Magnesium in PDB 6oo2: VPS4 with Cyclic Peptide Bound in the Central Pore
Other elements in 6oo2:
The structure of VPS4 with Cyclic Peptide Bound in the Central Pore also contains other interesting chemical elements:
Magnesium Binding Sites:
The binding sites of Magnesium atom in the VPS4 with Cyclic Peptide Bound in the Central Pore
(pdb code 6oo2). This binding sites where shown within
5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the
VPS4 with Cyclic Peptide Bound in the Central Pore, PDB code: 6oo2:
Jump to Magnesium binding site number:
1;
2;
3;
4;
Magnesium binding site 1 out
of 4 in 6oo2
Go back to
Magnesium Binding Sites List in 6oo2
Magnesium binding site 1 out
of 4 in the VPS4 with Cyclic Peptide Bound in the Central Pore
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 1 of VPS4 with Cyclic Peptide Bound in the Central Pore within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg503
b:62.5
occ:1.00
|
OG
|
A:SER180
|
2.0
|
68.3
|
1.0
|
O2B
|
A:ADP501
|
2.0
|
62.5
|
1.0
|
F1
|
A:BEF502
|
2.0
|
62.5
|
1.0
|
CB
|
A:SER180
|
3.0
|
68.3
|
1.0
|
PB
|
A:ADP501
|
3.1
|
62.5
|
1.0
|
BE
|
A:BEF502
|
3.2
|
62.5
|
1.0
|
O1B
|
A:ADP501
|
3.4
|
62.5
|
1.0
|
O3A
|
A:ADP501
|
3.8
|
62.5
|
1.0
|
OD2
|
A:ASP232
|
3.8
|
67.1
|
1.0
|
N
|
A:SER180
|
3.8
|
68.3
|
1.0
|
CA
|
A:SER180
|
4.0
|
68.3
|
1.0
|
F3
|
A:BEF502
|
4.0
|
62.5
|
1.0
|
OD1
|
A:ASP232
|
4.1
|
67.1
|
1.0
|
F2
|
A:BEF502
|
4.4
|
62.5
|
1.0
|
CG
|
A:ASP232
|
4.4
|
67.1
|
1.0
|
O3B
|
A:ADP501
|
4.4
|
62.5
|
1.0
|
NH2
|
B:ARG289
|
4.6
|
45.1
|
1.0
|
OE2
|
A:GLU233
|
4.8
|
69.4
|
1.0
|
O2A
|
A:ADP501
|
4.8
|
62.5
|
1.0
|
CB
|
A:LYS179
|
4.9
|
59.8
|
1.0
|
C
|
A:LYS179
|
4.9
|
59.8
|
1.0
|
NH2
|
B:ARG288
|
5.0
|
49.2
|
1.0
|
PA
|
A:ADP501
|
5.0
|
62.5
|
1.0
|
|
Magnesium binding site 2 out
of 4 in 6oo2
Go back to
Magnesium Binding Sites List in 6oo2
Magnesium binding site 2 out
of 4 in the VPS4 with Cyclic Peptide Bound in the Central Pore
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 2 of VPS4 with Cyclic Peptide Bound in the Central Pore within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg503
b:27.8
occ:1.00
|
OG
|
B:SER180
|
2.0
|
35.9
|
1.0
|
F1
|
B:BEF502
|
2.0
|
27.8
|
1.0
|
O2B
|
B:ADP501
|
2.0
|
27.8
|
1.0
|
O1B
|
B:ADP501
|
2.5
|
27.8
|
1.0
|
PB
|
B:ADP501
|
2.6
|
27.8
|
1.0
|
BE
|
B:BEF502
|
3.2
|
27.8
|
1.0
|
O3B
|
B:ADP501
|
3.3
|
27.8
|
1.0
|
CB
|
B:SER180
|
3.4
|
35.9
|
1.0
|
N
|
B:SER180
|
3.7
|
35.9
|
1.0
|
OD2
|
B:ASP232
|
4.1
|
35.8
|
1.0
|
CA
|
B:SER180
|
4.1
|
35.9
|
1.0
|
O3A
|
B:ADP501
|
4.1
|
27.8
|
1.0
|
OD1
|
B:ASP232
|
4.1
|
35.8
|
1.0
|
F3
|
B:BEF502
|
4.2
|
27.8
|
1.0
|
F2
|
B:BEF502
|
4.2
|
27.8
|
1.0
|
CB
|
B:LYS179
|
4.5
|
31.4
|
1.0
|
CG
|
B:ASP232
|
4.5
|
35.8
|
1.0
|
C
|
B:LYS179
|
4.6
|
31.4
|
1.0
|
NH2
|
C:ARG288
|
4.7
|
26.7
|
1.0
|
NH2
|
C:ARG289
|
4.7
|
23.4
|
1.0
|
CE
|
B:LYS179
|
4.8
|
31.4
|
1.0
|
OE2
|
B:GLU233
|
4.8
|
38.2
|
1.0
|
CB
|
B:ALA275
|
4.9
|
34.1
|
1.0
|
CA
|
B:LYS179
|
5.0
|
31.4
|
1.0
|
|
Magnesium binding site 3 out
of 4 in 6oo2
Go back to
Magnesium Binding Sites List in 6oo2
Magnesium binding site 3 out
of 4 in the VPS4 with Cyclic Peptide Bound in the Central Pore
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 3 of VPS4 with Cyclic Peptide Bound in the Central Pore within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mg503
b:39.5
occ:1.00
|
OG
|
C:SER180
|
2.0
|
36.2
|
1.0
|
F1
|
C:BEF502
|
2.0
|
39.5
|
1.0
|
O2B
|
C:ADP501
|
2.0
|
39.5
|
1.0
|
O1B
|
C:ADP501
|
2.5
|
39.5
|
1.0
|
PB
|
C:ADP501
|
2.6
|
39.5
|
1.0
|
CB
|
C:SER180
|
3.2
|
36.2
|
1.0
|
BE
|
C:BEF502
|
3.2
|
39.5
|
1.0
|
O3B
|
C:ADP501
|
3.3
|
39.5
|
1.0
|
N
|
C:SER180
|
3.6
|
36.2
|
1.0
|
CA
|
C:SER180
|
4.0
|
36.2
|
1.0
|
O3A
|
C:ADP501
|
4.1
|
39.5
|
1.0
|
F2
|
C:BEF502
|
4.2
|
39.5
|
1.0
|
OD2
|
C:ASP232
|
4.2
|
41.1
|
1.0
|
F3
|
C:BEF502
|
4.2
|
39.5
|
1.0
|
OD1
|
C:ASP232
|
4.3
|
41.1
|
1.0
|
CB
|
C:LYS179
|
4.5
|
32.5
|
1.0
|
C
|
C:LYS179
|
4.6
|
32.5
|
1.0
|
CG
|
C:ASP232
|
4.7
|
41.1
|
1.0
|
OE2
|
C:GLU233
|
4.9
|
42.8
|
1.0
|
CE
|
C:LYS179
|
4.9
|
32.5
|
1.0
|
CA
|
C:LYS179
|
5.0
|
32.5
|
1.0
|
|
Magnesium binding site 4 out
of 4 in 6oo2
Go back to
Magnesium Binding Sites List in 6oo2
Magnesium binding site 4 out
of 4 in the VPS4 with Cyclic Peptide Bound in the Central Pore
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 4 of VPS4 with Cyclic Peptide Bound in the Central Pore within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Mg502
b:43.8
occ:1.00
|
O2B
|
D:ADP501
|
2.1
|
46.8
|
1.0
|
OG
|
D:SER180
|
2.1
|
45.8
|
1.0
|
PB
|
D:ADP501
|
3.3
|
46.8
|
1.0
|
CB
|
D:SER180
|
3.4
|
45.8
|
1.0
|
O3B
|
D:ADP501
|
3.6
|
46.8
|
1.0
|
OD1
|
D:ASP232
|
3.8
|
40.6
|
1.0
|
OD2
|
D:ASP232
|
3.9
|
40.6
|
1.0
|
O2A
|
D:ADP501
|
3.9
|
46.8
|
1.0
|
N
|
D:SER180
|
4.1
|
45.8
|
1.0
|
O1B
|
D:ADP501
|
4.3
|
46.8
|
1.0
|
CG
|
D:ASP232
|
4.3
|
40.6
|
1.0
|
CA
|
D:SER180
|
4.3
|
45.8
|
1.0
|
O3A
|
D:ADP501
|
4.3
|
46.8
|
1.0
|
PA
|
D:ADP501
|
4.4
|
46.8
|
1.0
|
O1A
|
D:ADP501
|
4.4
|
46.8
|
1.0
|
NH2
|
E:ARG289
|
4.4
|
63.0
|
1.0
|
OE1
|
D:GLU233
|
4.6
|
47.4
|
1.0
|
|
Reference:
H.Han,
J.M.Fulcher,
V.P.Dandey,
J.H.Iwasa,
W.I.Sundquist,
M.S.Kay,
P.S.Shen,
C.P.Hill.
Structure of VPS4 with Circular Peptides and Implications For Translocation of Two Polypeptide Chains By Aaa+ Atpases. Elife V. 8 2019.
ISSN: ESSN 2050-084X
PubMed: 31184588
DOI: 10.7554/ELIFE.44071
Page generated: Tue Oct 1 13:28:17 2024
|