitor with Efficacy Against Multidrug-Resistant Tumors To Be Published.
Page generated: Mon Sep 30 09:31:21 2024
|