Magnesium in PDB 5s66: Tubulin-Z2856434929-Complex
Protein crystallography data
The structure of Tubulin-Z2856434929-Complex, PDB code: 5s66
was solved by
T.Muehlethaler,
D.Gioia,
A.E.Prota,
M.E.Sharpe,
A.Cavalli,
M.O.Steinmetz,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
68.00 /
2.10
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
104.69,
157.88,
178.85,
90,
90,
90
|
R / Rfree (%)
|
21.4 /
24.4
|
Magnesium Binding Sites:
The binding sites of Magnesium atom in the Tubulin-Z2856434929-Complex
(pdb code 5s66). 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-Z2856434929-Complex, PDB code: 5s66:
Jump to Magnesium binding site number:
1;
2;
3;
4;
5;
Magnesium binding site 1 out
of 5 in 5s66
Go back to
Magnesium Binding Sites List in 5s66
Magnesium binding site 1 out
of 5 in the Tubulin-Z2856434929-Complex
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 1 of Tubulin-Z2856434929-Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg502
b:45.1
occ:1.00
|
O
|
A:HOH625
|
2.0
|
46.2
|
1.0
|
O
|
A:HOH626
|
2.0
|
46.1
|
1.0
|
O1B
|
A:GTP501
|
2.0
|
43.9
|
1.0
|
O2G
|
A:GTP501
|
2.1
|
41.1
|
1.0
|
O
|
A:HOH638
|
2.1
|
44.3
|
1.0
|
O
|
A:HOH628
|
2.1
|
48.4
|
1.0
|
PB
|
A:GTP501
|
3.1
|
43.6
|
1.0
|
PG
|
A:GTP501
|
3.2
|
41.9
|
1.0
|
O3B
|
A:GTP501
|
3.5
|
48.2
|
1.0
|
O3A
|
A:GTP501
|
3.6
|
46.1
|
1.0
|
O3G
|
A:GTP501
|
3.6
|
46.2
|
1.0
|
NZ
|
B:LYS254
|
3.8
|
56.7
|
1.0
|
CB
|
A:GLN11
|
4.0
|
46.3
|
1.0
|
OE2
|
A:GLU71
|
4.0
|
59.8
|
1.0
|
OD1
|
A:ASP69
|
4.1
|
51.6
|
1.0
|
OD2
|
A:ASP69
|
4.2
|
52.8
|
1.0
|
OD2
|
A:ASP98
|
4.3
|
55.5
|
1.0
|
N
|
A:GLN11
|
4.3
|
45.5
|
1.0
|
O2A
|
A:GTP501
|
4.4
|
44.6
|
1.0
|
O2B
|
A:GTP501
|
4.4
|
45.1
|
1.0
|
CB
|
A:ASP98
|
4.5
|
52.1
|
1.0
|
O1G
|
A:GTP501
|
4.5
|
45.5
|
1.0
|
OE1
|
A:GLN11
|
4.6
|
52.7
|
1.0
|
PA
|
A:GTP501
|
4.6
|
43.3
|
1.0
|
CG
|
A:ASP69
|
4.6
|
53.8
|
1.0
|
CA
|
A:GLN11
|
4.7
|
48.2
|
1.0
|
CG
|
A:ASP98
|
4.8
|
54.4
|
1.0
|
CE
|
B:LYS254
|
4.8
|
54.5
|
1.0
|
|
Magnesium binding site 2 out
of 5 in 5s66
Go back to
Magnesium Binding Sites List in 5s66
Magnesium binding site 2 out
of 5 in the Tubulin-Z2856434929-Complex
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 2 of Tubulin-Z2856434929-Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg502
b:38.8
occ:1.00
|
O
|
B:HOH620
|
2.1
|
49.7
|
1.0
|
O
|
B:HOH612
|
2.1
|
57.2
|
1.0
|
OE1
|
B:GLN11
|
2.2
|
48.5
|
1.0
|
O1A
|
B:GDP501
|
2.3
|
44.0
|
1.0
|
O
|
C:HOH658
|
2.3
|
44.6
|
1.0
|
O
|
B:HOH634
|
2.4
|
47.5
|
1.0
|
CD
|
B:GLN11
|
3.4
|
48.5
|
1.0
|
PA
|
B:GDP501
|
3.6
|
45.9
|
1.0
|
O3A
|
B:GDP501
|
3.9
|
42.8
|
1.0
|
OD2
|
B:ASP179
|
4.1
|
52.4
|
1.0
|
CB
|
B:GLN11
|
4.1
|
42.1
|
1.0
|
ND2
|
B:ASN101
|
4.2
|
44.2
|
1.0
|
CG
|
B:GLN11
|
4.3
|
48.5
|
1.0
|
NE2
|
B:GLN11
|
4.3
|
56.2
|
1.0
|
OE1
|
C:GLU254
|
4.4
|
53.2
|
1.0
|
C5'
|
B:GDP501
|
4.5
|
46.7
|
1.0
|
O1B
|
B:GDP501
|
4.5
|
40.0
|
1.0
|
O5'
|
B:GDP501
|
4.5
|
41.6
|
1.0
|
O2A
|
B:GDP501
|
4.7
|
41.8
|
1.0
|
PB
|
B:GDP501
|
4.8
|
38.6
|
1.0
|
OD1
|
B:ASN101
|
4.9
|
52.9
|
1.0
|
CG
|
B:ASP179
|
5.0
|
48.9
|
1.0
|
CG
|
B:ASN101
|
5.0
|
47.8
|
1.0
|
|
Magnesium binding site 3 out
of 5 in 5s66
Go back to
Magnesium Binding Sites List in 5s66
Magnesium binding site 3 out
of 5 in the Tubulin-Z2856434929-Complex
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 3 of Tubulin-Z2856434929-Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mg502
b:38.0
occ:1.00
|
O
|
C:HOH631
|
1.9
|
39.6
|
1.0
|
O
|
C:HOH623
|
2.0
|
41.4
|
1.0
|
O1G
|
C:GTP501
|
2.1
|
40.3
|
1.0
|
O
|
C:HOH704
|
2.1
|
40.8
|
1.0
|
O
|
C:HOH645
|
2.1
|
42.3
|
1.0
|
O2B
|
C:GTP501
|
2.2
|
38.4
|
1.0
|
PG
|
C:GTP501
|
3.2
|
45.3
|
1.0
|
PB
|
C:GTP501
|
3.3
|
42.2
|
1.0
|
O3G
|
C:GTP501
|
3.6
|
42.9
|
1.0
|
O3B
|
C:GTP501
|
3.7
|
42.4
|
1.0
|
O3A
|
C:GTP501
|
3.8
|
44.0
|
1.0
|
NZ
|
D:LYS254
|
3.9
|
46.0
|
1.0
|
OE1
|
C:GLU71
|
4.1
|
51.2
|
1.0
|
OD2
|
C:ASP69
|
4.1
|
40.6
|
1.0
|
OD1
|
C:ASP69
|
4.1
|
44.4
|
1.0
|
CB
|
C:GLN11
|
4.2
|
40.1
|
1.0
|
CG
|
C:GLU71
|
4.2
|
47.8
|
1.0
|
OD2
|
C:ASP98
|
4.2
|
48.2
|
1.0
|
N
|
C:GLN11
|
4.4
|
38.0
|
1.0
|
CB
|
C:ASP98
|
4.5
|
44.8
|
1.0
|
CG
|
C:ASP69
|
4.5
|
42.3
|
1.0
|
O2G
|
C:GTP501
|
4.5
|
39.5
|
1.0
|
O1B
|
C:GTP501
|
4.6
|
41.0
|
1.0
|
NE2
|
C:GLN11
|
4.6
|
48.5
|
1.0
|
CD
|
C:GLU71
|
4.6
|
48.5
|
1.0
|
O1A
|
C:GTP501
|
4.7
|
42.1
|
1.0
|
CG
|
C:ASP98
|
4.7
|
44.9
|
1.0
|
PA
|
C:GTP501
|
4.8
|
39.0
|
1.0
|
CA
|
C:GLN11
|
4.9
|
39.8
|
1.0
|
|
Magnesium binding site 4 out
of 5 in 5s66
Go back to
Magnesium Binding Sites List in 5s66
Magnesium binding site 4 out
of 5 in the Tubulin-Z2856434929-Complex
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 4 of Tubulin-Z2856434929-Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Mg502
b:64.7
occ:1.00
|
O1A
|
D:GDP501
|
2.0
|
74.9
|
1.0
|
O
|
D:HOH636
|
2.0
|
65.9
|
1.0
|
OE1
|
D:GLN11
|
2.1
|
68.2
|
1.0
|
CD
|
D:GLN11
|
3.3
|
70.2
|
1.0
|
PA
|
D:GDP501
|
3.5
|
62.7
|
1.0
|
CB
|
D:GLN11
|
4.0
|
64.4
|
1.0
|
CG
|
D:GLN11
|
4.1
|
66.0
|
1.0
|
C5'
|
D:GDP501
|
4.2
|
67.5
|
1.0
|
O2A
|
D:GDP501
|
4.3
|
65.5
|
1.0
|
NE2
|
D:GLN11
|
4.3
|
68.3
|
1.0
|
O
|
D:HOH632
|
4.3
|
64.9
|
1.0
|
O5'
|
D:GDP501
|
4.4
|
66.8
|
1.0
|
O1B
|
D:GDP501
|
4.4
|
60.6
|
1.0
|
O3A
|
D:GDP501
|
4.4
|
67.4
|
1.0
|
OD1
|
D:ASN101
|
4.5
|
75.9
|
1.0
|
C8
|
D:GDP501
|
4.8
|
63.4
|
1.0
|
PB
|
D:GDP501
|
4.9
|
65.0
|
1.0
|
|
Magnesium binding site 5 out
of 5 in 5s66
Go back to
Magnesium Binding Sites List in 5s66
Magnesium binding site 5 out
of 5 in the Tubulin-Z2856434929-Complex
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 5 of Tubulin-Z2856434929-Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Mg402
b:89.2
occ:1.00
|
O3G
|
F:ACP401
|
2.4
|
90.7
|
1.0
|
OE1
|
F:GLU331
|
2.5
|
84.4
|
1.0
|
ND2
|
F:ASN333
|
2.7
|
84.6
|
1.0
|
O1B
|
F:ACP401
|
2.7
|
95.0
|
1.0
|
OE2
|
F:GLU331
|
3.0
|
90.0
|
1.0
|
CD
|
F:GLU331
|
3.1
|
84.3
|
1.0
|
NZ
|
F:LYS74
|
3.1
|
99.3
|
1.0
|
PG
|
F:ACP401
|
3.8
|
104.7
|
1.0
|
CG
|
F:ASN333
|
3.9
|
81.2
|
1.0
|
PB
|
F:ACP401
|
3.9
|
96.3
|
1.0
|
CE
|
F:LYS74
|
4.2
|
97.0
|
1.0
|
O1G
|
F:ACP401
|
4.2
|
97.8
|
1.0
|
CG
|
A:GLU450
|
4.2
|
85.9
|
1.0
|
O2B
|
F:ACP401
|
4.4
|
102.1
|
1.0
|
OD1
|
F:ASN333
|
4.5
|
82.6
|
1.0
|
C3B
|
F:ACP401
|
4.5
|
96.8
|
1.0
|
CG
|
F:GLU331
|
4.6
|
77.5
|
1.0
|
CD
|
A:GLU450
|
4.7
|
85.0
|
1.0
|
CB
|
A:GLU450
|
4.9
|
83.6
|
1.0
|
OE1
|
A:GLU450
|
4.9
|
85.2
|
1.0
|
O2G
|
F:ACP401
|
5.0
|
94.0
|
1.0
|
|
Reference:
T.Muhlethaler,
D.Gioia,
A.E.Prota,
M.E.Sharpe,
A.Cavalli,
M.O.Steinmetz.
Comprehensive Analysis of Binding Sites in Tubulin. Angew.Chem.Int.Ed.Engl. V. 60 13331 2021.
ISSN: ESSN 1521-3773
PubMed: 33951246
DOI: 10.1002/ANIE.202100273
Page generated: Mon Sep 30 02:57:42 2024
|