Magnesium in PDB 5xp3: Crystal Structure of Apo T2R-Ttl
Protein crystallography data
The structure of Crystal Structure of Apo T2R-Ttl, PDB code: 5xp3
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 /
2.30
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
105.168,
157.964,
181.408,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
18.9 /
24
|
Other elements in 5xp3:
The structure of Crystal Structure of Apo T2R-Ttl also contains other interesting chemical elements:
Magnesium Binding Sites:
The binding sites of Magnesium atom in the Crystal Structure of Apo T2R-Ttl
(pdb code 5xp3). 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 Apo T2R-Ttl, PDB code: 5xp3:
Jump to Magnesium binding site number:
1;
2;
3;
4;
Magnesium binding site 1 out
of 4 in 5xp3
Go back to
Magnesium Binding Sites List in 5xp3
Magnesium binding site 1 out
of 4 in the Crystal Structure of Apo T2R-Ttl
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 Apo T2R-Ttl within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg502
b:42.2
occ:1.00
|
O1G
|
A:GTP501
|
2.0
|
39.9
|
1.0
|
O
|
A:HOH630
|
2.0
|
37.7
|
1.0
|
O
|
A:HOH642
|
2.1
|
33.0
|
1.0
|
O
|
A:HOH608
|
2.1
|
40.6
|
1.0
|
O
|
A:HOH604
|
2.2
|
42.3
|
1.0
|
O1B
|
A:GTP501
|
2.2
|
39.8
|
1.0
|
PG
|
A:GTP501
|
3.1
|
42.0
|
1.0
|
PB
|
A:GTP501
|
3.3
|
37.8
|
1.0
|
O2G
|
A:GTP501
|
3.4
|
43.7
|
1.0
|
O3B
|
A:GTP501
|
3.5
|
45.1
|
1.0
|
NZ
|
B:LYS252
|
3.8
|
52.1
|
1.0
|
O3A
|
A:GTP501
|
3.9
|
40.7
|
1.0
|
OE2
|
A:GLU71
|
4.1
|
78.5
|
1.0
|
OD1
|
A:ASP69
|
4.2
|
44.7
|
1.0
|
OD2
|
A:ASP98
|
4.2
|
46.5
|
1.0
|
OD2
|
A:ASP69
|
4.3
|
47.3
|
1.0
|
CB
|
A:GLN11
|
4.4
|
40.0
|
1.0
|
O3G
|
A:GTP501
|
4.4
|
40.5
|
1.0
|
CB
|
A:ASP98
|
4.4
|
45.8
|
1.0
|
N
|
A:GLN11
|
4.5
|
40.2
|
1.0
|
O1A
|
A:GTP501
|
4.5
|
39.9
|
1.0
|
O2B
|
A:GTP501
|
4.6
|
44.2
|
1.0
|
CG
|
A:ASP98
|
4.6
|
47.2
|
1.0
|
CG
|
A:ASP69
|
4.7
|
47.7
|
1.0
|
PA
|
A:GTP501
|
4.8
|
38.0
|
1.0
|
CD
|
A:GLU71
|
4.9
|
72.0
|
1.0
|
CE
|
B:LYS252
|
4.9
|
49.5
|
1.0
|
O
|
B:HOH610
|
5.0
|
50.3
|
1.0
|
|
Magnesium binding site 2 out
of 4 in 5xp3
Go back to
Magnesium Binding Sites List in 5xp3
Magnesium binding site 2 out
of 4 in the Crystal Structure of Apo T2R-Ttl
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 Apo T2R-Ttl within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg502
b:37.5
occ:1.00
|
O
|
B:HOH627
|
2.0
|
53.2
|
1.0
|
OE1
|
B:GLN11
|
2.1
|
47.9
|
1.0
|
O1A
|
B:GDP501
|
2.2
|
39.7
|
1.0
|
O
|
C:HOH678
|
2.3
|
47.9
|
1.0
|
O
|
B:HOH652
|
2.5
|
49.1
|
1.0
|
O
|
B:HOH606
|
2.6
|
52.1
|
1.0
|
CD
|
B:GLN11
|
3.4
|
52.7
|
1.0
|
O
|
B:HOH665
|
3.6
|
62.4
|
1.0
|
PA
|
B:GDP501
|
3.6
|
34.8
|
1.0
|
OD2
|
B:ASP177
|
3.8
|
54.1
|
1.0
|
O3A
|
B:GDP501
|
3.8
|
36.4
|
1.0
|
CB
|
B:GLN11
|
4.2
|
39.6
|
1.0
|
CG
|
B:GLN11
|
4.2
|
48.6
|
1.0
|
NE2
|
B:GLN11
|
4.3
|
49.0
|
1.0
|
C5'
|
B:GDP501
|
4.4
|
35.6
|
1.0
|
O5'
|
B:GDP501
|
4.4
|
36.1
|
1.0
|
OD1
|
B:ASN99
|
4.4
|
42.5
|
1.0
|
O
|
B:HOH663
|
4.6
|
61.8
|
1.0
|
CG
|
B:ASP177
|
4.7
|
53.5
|
1.0
|
OE1
|
C:GLU254
|
4.7
|
58.1
|
1.0
|
O2A
|
B:GDP501
|
4.8
|
36.5
|
1.0
|
C8
|
B:GDP501
|
4.8
|
39.0
|
1.0
|
O1B
|
B:GDP501
|
4.8
|
30.2
|
1.0
|
PB
|
B:GDP501
|
5.0
|
34.5
|
1.0
|
|
Magnesium binding site 3 out
of 4 in 5xp3
Go back to
Magnesium Binding Sites List in 5xp3
Magnesium binding site 3 out
of 4 in the Crystal Structure of Apo T2R-Ttl
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 Apo T2R-Ttl within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mg502
b:36.7
occ:1.00
|
O1G
|
C:GTP501
|
2.0
|
36.0
|
1.0
|
O
|
C:HOH603
|
2.0
|
35.5
|
1.0
|
O
|
C:HOH611
|
2.1
|
40.4
|
1.0
|
O
|
C:HOH665
|
2.1
|
36.3
|
1.0
|
O1B
|
C:GTP501
|
2.1
|
34.8
|
1.0
|
O
|
C:HOH651
|
2.1
|
33.0
|
1.0
|
PG
|
C:GTP501
|
3.2
|
38.3
|
1.0
|
PB
|
C:GTP501
|
3.3
|
33.6
|
1.0
|
O3B
|
C:GTP501
|
3.6
|
38.1
|
1.0
|
O2G
|
C:GTP501
|
3.7
|
38.4
|
1.0
|
O3A
|
C:GTP501
|
3.8
|
34.9
|
1.0
|
NZ
|
D:LYS252
|
3.9
|
41.8
|
1.0
|
OD1
|
C:ASP69
|
4.1
|
37.2
|
1.0
|
OE1
|
C:GLU71
|
4.1
|
59.3
|
1.0
|
OD2
|
C:ASP69
|
4.1
|
34.0
|
1.0
|
CB
|
C:GLN11
|
4.2
|
34.5
|
1.0
|
OD2
|
C:ASP98
|
4.2
|
45.8
|
1.0
|
N
|
C:GLN11
|
4.4
|
32.4
|
1.0
|
O1A
|
C:GTP501
|
4.5
|
38.8
|
1.0
|
O3G
|
C:GTP501
|
4.5
|
32.8
|
1.0
|
CB
|
C:ASP98
|
4.5
|
42.5
|
1.0
|
CG
|
C:ASP69
|
4.5
|
37.5
|
1.0
|
O2B
|
C:GTP501
|
4.6
|
36.0
|
1.0
|
PA
|
C:GTP501
|
4.7
|
36.4
|
1.0
|
NE2
|
C:GLN11
|
4.7
|
43.6
|
1.0
|
CG
|
C:ASP98
|
4.7
|
42.5
|
1.0
|
CA
|
C:GLN11
|
4.9
|
35.3
|
1.0
|
CB
|
C:GLU71
|
4.9
|
52.9
|
1.0
|
|
Magnesium binding site 4 out
of 4 in 5xp3
Go back to
Magnesium Binding Sites List in 5xp3
Magnesium binding site 4 out
of 4 in the Crystal Structure of Apo T2R-Ttl
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 Apo T2R-Ttl within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Mg502
b:69.7
occ:1.00
|
O1G
|
D:GTP501
|
2.2
|
77.9
|
1.0
|
O1B
|
D:GTP501
|
2.7
|
65.1
|
1.0
|
PG
|
D:GTP501
|
3.5
|
88.0
|
1.0
|
CB
|
D:GLN11
|
3.6
|
68.2
|
1.0
|
PB
|
D:GTP501
|
3.7
|
61.6
|
1.0
|
O3G
|
D:GTP501
|
4.0
|
79.3
|
1.0
|
O3A
|
D:GTP501
|
4.0
|
61.7
|
1.0
|
O3B
|
D:GTP501
|
4.0
|
74.9
|
1.0
|
O1A
|
D:GTP501
|
4.1
|
63.3
|
1.0
|
CD
|
D:GLN11
|
4.2
|
85.3
|
1.0
|
NE2
|
D:GLN11
|
4.3
|
84.7
|
1.0
|
O
|
D:HOH607
|
4.3
|
55.9
|
1.0
|
OE1
|
D:GLN11
|
4.4
|
84.3
|
1.0
|
N
|
D:GLN11
|
4.4
|
61.4
|
1.0
|
CG
|
D:GLN11
|
4.5
|
76.1
|
1.0
|
PA
|
D:GTP501
|
4.6
|
59.5
|
1.0
|
CA
|
D:GLN11
|
4.6
|
61.8
|
1.0
|
O2G
|
D:GTP501
|
4.7
|
74.9
|
1.0
|
OD2
|
D:ASP67
|
4.8
|
64.1
|
1.0
|
CB
|
D:GLU69
|
4.8
|
82.1
|
1.0
|
CG
|
D:GLU69
|
5.0
|
98.8
|
1.0
|
|
Reference:
Y.Jianhong,
Y.Wei,
Y.Yamei,
W.Yuxi,
Y.Tao,
X.Linlin,
Y.Xue,
L.Caofeng,
L.Zuowei,
C.Xiaoxin,
H.Mengshi,
Z.Li,
Q.Qiang,
P.Heying,
L.Dan,
W.Fang,
B.Peng,
W.Jiaolin,
Y.Haoyu,
C.Lijuan.
The Compound Millepachine and Its Derivatives Inhibit Tubulin Polymerization By Irreversibly Binding to the Colchicine-Binding Site in Beta-Tubulin. J. Biol. Chem. 2018.
ISSN: ESSN 1083-351X
PubMed: 29691282
DOI: 10.1074/JBC.RA117.001658
Page generated: Mon Sep 30 09:38:00 2024
|