Magnesium in PDB 6zp8: Yeast 20S Proteasome in Complex with Glidobactin-Like Natural Product HB335
Enzymatic activity of Yeast 20S Proteasome in Complex with Glidobactin-Like Natural Product HB335
All present enzymatic activity of Yeast 20S Proteasome in Complex with Glidobactin-Like Natural Product HB335:
3.4.25.1;
Protein crystallography data
The structure of Yeast 20S Proteasome in Complex with Glidobactin-Like Natural Product HB335, PDB code: 6zp8
was solved by
L.Zhao,
C.Le Chapelain,
A.O.Brachmann,
M.Kaiser,
M.Groll,
H.B.Bode,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
15.00 /
3.00
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
136.16,
300.12,
144.83,
90,
113.11,
90
|
R / Rfree (%)
|
16.7 /
20
|
Other elements in 6zp8:
The structure of Yeast 20S Proteasome in Complex with Glidobactin-Like Natural Product HB335 also contains other interesting chemical elements:
Magnesium Binding Sites:
The binding sites of Magnesium atom in the Yeast 20S Proteasome in Complex with Glidobactin-Like Natural Product HB335
(pdb code 6zp8). This binding sites where shown within
5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the
Yeast 20S Proteasome in Complex with Glidobactin-Like Natural Product HB335, PDB code: 6zp8:
Jump to Magnesium binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
Magnesium binding site 1 out
of 8 in 6zp8
Go back to
Magnesium Binding Sites List in 6zp8
Magnesium binding site 1 out
of 8 in the Yeast 20S Proteasome in Complex with Glidobactin-Like Natural Product HB335
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 1 of Yeast 20S Proteasome in Complex with Glidobactin-Like Natural Product HB335 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
G:Mg301
b:48.1
occ:1.00
|
O
|
G:MET125
|
2.1
|
58.0
|
1.0
|
OG1
|
G:THR8
|
2.7
|
48.5
|
1.0
|
O
|
G:ARG122
|
2.8
|
49.8
|
1.0
|
O
|
G:TYR119
|
2.8
|
46.1
|
1.0
|
CG2
|
G:THR8
|
3.2
|
49.3
|
1.0
|
O
|
G:ALA123
|
3.3
|
59.4
|
1.0
|
C
|
G:MET125
|
3.3
|
54.6
|
1.0
|
CB
|
G:THR8
|
3.5
|
48.6
|
1.0
|
C
|
G:ALA123
|
3.7
|
55.3
|
1.0
|
CA
|
G:ALA123
|
3.9
|
52.4
|
1.0
|
C
|
G:ARG122
|
3.9
|
50.5
|
1.0
|
CA
|
G:ARG126
|
4.0
|
48.3
|
1.0
|
C
|
G:TYR119
|
4.0
|
45.2
|
1.0
|
N
|
G:ARG126
|
4.0
|
50.2
|
1.0
|
N
|
G:THR8
|
4.2
|
52.5
|
1.0
|
N
|
G:MET125
|
4.3
|
56.3
|
1.0
|
CD
|
G:PRO127
|
4.3
|
46.3
|
1.0
|
N
|
G:ALA123
|
4.3
|
50.9
|
1.0
|
CA
|
G:MET125
|
4.3
|
58.0
|
1.0
|
CA
|
G:THR8
|
4.5
|
50.6
|
1.0
|
C
|
G:ARG126
|
4.6
|
45.6
|
1.0
|
N
|
G:TYR124
|
4.7
|
56.5
|
1.0
|
CA
|
G:TYR119
|
4.8
|
44.2
|
1.0
|
N
|
G:PRO127
|
4.8
|
45.0
|
1.0
|
C
|
G:TYR124
|
4.9
|
55.7
|
1.0
|
CB
|
G:MET125
|
5.0
|
64.2
|
1.0
|
|
Magnesium binding site 2 out
of 8 in 6zp8
Go back to
Magnesium Binding Sites List in 6zp8
Magnesium binding site 2 out
of 8 in the Yeast 20S Proteasome in Complex with Glidobactin-Like Natural Product HB335
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 2 of Yeast 20S Proteasome in Complex with Glidobactin-Like Natural Product HB335 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
I:Mg301
b:77.7
occ:1.00
|
O
|
I:ASP177
|
2.9
|
51.8
|
1.0
|
O
|
I:SER180
|
2.9
|
51.1
|
1.0
|
O
|
I:ALA174
|
3.2
|
53.8
|
1.0
|
OXT
|
I:ASP204
|
3.3
|
75.8
|
1.0
|
O
|
I:ASP204
|
3.9
|
72.4
|
1.0
|
C
|
I:ASP177
|
4.0
|
53.5
|
1.0
|
C
|
I:ASP204
|
4.0
|
69.3
|
1.0
|
NH1
|
Y:ARG19
|
4.1
|
62.8
|
1.0
|
C
|
I:SER180
|
4.1
|
54.5
|
1.0
|
C
|
I:ALA174
|
4.2
|
56.2
|
1.0
|
O
|
I:ALA178
|
4.2
|
61.0
|
1.0
|
CA
|
I:ASP175
|
4.3
|
58.6
|
1.0
|
NH2
|
Y:ARG19
|
4.3
|
63.7
|
1.0
|
O
|
I:ASP175
|
4.5
|
64.1
|
1.0
|
CA
|
I:ALA178
|
4.5
|
53.7
|
1.0
|
C
|
I:ALA178
|
4.6
|
55.9
|
1.0
|
C
|
I:ASP175
|
4.6
|
59.3
|
1.0
|
CZ
|
Y:ARG19
|
4.6
|
61.3
|
1.0
|
N
|
I:ALA178
|
4.7
|
50.7
|
1.0
|
N
|
I:ASP175
|
4.7
|
57.6
|
1.0
|
CA
|
I:GLY181
|
4.8
|
56.3
|
1.0
|
N
|
I:ASP177
|
4.8
|
55.0
|
1.0
|
OD1
|
I:ASP175
|
4.9
|
63.5
|
1.0
|
N
|
I:GLY181
|
4.9
|
54.7
|
1.0
|
N
|
I:SER180
|
4.9
|
52.0
|
1.0
|
|
Magnesium binding site 3 out
of 8 in 6zp8
Go back to
Magnesium Binding Sites List in 6zp8
Magnesium binding site 3 out
of 8 in the Yeast 20S Proteasome in Complex with Glidobactin-Like Natural Product HB335
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 3 of Yeast 20S Proteasome in Complex with Glidobactin-Like Natural Product HB335 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
K:Mg902
b:68.5
occ:1.00
|
O
|
K:ASP168
|
2.3
|
48.2
|
1.0
|
O
|
K:ALA165
|
2.3
|
50.2
|
1.0
|
O
|
W:ASP204
|
2.7
|
72.1
|
1.0
|
O
|
K:SER171
|
3.0
|
52.9
|
1.0
|
C
|
W:ASP204
|
3.2
|
68.7
|
1.0
|
C
|
K:ASP168
|
3.2
|
50.3
|
1.0
|
CA
|
W:ASP204
|
3.5
|
64.1
|
1.0
|
C
|
K:ALA165
|
3.5
|
51.0
|
1.0
|
O
|
K:HIS166
|
3.6
|
57.0
|
1.0
|
CA
|
K:ALA169
|
3.6
|
52.5
|
1.0
|
N
|
K:ALA169
|
3.7
|
53.1
|
1.0
|
CB
|
W:ASP204
|
3.8
|
62.9
|
1.0
|
C
|
K:ALA169
|
3.9
|
53.5
|
1.0
|
O
|
K:ALA169
|
3.9
|
57.9
|
1.0
|
OXT
|
W:ASP204
|
4.0
|
79.2
|
1.0
|
C
|
K:HIS166
|
4.0
|
51.8
|
1.0
|
NH1
|
K:ARG19
|
4.2
|
64.9
|
1.0
|
C
|
K:SER171
|
4.2
|
52.8
|
1.0
|
N
|
K:ASP168
|
4.3
|
49.4
|
1.0
|
CA
|
K:ASP168
|
4.3
|
49.6
|
1.0
|
CA
|
K:ALA165
|
4.4
|
51.7
|
1.0
|
N
|
K:HIS166
|
4.4
|
50.2
|
1.0
|
CA
|
K:HIS166
|
4.5
|
51.0
|
1.0
|
C
|
K:ARG167
|
4.5
|
51.3
|
1.0
|
N
|
K:SER171
|
4.6
|
51.9
|
1.0
|
O
|
K:ALA164
|
4.6
|
52.6
|
1.0
|
N
|
K:ARG167
|
4.7
|
50.2
|
1.0
|
N
|
K:TYR170
|
4.7
|
52.6
|
1.0
|
O
|
K:ARG167
|
4.8
|
54.2
|
1.0
|
N
|
W:ASP204
|
4.9
|
64.3
|
1.0
|
CA
|
K:SER171
|
4.9
|
51.1
|
1.0
|
CB
|
K:ALA169
|
4.9
|
51.5
|
1.0
|
CZ
|
K:ARG19
|
5.0
|
61.0
|
1.0
|
|
Magnesium binding site 4 out
of 8 in 6zp8
Go back to
Magnesium Binding Sites List in 6zp8
Magnesium binding site 4 out
of 8 in the Yeast 20S Proteasome in Complex with Glidobactin-Like Natural Product HB335
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 4 of Yeast 20S Proteasome in Complex with Glidobactin-Like Natural Product HB335 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
N:Mg201
b:36.6
occ:1.00
|
O
|
N:SER169
|
2.5
|
50.0
|
1.0
|
O
|
N:ILE163
|
2.7
|
47.8
|
1.0
|
O
|
N:ASP166
|
2.8
|
48.2
|
1.0
|
NH1
|
N:ARG19
|
3.4
|
51.2
|
1.0
|
CD1
|
a:LEU34
|
3.6
|
53.5
|
1.0
|
C
|
N:SER169
|
3.7
|
47.4
|
1.0
|
C
|
N:ASP166
|
3.8
|
46.4
|
1.0
|
C
|
N:ILE163
|
3.9
|
47.3
|
1.0
|
CA
|
N:GLY167
|
4.0
|
45.4
|
1.0
|
CZ
|
N:ARG19
|
4.1
|
50.2
|
1.0
|
CG2
|
N:ILE163
|
4.1
|
47.0
|
1.0
|
O
|
N:GLY167
|
4.2
|
44.2
|
1.0
|
N
|
N:GLY167
|
4.3
|
45.5
|
1.0
|
C
|
N:GLY167
|
4.3
|
45.1
|
1.0
|
CA
|
N:GLY170
|
4.4
|
49.1
|
1.0
|
NH2
|
N:ARG19
|
4.5
|
52.0
|
1.0
|
CA
|
N:ILE163
|
4.5
|
46.1
|
1.0
|
N
|
N:GLY170
|
4.5
|
47.3
|
1.0
|
N
|
N:SER169
|
4.7
|
46.1
|
1.0
|
CA
|
N:SER169
|
4.7
|
45.3
|
1.0
|
CG
|
a:LEU34
|
4.8
|
53.5
|
1.0
|
N
|
N:LYS164
|
4.9
|
47.8
|
1.0
|
CB
|
N:ILE163
|
5.0
|
45.5
|
1.0
|
NE
|
N:ARG19
|
5.0
|
50.0
|
1.0
|
CA
|
N:ASP166
|
5.0
|
46.1
|
1.0
|
N
|
N:ASP166
|
5.0
|
46.2
|
1.0
|
|
Magnesium binding site 5 out
of 8 in 6zp8
Go back to
Magnesium Binding Sites List in 6zp8
Magnesium binding site 5 out
of 8 in the Yeast 20S Proteasome in Complex with Glidobactin-Like Natural Product HB335
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 5 of Yeast 20S Proteasome in Complex with Glidobactin-Like Natural Product HB335 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
V:Mg902
b:78.9
occ:1.00
|
OXT
|
L:ASP222
|
2.3
|
73.6
|
1.0
|
O
|
V:ILE163
|
2.3
|
44.7
|
1.0
|
O
|
V:ASP166
|
2.3
|
44.3
|
1.0
|
C
|
L:ASP222
|
3.0
|
71.3
|
1.0
|
C
|
V:ASP166
|
3.1
|
48.8
|
1.0
|
O
|
V:SER169
|
3.2
|
55.4
|
1.0
|
O
|
V:TRP164
|
3.4
|
55.1
|
1.0
|
C
|
V:ILE163
|
3.4
|
50.0
|
1.0
|
C
|
V:TRP164
|
3.6
|
52.5
|
1.0
|
CA
|
L:ASP222
|
3.7
|
68.5
|
1.0
|
N
|
V:LEU167
|
3.7
|
50.7
|
1.0
|
O
|
L:ASP222
|
3.8
|
76.4
|
1.0
|
CA
|
V:LEU167
|
3.8
|
49.5
|
1.0
|
N
|
V:ASP166
|
3.9
|
47.1
|
1.0
|
O
|
V:GLY162
|
4.1
|
49.3
|
1.0
|
CA
|
V:TRP164
|
4.1
|
52.1
|
1.0
|
CA
|
V:ASP166
|
4.1
|
48.3
|
1.0
|
N
|
V:ASN165
|
4.1
|
52.1
|
1.0
|
N
|
V:TRP164
|
4.2
|
51.5
|
1.0
|
C
|
V:ASN165
|
4.2
|
49.1
|
1.0
|
C
|
V:SER169
|
4.4
|
51.6
|
1.0
|
NH1
|
V:ARG19
|
4.5
|
60.1
|
1.0
|
CA
|
V:ILE163
|
4.5
|
50.1
|
1.0
|
O
|
L:ARG221
|
4.5
|
68.2
|
1.0
|
CB
|
L:ASP222
|
4.5
|
69.1
|
1.0
|
C
|
V:LEU167
|
4.5
|
49.2
|
1.0
|
CD2
|
V:LEU167
|
4.6
|
47.9
|
1.0
|
CA
|
V:ASN165
|
4.7
|
50.7
|
1.0
|
O
|
V:LEU167
|
4.7
|
48.5
|
1.0
|
O
|
V:ASN165
|
4.8
|
47.7
|
1.0
|
N
|
L:ASP222
|
4.9
|
67.1
|
1.0
|
CD1
|
L:ILE35
|
4.9
|
56.6
|
1.0
|
CB
|
V:LEU167
|
5.0
|
48.9
|
1.0
|
|
Magnesium binding site 6 out
of 8 in 6zp8
Go back to
Magnesium Binding Sites List in 6zp8
Magnesium binding site 6 out
of 8 in the Yeast 20S Proteasome in Complex with Glidobactin-Like Natural Product HB335
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 6 of Yeast 20S Proteasome in Complex with Glidobactin-Like Natural Product HB335 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
W:Mg301
b:70.5
occ:1.00
|
O
|
W:ASP177
|
2.6
|
50.2
|
1.0
|
O
|
W:SER180
|
2.8
|
56.4
|
1.0
|
O
|
W:ALA174
|
3.1
|
53.2
|
1.0
|
O
|
W:HOH405
|
3.2
|
41.6
|
1.0
|
OXT
|
W:ASP204
|
3.6
|
79.2
|
1.0
|
C
|
W:ASP177
|
3.7
|
52.2
|
1.0
|
C
|
W:SER180
|
4.0
|
54.9
|
1.0
|
O
|
W:ALA178
|
4.0
|
53.1
|
1.0
|
O
|
W:ASP204
|
4.1
|
72.1
|
1.0
|
NH1
|
K:ARG19
|
4.1
|
64.9
|
1.0
|
C
|
W:ALA174
|
4.2
|
54.6
|
1.0
|
CA
|
W:ALA178
|
4.2
|
53.0
|
1.0
|
C
|
W:ASP204
|
4.3
|
68.7
|
1.0
|
C
|
W:ALA178
|
4.3
|
53.4
|
1.0
|
CA
|
W:ASP175
|
4.3
|
57.7
|
1.0
|
N
|
W:ALA178
|
4.4
|
51.3
|
1.0
|
NH2
|
K:ARG19
|
4.4
|
63.1
|
1.0
|
O
|
W:ASP175
|
4.5
|
64.2
|
1.0
|
C
|
W:ASP175
|
4.5
|
58.0
|
1.0
|
N
|
W:ASP177
|
4.6
|
55.3
|
1.0
|
CZ
|
K:ARG19
|
4.6
|
61.0
|
1.0
|
N
|
W:SER180
|
4.7
|
53.8
|
1.0
|
N
|
W:ASP175
|
4.7
|
56.3
|
1.0
|
CA
|
W:ASP177
|
4.7
|
54.1
|
1.0
|
CA
|
W:GLY181
|
4.9
|
55.4
|
1.0
|
N
|
W:GLY181
|
4.9
|
54.6
|
1.0
|
CA
|
W:SER180
|
4.9
|
55.4
|
1.0
|
|
Magnesium binding site 7 out
of 8 in 6zp8
Go back to
Magnesium Binding Sites List in 6zp8
Magnesium binding site 7 out
of 8 in the Yeast 20S Proteasome in Complex with Glidobactin-Like Natural Product HB335
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 7 of Yeast 20S Proteasome in Complex with Glidobactin-Like Natural Product HB335 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
Y:Mg902
b:68.7
occ:1.00
|
O
|
Y:ASP168
|
2.3
|
49.0
|
1.0
|
O
|
I:ASP204
|
2.5
|
72.4
|
1.0
|
O
|
Y:ALA165
|
2.6
|
51.2
|
1.0
|
O
|
Y:SER171
|
2.9
|
56.4
|
1.0
|
C
|
I:ASP204
|
3.1
|
69.3
|
1.0
|
C
|
Y:ASP168
|
3.2
|
49.6
|
1.0
|
CA
|
Y:ALA169
|
3.4
|
49.8
|
1.0
|
O
|
Y:ALA169
|
3.5
|
52.5
|
1.0
|
CA
|
I:ASP204
|
3.6
|
65.3
|
1.0
|
C
|
Y:ALA169
|
3.6
|
49.7
|
1.0
|
N
|
Y:ALA169
|
3.7
|
51.2
|
1.0
|
C
|
Y:ALA165
|
3.8
|
49.7
|
1.0
|
NH1
|
Y:ARG19
|
3.8
|
62.8
|
1.0
|
CB
|
I:ASP204
|
3.9
|
65.8
|
1.0
|
O
|
Y:HIS166
|
4.0
|
51.2
|
1.0
|
OXT
|
I:ASP204
|
4.0
|
75.8
|
1.0
|
C
|
Y:SER171
|
4.1
|
53.3
|
1.0
|
N
|
Y:SER171
|
4.4
|
49.3
|
1.0
|
C
|
Y:HIS166
|
4.4
|
49.6
|
1.0
|
CA
|
Y:ASP168
|
4.5
|
50.2
|
1.0
|
N
|
Y:TYR170
|
4.5
|
48.5
|
1.0
|
N
|
Y:ASP168
|
4.5
|
50.9
|
1.0
|
CA
|
Y:ALA165
|
4.6
|
49.3
|
1.0
|
CZ
|
Y:ARG19
|
4.6
|
61.3
|
1.0
|
N
|
Y:HIS166
|
4.7
|
50.1
|
1.0
|
CB
|
Y:ALA169
|
4.8
|
48.6
|
1.0
|
CA
|
Y:SER171
|
4.8
|
49.6
|
1.0
|
C
|
Y:ARG167
|
4.8
|
51.7
|
1.0
|
O
|
Y:ALA164
|
4.8
|
51.1
|
1.0
|
CA
|
Y:HIS166
|
4.9
|
49.2
|
1.0
|
CG
|
I:ASP204
|
5.0
|
69.2
|
1.0
|
|
Magnesium binding site 8 out
of 8 in 6zp8
Go back to
Magnesium Binding Sites List in 6zp8
Magnesium binding site 8 out
of 8 in the Yeast 20S Proteasome in Complex with Glidobactin-Like Natural Product HB335
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 8 of Yeast 20S Proteasome in Complex with Glidobactin-Like Natural Product HB335 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
Z:Mg301
b:56.1
occ:1.00
|
O
|
Z:VAL198
|
2.7
|
56.4
|
1.0
|
O
|
Z:THR192
|
3.0
|
54.3
|
1.0
|
O
|
Z:HIS195
|
3.2
|
45.8
|
1.0
|
O
|
Z:ASP222
|
3.3
|
74.0
|
1.0
|
NH2
|
Z:ARG28
|
3.5
|
60.1
|
1.0
|
O
|
Z:ILE196
|
3.8
|
57.1
|
1.0
|
C
|
Z:VAL198
|
3.9
|
55.1
|
1.0
|
CG2
|
Z:THR192
|
3.9
|
62.5
|
1.0
|
NH2
|
H:ARG19
|
4.0
|
65.6
|
1.0
|
OD1
|
Z:ASP222
|
4.0
|
74.1
|
1.0
|
C
|
Z:THR192
|
4.0
|
58.9
|
1.0
|
CA
|
Z:ILE196
|
4.1
|
49.6
|
1.0
|
C
|
Z:ILE196
|
4.1
|
50.0
|
1.0
|
C
|
Z:HIS195
|
4.2
|
49.4
|
1.0
|
C
|
Z:ASP222
|
4.3
|
72.5
|
1.0
|
CA
|
Z:THR192
|
4.4
|
59.2
|
1.0
|
CZ
|
Z:ARG28
|
4.5
|
58.1
|
1.0
|
N
|
Z:VAL198
|
4.6
|
51.4
|
1.0
|
NH1
|
Z:ARG28
|
4.6
|
61.6
|
1.0
|
O
|
Z:LYS220
|
4.6
|
62.9
|
1.0
|
N
|
Z:ILE196
|
4.6
|
48.7
|
1.0
|
CA
|
Z:GLY199
|
4.7
|
56.9
|
1.0
|
OXT
|
Z:ASP222
|
4.7
|
74.3
|
1.0
|
N
|
Z:GLY199
|
4.7
|
54.8
|
1.0
|
CB
|
Z:THR192
|
4.8
|
60.3
|
1.0
|
CA
|
Z:VAL198
|
4.8
|
52.4
|
1.0
|
CZ
|
H:ARG19
|
4.8
|
62.1
|
1.0
|
NH1
|
H:ARG19
|
4.8
|
63.8
|
1.0
|
CG
|
Z:ASP222
|
5.0
|
68.9
|
1.0
|
|
Reference:
L.Zhao,
C.Le Chapelain,
A.O.Brachmann,
M.Kaiser,
M.Groll,
H.B.Bode.
Activation, Structure, Biosynthesis and Bioactivity of Glidobactin-Like Proteasome Inhibitors From Photorhabdus Laumondii. Chembiochem V. 22 1582 2021.
ISSN: ESSN 1439-7633
PubMed: 33452852
DOI: 10.1002/CBIC.202100014
Page generated: Wed Oct 2 02:29:58 2024
|