Magnesium in PDB 7zcw: Cryo-Em Structure of Gmpcpp-Microtubules in Complex with VASH2-Svbp
Enzymatic activity of Cryo-Em Structure of Gmpcpp-Microtubules in Complex with VASH2-Svbp
All present enzymatic activity of Cryo-Em Structure of Gmpcpp-Microtubules in Complex with VASH2-Svbp:
3.4.17.17;
Magnesium Binding Sites:
The binding sites of Magnesium atom in the Cryo-Em Structure of Gmpcpp-Microtubules in Complex with VASH2-Svbp
(pdb code 7zcw). This binding sites where shown within
5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the
Cryo-Em Structure of Gmpcpp-Microtubules in Complex with VASH2-Svbp, PDB code: 7zcw:
Jump to Magnesium binding site number:
1;
2;
3;
4;
5;
6;
Magnesium binding site 1 out
of 6 in 7zcw
Go back to
Magnesium Binding Sites List in 7zcw
Magnesium binding site 1 out
of 6 in the Cryo-Em Structure of Gmpcpp-Microtubules in Complex with VASH2-Svbp
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 1 of Cryo-Em Structure of Gmpcpp-Microtubules in Complex with VASH2-Svbp within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg502
b:39.4
occ:1.00
|
O1G
|
A:GTP501
|
1.9
|
54.9
|
1.0
|
O2B
|
A:GTP501
|
2.3
|
54.9
|
1.0
|
OE1
|
A:GLU71
|
3.3
|
51.7
|
1.0
|
PG
|
A:GTP501
|
3.3
|
54.9
|
1.0
|
HB2
|
A:GLN11
|
3.4
|
46.4
|
1.0
|
PB
|
A:GTP501
|
3.6
|
54.9
|
1.0
|
HZ1
|
B:LYS252
|
3.6
|
47.2
|
1.0
|
O3B
|
A:GTP501
|
3.8
|
54.9
|
1.0
|
H
|
A:GLN11
|
4.0
|
46.4
|
1.0
|
HB3
|
A:GLN11
|
4.0
|
46.4
|
1.0
|
O3G
|
A:GTP501
|
4.1
|
54.9
|
1.0
|
CB
|
A:GLN11
|
4.1
|
46.4
|
1.0
|
OE1
|
A:GLN11
|
4.3
|
46.4
|
1.0
|
HB3
|
A:GLU71
|
4.3
|
51.7
|
1.0
|
HB2
|
A:ASP98
|
4.3
|
49.4
|
1.0
|
O2G
|
A:GTP501
|
4.3
|
54.9
|
1.0
|
CD
|
A:GLU71
|
4.4
|
51.7
|
1.0
|
NZ
|
B:LYS252
|
4.4
|
47.2
|
1.0
|
HB2
|
B:ASN247
|
4.5
|
50.4
|
1.0
|
O3A
|
A:GTP501
|
4.5
|
54.9
|
1.0
|
HE3
|
B:LYS252
|
4.5
|
47.2
|
1.0
|
HZ2
|
B:LYS252
|
4.6
|
47.2
|
1.0
|
O1B
|
A:GTP501
|
4.6
|
54.9
|
1.0
|
HB2
|
A:GLU71
|
4.6
|
51.7
|
1.0
|
N
|
A:GLN11
|
4.7
|
46.4
|
1.0
|
HG1
|
A:THR145
|
4.8
|
43.3
|
1.0
|
OD2
|
A:ASP69
|
4.8
|
45.8
|
1.0
|
HD21
|
B:ASN247
|
4.8
|
50.4
|
1.0
|
O2A
|
A:GTP501
|
4.8
|
54.9
|
1.0
|
OD1
|
A:ASP69
|
4.8
|
45.8
|
1.0
|
HB3
|
A:ASP98
|
4.8
|
49.4
|
1.0
|
CB
|
A:GLU71
|
4.9
|
51.7
|
1.0
|
CD
|
A:GLN11
|
4.9
|
46.4
|
1.0
|
CE
|
B:LYS252
|
5.0
|
47.2
|
1.0
|
|
Magnesium binding site 2 out
of 6 in 7zcw
Go back to
Magnesium Binding Sites List in 7zcw
Magnesium binding site 2 out
of 6 in the Cryo-Em Structure of Gmpcpp-Microtubules in Complex with VASH2-Svbp
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 2 of Cryo-Em Structure of Gmpcpp-Microtubules in Complex with VASH2-Svbp within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg502
b:48.2
occ:1.00
|
O3G
|
B:G2P501
|
2.0
|
57.7
|
1.0
|
O2G
|
B:G2P501
|
2.0
|
57.7
|
1.0
|
O2B
|
B:G2P501
|
2.0
|
57.7
|
1.0
|
PG
|
B:G2P501
|
2.3
|
57.7
|
1.0
|
PB
|
B:G2P501
|
3.1
|
57.7
|
1.0
|
O3B
|
B:G2P501
|
3.1
|
57.7
|
1.0
|
O1G
|
B:G2P501
|
3.7
|
57.7
|
1.0
|
HB2
|
B:GLN11
|
3.8
|
57.9
|
1.0
|
H
|
B:GLN11
|
3.9
|
57.9
|
1.0
|
O2A
|
B:G2P501
|
3.9
|
57.7
|
1.0
|
HG1
|
B:THR143
|
4.0
|
56.9
|
1.0
|
HB
|
B:THR143
|
4.1
|
56.9
|
1.0
|
C3A
|
B:G2P501
|
4.2
|
57.7
|
1.0
|
H3A2
|
B:G2P501
|
4.2
|
57.7
|
1.0
|
O1B
|
B:G2P501
|
4.2
|
57.7
|
1.0
|
HB3
|
B:GLN11
|
4.4
|
57.9
|
1.0
|
PA
|
B:G2P501
|
4.4
|
57.7
|
1.0
|
OE1
|
B:GLU69
|
4.5
|
63.5
|
1.0
|
O1A
|
B:G2P501
|
4.5
|
57.7
|
1.0
|
OG1
|
B:THR143
|
4.5
|
56.9
|
1.0
|
CB
|
B:GLN11
|
4.6
|
57.9
|
1.0
|
N
|
B:GLN11
|
4.7
|
57.9
|
1.0
|
OD2
|
B:ASP67
|
4.7
|
61.2
|
1.0
|
HA2
|
B:GLY10
|
4.7
|
56.0
|
1.0
|
CB
|
B:THR143
|
4.8
|
56.9
|
1.0
|
OD1
|
B:ASP67
|
4.8
|
61.2
|
1.0
|
HB3
|
B:GLU69
|
4.9
|
63.5
|
1.0
|
HD22
|
B:ASN99
|
4.9
|
54.5
|
1.0
|
HD21
|
B:ASN99
|
4.9
|
54.5
|
1.0
|
|
Magnesium binding site 3 out
of 6 in 7zcw
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Magnesium Binding Sites List in 7zcw
Magnesium binding site 3 out
of 6 in the Cryo-Em Structure of Gmpcpp-Microtubules in Complex with VASH2-Svbp
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 3 of Cryo-Em Structure of Gmpcpp-Microtubules in Complex with VASH2-Svbp within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Mg502
b:44.3
occ:1.00
|
O1G
|
E:GTP501
|
1.9
|
54.9
|
1.0
|
O2B
|
E:GTP501
|
3.0
|
54.9
|
1.0
|
OE1
|
E:GLU71
|
3.1
|
47.7
|
1.0
|
PG
|
E:GTP501
|
3.4
|
54.9
|
1.0
|
HB2
|
E:GLN11
|
3.4
|
44.8
|
1.0
|
HE21
|
E:GLN11
|
3.6
|
44.8
|
1.0
|
HZ1
|
F:LYS252
|
3.7
|
45.5
|
1.0
|
HB2
|
E:ASP98
|
4.0
|
46.2
|
1.0
|
HB3
|
E:GLN11
|
4.0
|
44.8
|
1.0
|
H
|
E:GLN11
|
4.1
|
44.8
|
1.0
|
PB
|
E:GTP501
|
4.1
|
54.9
|
1.0
|
O3G
|
E:GTP501
|
4.1
|
54.9
|
1.0
|
NE2
|
E:GLN11
|
4.1
|
44.8
|
1.0
|
O3B
|
E:GTP501
|
4.2
|
54.9
|
1.0
|
CB
|
E:GLN11
|
4.2
|
44.8
|
1.0
|
HB3
|
E:ASP98
|
4.2
|
46.2
|
1.0
|
HB3
|
E:GLU71
|
4.3
|
47.7
|
1.0
|
CD
|
E:GLU71
|
4.3
|
47.7
|
1.0
|
O2G
|
E:GTP501
|
4.3
|
54.9
|
1.0
|
HE22
|
E:GLN11
|
4.3
|
44.8
|
1.0
|
HB2
|
F:ASN247
|
4.6
|
49.3
|
1.0
|
CB
|
E:ASP98
|
4.6
|
46.2
|
1.0
|
NZ
|
F:LYS252
|
4.6
|
45.5
|
1.0
|
HD21
|
F:ASN247
|
4.6
|
49.3
|
1.0
|
O3A
|
E:GTP501
|
4.6
|
54.9
|
1.0
|
OD1
|
E:ASP69
|
4.7
|
42.7
|
1.0
|
OD2
|
E:ASP69
|
4.7
|
42.7
|
1.0
|
N
|
E:GLN11
|
4.7
|
44.8
|
1.0
|
HG1
|
E:THR145
|
4.8
|
41.4
|
1.0
|
HD2
|
F:LYS252
|
4.8
|
45.5
|
1.0
|
HZ3
|
F:LYS252
|
4.9
|
45.5
|
1.0
|
HZ2
|
F:LYS252
|
4.9
|
45.5
|
1.0
|
|
Magnesium binding site 4 out
of 6 in 7zcw
Go back to
Magnesium Binding Sites List in 7zcw
Magnesium binding site 4 out
of 6 in the Cryo-Em Structure of Gmpcpp-Microtubules in Complex with VASH2-Svbp
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 4 of Cryo-Em Structure of Gmpcpp-Microtubules in Complex with VASH2-Svbp within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Mg502
b:51.5
occ:1.00
|
O3G
|
F:G2P501
|
1.9
|
56.6
|
1.0
|
O2B
|
F:G2P501
|
2.7
|
56.6
|
1.0
|
PG
|
F:G2P501
|
3.3
|
56.6
|
1.0
|
HG1
|
F:THR143
|
3.5
|
55.8
|
1.0
|
O2G
|
F:G2P501
|
3.7
|
56.6
|
1.0
|
HB2
|
F:GLN11
|
3.7
|
54.4
|
1.0
|
PB
|
F:G2P501
|
3.9
|
56.6
|
1.0
|
O3B
|
F:G2P501
|
4.0
|
56.6
|
1.0
|
OG1
|
F:THR143
|
4.2
|
55.8
|
1.0
|
OD2
|
F:ASP67
|
4.3
|
57.8
|
1.0
|
HB
|
F:THR143
|
4.3
|
55.8
|
1.0
|
OD1
|
F:ASP67
|
4.3
|
57.8
|
1.0
|
O1G
|
F:G2P501
|
4.4
|
56.6
|
1.0
|
H
|
F:GLN11
|
4.4
|
54.4
|
1.0
|
HA2
|
F:GLY10
|
4.5
|
52.3
|
1.0
|
HB2
|
F:GLU69
|
4.5
|
62.8
|
1.0
|
HG21
|
F:THR72
|
4.7
|
61.7
|
1.0
|
CB
|
F:GLN11
|
4.7
|
54.4
|
1.0
|
CB
|
F:THR143
|
4.8
|
55.8
|
1.0
|
N
|
F:GLN11
|
4.8
|
54.4
|
1.0
|
CG
|
F:ASP67
|
4.8
|
57.8
|
1.0
|
O2A
|
F:G2P501
|
4.8
|
56.6
|
1.0
|
HG21
|
F:THR143
|
4.8
|
55.8
|
1.0
|
O1B
|
F:G2P501
|
4.8
|
56.6
|
1.0
|
HG3
|
F:GLN11
|
4.9
|
54.4
|
1.0
|
HG23
|
F:THR72
|
4.9
|
61.7
|
1.0
|
HA3
|
F:GLY96
|
5.0
|
61.8
|
1.0
|
|
Magnesium binding site 5 out
of 6 in 7zcw
Go back to
Magnesium Binding Sites List in 7zcw
Magnesium binding site 5 out
of 6 in the Cryo-Em Structure of Gmpcpp-Microtubules in Complex with VASH2-Svbp
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 5 of Cryo-Em Structure of Gmpcpp-Microtubules in Complex with VASH2-Svbp within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
G:Mg502
b:38.4
occ:1.00
|
O3G
|
G:G2P501
|
1.9
|
52.8
|
1.0
|
OE2
|
G:GLU69
|
2.4
|
59.6
|
1.0
|
O2B
|
G:G2P501
|
2.5
|
52.8
|
1.0
|
PG
|
G:G2P501
|
3.1
|
52.8
|
1.0
|
O2G
|
G:G2P501
|
3.2
|
52.8
|
1.0
|
CD
|
G:GLU69
|
3.4
|
59.6
|
1.0
|
HB2
|
G:GLN11
|
3.5
|
53.3
|
1.0
|
PB
|
G:G2P501
|
3.8
|
52.8
|
1.0
|
O3B
|
G:G2P501
|
3.9
|
52.8
|
1.0
|
H
|
G:GLN11
|
3.9
|
53.3
|
1.0
|
HG2
|
G:GLU69
|
4.1
|
59.6
|
1.0
|
OE1
|
G:GLU69
|
4.2
|
59.6
|
1.0
|
O1G
|
G:G2P501
|
4.2
|
52.8
|
1.0
|
CG
|
G:GLU69
|
4.3
|
59.6
|
1.0
|
CB
|
G:GLN11
|
4.4
|
53.3
|
1.0
|
HB3
|
G:GLN11
|
4.4
|
53.3
|
1.0
|
OE1
|
G:GLN11
|
4.5
|
53.3
|
1.0
|
HG3
|
G:GLU69
|
4.5
|
59.6
|
1.0
|
OD2
|
G:ASP67
|
4.6
|
57.6
|
1.0
|
O2A
|
G:G2P501
|
4.7
|
52.8
|
1.0
|
N
|
G:GLN11
|
4.7
|
53.3
|
1.0
|
O1B
|
G:G2P501
|
4.8
|
52.8
|
1.0
|
O1A
|
G:G2P501
|
4.8
|
52.8
|
1.0
|
HA2
|
G:GLY10
|
4.9
|
52.0
|
1.0
|
OD1
|
G:ASP67
|
4.9
|
57.6
|
1.0
|
C3A
|
G:G2P501
|
5.0
|
52.8
|
1.0
|
HB
|
G:THR143
|
5.0
|
52.4
|
1.0
|
|
Magnesium binding site 6 out
of 6 in 7zcw
Go back to
Magnesium Binding Sites List in 7zcw
Magnesium binding site 6 out
of 6 in the Cryo-Em Structure of Gmpcpp-Microtubules in Complex with VASH2-Svbp
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 6 of Cryo-Em Structure of Gmpcpp-Microtubules in Complex with VASH2-Svbp within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
H:Mg502
b:50.5
occ:1.00
|
O3G
|
H:G2P501
|
2.0
|
54.1
|
1.0
|
O2B
|
H:G2P501
|
2.6
|
54.1
|
1.0
|
PG
|
H:G2P501
|
3.2
|
54.1
|
1.0
|
O2G
|
H:G2P501
|
3.4
|
54.1
|
1.0
|
HB2
|
H:GLN11
|
3.6
|
53.3
|
1.0
|
PB
|
H:G2P501
|
3.8
|
54.1
|
1.0
|
O3B
|
H:G2P501
|
4.0
|
54.1
|
1.0
|
H
|
H:GLN11
|
4.0
|
53.3
|
1.0
|
O1G
|
H:G2P501
|
4.3
|
54.1
|
1.0
|
CB
|
H:GLN11
|
4.5
|
53.3
|
1.0
|
HB2
|
H:GLU69
|
4.5
|
61.7
|
1.0
|
HB3
|
H:GLN11
|
4.5
|
53.3
|
1.0
|
O2A
|
H:G2P501
|
4.6
|
54.1
|
1.0
|
OD2
|
H:ASP67
|
4.6
|
57.1
|
1.0
|
HG1
|
H:THR143
|
4.7
|
53.0
|
1.0
|
HB
|
H:THR143
|
4.7
|
53.0
|
1.0
|
N
|
H:GLN11
|
4.7
|
53.3
|
1.0
|
OD1
|
H:ASP67
|
4.7
|
57.1
|
1.0
|
OE1
|
H:GLN11
|
4.7
|
53.3
|
1.0
|
O1A
|
H:G2P501
|
4.8
|
54.1
|
1.0
|
HA2
|
H:GLY10
|
4.8
|
53.4
|
1.0
|
O1B
|
H:G2P501
|
4.8
|
54.1
|
1.0
|
HG1
|
H:THR72
|
4.8
|
60.7
|
1.0
|
HA3
|
H:GLY96
|
4.9
|
56.9
|
1.0
|
|
Reference:
S.R.Choi,
T.Blum,
M.O.Steinmetz.
Structural and Functional Comparison of Vash-Svbp Microtubule-Detyrosinating Enzyme Complexes To Be Published.
Page generated: Thu Oct 3 16:23:18 2024
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