Magnesium in PDB 8v2i: Structure of ALPHA1B and Betai/Ivb Microtubule Bound to Gmpcpp
Magnesium Binding Sites:
The binding sites of Magnesium atom in the Structure of ALPHA1B and Betai/Ivb Microtubule Bound to Gmpcpp
(pdb code 8v2i). This binding sites where shown within
5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the
Structure of ALPHA1B and Betai/Ivb Microtubule Bound to Gmpcpp, PDB code: 8v2i:
Jump to Magnesium binding site number:
1;
2;
3;
4;
Magnesium binding site 1 out
of 4 in 8v2i
Go back to
Magnesium Binding Sites List in 8v2i
Magnesium binding site 1 out
of 4 in the Structure of ALPHA1B and Betai/Ivb Microtubule Bound to Gmpcpp
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 1 of Structure of ALPHA1B and Betai/Ivb Microtubule Bound to Gmpcpp within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg502
b:84.0
occ:1.00
|
O1G
|
A:GTP501
|
2.0
|
97.6
|
1.0
|
O2B
|
A:GTP501
|
2.0
|
87.1
|
1.0
|
OD1
|
A:ASP98
|
2.3
|
148.7
|
1.0
|
PG
|
A:GTP501
|
2.6
|
112.2
|
1.0
|
O3B
|
A:GTP501
|
2.6
|
93.4
|
1.0
|
OD2
|
A:ASP98
|
2.7
|
139.4
|
1.0
|
PB
|
A:GTP501
|
2.8
|
101.6
|
1.0
|
CG
|
A:ASP98
|
2.8
|
143.2
|
1.0
|
O2G
|
A:GTP501
|
3.0
|
94.2
|
1.0
|
OG1
|
A:THR145
|
3.8
|
113.5
|
1.0
|
O3A
|
A:GTP501
|
3.8
|
100.1
|
1.0
|
NZ
|
B:LYS252
|
3.9
|
117.8
|
1.0
|
O1B
|
A:GTP501
|
3.9
|
101.7
|
1.0
|
OD1
|
A:ASP69
|
3.9
|
118.2
|
1.0
|
O3G
|
A:GTP501
|
4.0
|
109.0
|
1.0
|
OE1
|
A:GLU71
|
4.3
|
130.8
|
1.0
|
CB
|
A:THR145
|
4.3
|
105.2
|
1.0
|
CB
|
A:ASP98
|
4.4
|
137.3
|
1.0
|
OD2
|
A:ASP69
|
4.5
|
114.1
|
1.0
|
CB
|
A:GLU71
|
4.6
|
129.5
|
1.0
|
CG
|
A:ASP69
|
4.6
|
114.6
|
1.0
|
CE
|
B:LYS252
|
4.9
|
110.8
|
1.0
|
N
|
A:GLN11
|
4.9
|
94.7
|
1.0
|
N
|
A:ALA99
|
4.9
|
109.1
|
1.0
|
|
Magnesium binding site 2 out
of 4 in 8v2i
Go back to
Magnesium Binding Sites List in 8v2i
Magnesium binding site 2 out
of 4 in the Structure of ALPHA1B and Betai/Ivb Microtubule Bound to Gmpcpp
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 2 of Structure of ALPHA1B and Betai/Ivb Microtubule Bound to Gmpcpp within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg502
b:80.9
occ:1.00
|
O3G
|
B:G2P501
|
2.0
|
103.9
|
1.0
|
O2B
|
B:G2P501
|
2.4
|
100.9
|
1.0
|
OE1
|
B:GLU69
|
3.0
|
127.9
|
1.0
|
PG
|
B:G2P501
|
3.3
|
110.0
|
1.0
|
PB
|
B:G2P501
|
3.6
|
93.7
|
1.0
|
O3B
|
B:G2P501
|
3.9
|
99.1
|
1.0
|
CD
|
B:GLU69
|
4.0
|
128.1
|
1.0
|
O2G
|
B:G2P501
|
4.0
|
111.8
|
1.0
|
OD1
|
B:ASP67
|
4.0
|
114.9
|
1.0
|
O2A
|
B:G2P501
|
4.1
|
111.1
|
1.0
|
OD2
|
B:ASP67
|
4.1
|
123.0
|
1.0
|
CB
|
B:GLN11
|
4.2
|
101.1
|
1.0
|
N
|
B:GLN11
|
4.2
|
98.2
|
1.0
|
C3A
|
B:G2P501
|
4.4
|
96.2
|
1.0
|
OE1
|
B:GLN11
|
4.4
|
108.8
|
1.0
|
O1G
|
B:G2P501
|
4.5
|
108.7
|
1.0
|
CG
|
B:ASP67
|
4.5
|
117.1
|
1.0
|
OG1
|
B:THR143
|
4.7
|
117.2
|
1.0
|
CG
|
B:GLU69
|
4.7
|
125.1
|
1.0
|
OE2
|
B:GLU69
|
4.7
|
127.5
|
1.0
|
O
|
B:GLY96
|
4.7
|
119.7
|
1.0
|
PA
|
B:G2P501
|
4.8
|
110.2
|
1.0
|
CA
|
B:GLN11
|
4.8
|
99.5
|
1.0
|
O1B
|
B:G2P501
|
4.8
|
107.0
|
1.0
|
CB
|
B:THR143
|
4.9
|
106.7
|
1.0
|
|
Magnesium binding site 3 out
of 4 in 8v2i
Go back to
Magnesium Binding Sites List in 8v2i
Magnesium binding site 3 out
of 4 in the Structure of ALPHA1B and Betai/Ivb Microtubule Bound to Gmpcpp
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 3 of Structure of ALPHA1B and Betai/Ivb Microtubule Bound to Gmpcpp within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
I:Mg502
b:60.0
occ:1.00
|
O2B
|
I:GTP501
|
2.0
|
114.5
|
1.0
|
O1G
|
I:GTP501
|
2.0
|
125.7
|
1.0
|
OE2
|
I:GLU71
|
2.0
|
126.6
|
1.0
|
PB
|
I:GTP501
|
3.0
|
126.6
|
1.0
|
CD
|
I:GLU71
|
3.0
|
130.7
|
1.0
|
PG
|
I:GTP501
|
3.0
|
130.3
|
1.0
|
O3B
|
I:GTP501
|
3.0
|
121.9
|
1.0
|
CG
|
I:GLU71
|
3.4
|
131.3
|
1.0
|
OD1
|
I:ASP69
|
3.6
|
117.9
|
1.0
|
O2G
|
I:GTP501
|
3.8
|
122.9
|
1.0
|
O1B
|
I:GTP501
|
3.9
|
124.8
|
1.0
|
OD2
|
I:ASP69
|
4.0
|
112.9
|
1.0
|
CB
|
I:ASP98
|
4.0
|
129.2
|
1.0
|
NZ
|
Q:LYS252
|
4.0
|
125.3
|
1.0
|
OG1
|
I:THR145
|
4.1
|
121.9
|
1.0
|
OE1
|
I:GLU71
|
4.1
|
124.9
|
1.0
|
O3A
|
I:GTP501
|
4.1
|
133.1
|
1.0
|
O3G
|
I:GTP501
|
4.2
|
129.3
|
1.0
|
CG
|
I:ASP69
|
4.3
|
113.7
|
1.0
|
CB
|
I:THR145
|
4.6
|
111.5
|
1.0
|
N
|
I:GLN11
|
4.7
|
105.4
|
1.0
|
CB
|
I:GLU71
|
4.7
|
123.0
|
1.0
|
CB
|
I:GLN11
|
4.8
|
101.4
|
1.0
|
OD2
|
I:ASP98
|
4.9
|
140.8
|
1.0
|
O2A
|
I:GTP501
|
4.9
|
131.2
|
1.0
|
|
Magnesium binding site 4 out
of 4 in 8v2i
Go back to
Magnesium Binding Sites List in 8v2i
Magnesium binding site 4 out
of 4 in the Structure of ALPHA1B and Betai/Ivb Microtubule Bound to Gmpcpp
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 4 of Structure of ALPHA1B and Betai/Ivb Microtubule Bound to Gmpcpp within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
Q:Mg502
b:106.9
occ:1.00
|
O3G
|
Q:G2P501
|
1.9
|
108.7
|
1.0
|
O2B
|
Q:G2P501
|
2.0
|
111.7
|
1.0
|
OE2
|
Q:GLU69
|
2.0
|
135.6
|
1.0
|
PB
|
Q:G2P501
|
3.2
|
106.0
|
1.0
|
CD
|
Q:GLU69
|
3.2
|
135.3
|
1.0
|
PG
|
Q:G2P501
|
3.3
|
118.0
|
1.0
|
O3B
|
Q:G2P501
|
3.6
|
106.4
|
1.0
|
C3A
|
Q:G2P501
|
3.9
|
98.7
|
1.0
|
CG
|
Q:GLU69
|
4.0
|
131.3
|
1.0
|
OD1
|
Q:ASP67
|
4.1
|
116.3
|
1.0
|
OE1
|
Q:GLU69
|
4.1
|
134.5
|
1.0
|
N
|
Q:GLN11
|
4.2
|
99.3
|
1.0
|
OD2
|
Q:ASP67
|
4.2
|
123.4
|
1.0
|
O2G
|
Q:G2P501
|
4.2
|
119.1
|
1.0
|
CB
|
Q:GLN11
|
4.3
|
100.0
|
1.0
|
O1G
|
Q:G2P501
|
4.3
|
115.1
|
1.0
|
O2A
|
Q:G2P501
|
4.4
|
116.1
|
1.0
|
PA
|
Q:G2P501
|
4.5
|
112.0
|
1.0
|
O1B
|
Q:G2P501
|
4.5
|
113.1
|
1.0
|
O1A
|
Q:G2P501
|
4.6
|
111.1
|
1.0
|
CG
|
Q:ASP67
|
4.6
|
120.4
|
1.0
|
OG1
|
Q:THR143
|
4.6
|
126.2
|
1.0
|
OE1
|
Q:GLN11
|
4.7
|
108.2
|
1.0
|
O
|
Q:GLY96
|
4.7
|
128.5
|
1.0
|
CA
|
Q:GLN11
|
4.8
|
101.1
|
1.0
|
CB
|
Q:THR143
|
4.9
|
112.4
|
1.0
|
CA
|
Q:GLY10
|
4.9
|
94.9
|
1.0
|
|
Reference:
E.A.Zehr,
A.Roll-Mecak.
Cryo-Em Structures of Human A1B/Bi+Bivb Microtubules Shed Light on Isoform Specific Assembly Biorxiv 2023.
ISSN: ISSN 2692-8205
Page generated: Thu Dec 28 10:43:35 2023
|