Magnesium in PDB 4qz1: Ycp BETA5-M45T Mutant in Complex with the Epoxyketone Inhibitor Onx 0914
Enzymatic activity of Ycp BETA5-M45T Mutant in Complex with the Epoxyketone Inhibitor Onx 0914
All present enzymatic activity of Ycp BETA5-M45T Mutant in Complex with the Epoxyketone Inhibitor Onx 0914:
3.4.25.1;
Protein crystallography data
The structure of Ycp BETA5-M45T Mutant in Complex with the Epoxyketone Inhibitor Onx 0914, PDB code: 4qz1
was solved by
E.M.Huber,
W.Heinemeyer,
M.Groll,
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 (°)
|
137.180,
298.800,
146.830,
90.00,
113.02,
90.00
|
R / Rfree (%)
|
17.6 /
21.6
|
Other elements in 4qz1:
The structure of Ycp BETA5-M45T Mutant in Complex with the Epoxyketone Inhibitor Onx 0914 also contains other interesting chemical elements:
Magnesium Binding Sites:
The binding sites of Magnesium atom in the Ycp BETA5-M45T Mutant in Complex with the Epoxyketone Inhibitor Onx 0914
(pdb code 4qz1). This binding sites where shown within
5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the
Ycp BETA5-M45T Mutant in Complex with the Epoxyketone Inhibitor Onx 0914, PDB code: 4qz1:
Jump to Magnesium binding site number:
1;
2;
3;
Magnesium binding site 1 out
of 3 in 4qz1
Go back to
Magnesium Binding Sites List in 4qz1
Magnesium binding site 1 out
of 3 in the Ycp BETA5-M45T Mutant in Complex with the Epoxyketone Inhibitor Onx 0914
 Mono view
 Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 1 of Ycp BETA5-M45T Mutant in Complex with the Epoxyketone Inhibitor Onx 0914 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
K:Mg302
b:61.7
occ:1.00
|
O
|
K:ASP168
|
2.2
|
70.3
|
1.0
|
O
|
K:ALA165
|
2.3
|
64.8
|
1.0
|
O
|
W:ASP204
|
2.5
|
75.9
|
1.0
|
O
|
K:SER171
|
2.7
|
62.9
|
1.0
|
C
|
W:ASP204
|
3.2
|
78.9
|
1.0
|
C
|
K:ASP168
|
3.3
|
67.1
|
1.0
|
C
|
K:ALA165
|
3.5
|
66.6
|
1.0
|
CA
|
W:ASP204
|
3.6
|
77.4
|
1.0
|
O
|
K:HIS166
|
3.6
|
63.5
|
1.0
|
CA
|
K:ALA169
|
3.7
|
68.1
|
1.0
|
N
|
K:ALA169
|
3.9
|
68.1
|
1.0
|
C
|
K:SER171
|
3.9
|
64.3
|
1.0
|
CB
|
W:ASP204
|
4.0
|
76.2
|
1.0
|
C
|
K:ALA169
|
4.0
|
71.4
|
1.0
|
NH1
|
K:ARG19
|
4.0
|
85.2
|
1.0
|
C
|
K:HIS166
|
4.1
|
64.6
|
1.0
|
O
|
K:ALA169
|
4.1
|
72.0
|
1.0
|
OXT
|
W:ASP204
|
4.2
|
94.4
|
1.0
|
N
|
K:SER171
|
4.4
|
63.7
|
1.0
|
N
|
K:ASP168
|
4.4
|
67.9
|
1.0
|
N
|
K:HIS166
|
4.4
|
64.5
|
1.0
|
CA
|
K:ASP168
|
4.4
|
65.1
|
1.0
|
CA
|
K:ALA165
|
4.4
|
68.0
|
1.0
|
CA
|
K:HIS166
|
4.5
|
65.6
|
1.0
|
O
|
K:ALA164
|
4.6
|
73.7
|
1.0
|
C
|
K:ARG167
|
4.6
|
68.2
|
1.0
|
CZ
|
K:ARG19
|
4.7
|
85.2
|
1.0
|
CA
|
K:SER171
|
4.7
|
63.4
|
1.0
|
N
|
K:ARG167
|
4.8
|
66.4
|
1.0
|
N
|
K:TYR170
|
4.8
|
64.8
|
1.0
|
O
|
K:ARG167
|
4.9
|
67.8
|
1.0
|
NH2
|
K:ARG19
|
4.9
|
94.8
|
1.0
|
N
|
K:GLY172
|
4.9
|
63.9
|
1.0
|
|
Magnesium binding site 2 out
of 3 in 4qz1
Go back to
Magnesium Binding Sites List in 4qz1
Magnesium binding site 2 out
of 3 in the Ycp BETA5-M45T Mutant in Complex with the Epoxyketone Inhibitor Onx 0914
 Mono view
 Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 2 of Ycp BETA5-M45T Mutant in Complex with the Epoxyketone Inhibitor Onx 0914 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
N:Mg202
b:62.6
occ:1.00
|
O
|
N:ILE163
|
2.6
|
57.4
|
1.0
|
O
|
N:SER169
|
2.6
|
64.1
|
1.0
|
O
|
N:ASP166
|
2.7
|
64.4
|
1.0
|
NH1
|
N:ARG19
|
3.7
|
64.2
|
1.0
|
CD1
|
a:LEU34
|
3.7
|
76.6
|
1.0
|
C
|
N:ILE163
|
3.7
|
62.6
|
1.0
|
C
|
N:ASP166
|
3.8
|
63.2
|
1.0
|
C
|
N:SER169
|
3.8
|
62.5
|
1.0
|
CG2
|
N:ILE163
|
4.1
|
65.5
|
1.0
|
CA
|
N:GLY167
|
4.1
|
63.5
|
1.0
|
CZ
|
N:ARG19
|
4.4
|
67.7
|
1.0
|
N
|
N:GLY167
|
4.4
|
61.0
|
1.0
|
O
|
N:GLY167
|
4.4
|
60.5
|
1.0
|
CA
|
N:ILE163
|
4.5
|
65.1
|
1.0
|
C
|
N:GLY167
|
4.5
|
63.6
|
1.0
|
CA
|
N:GLY170
|
4.6
|
67.5
|
1.0
|
NH2
|
N:ARG19
|
4.6
|
69.5
|
1.0
|
N
|
N:GLY170
|
4.7
|
65.0
|
1.0
|
N
|
N:SER169
|
4.7
|
59.9
|
1.0
|
O
|
N:LYS164
|
4.7
|
70.0
|
1.0
|
N
|
N:LYS164
|
4.7
|
65.4
|
1.0
|
C
|
N:LYS164
|
4.8
|
67.3
|
1.0
|
CA
|
N:SER169
|
4.8
|
59.6
|
1.0
|
CG
|
a:LEU34
|
4.9
|
78.3
|
1.0
|
CA
|
N:LYS164
|
4.9
|
67.8
|
1.0
|
CB
|
N:ILE163
|
4.9
|
65.4
|
1.0
|
N
|
N:ASP166
|
4.9
|
61.6
|
1.0
|
CA
|
N:ASP166
|
5.0
|
63.6
|
1.0
|
|
Magnesium binding site 3 out
of 3 in 4qz1
Go back to
Magnesium Binding Sites List in 4qz1
Magnesium binding site 3 out
of 3 in the Ycp BETA5-M45T Mutant in Complex with the Epoxyketone Inhibitor Onx 0914
 Mono view
 Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 3 of Ycp BETA5-M45T Mutant in Complex with the Epoxyketone Inhibitor Onx 0914 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
Y:Mg302
b:68.2
occ:1.00
|
O
|
Y:ASP168
|
2.2
|
66.8
|
1.0
|
O
|
Y:ALA165
|
2.4
|
66.1
|
1.0
|
O
|
I:ASP204
|
2.4
|
82.7
|
1.0
|
O
|
Y:SER171
|
2.8
|
67.0
|
1.0
|
C
|
Y:ASP168
|
3.2
|
62.8
|
1.0
|
C
|
I:ASP204
|
3.2
|
83.9
|
1.0
|
O
|
Y:HIS166
|
3.6
|
67.6
|
1.0
|
C
|
Y:ALA165
|
3.6
|
68.8
|
1.0
|
CA
|
Y:ALA169
|
3.6
|
64.7
|
1.0
|
CA
|
I:ASP204
|
3.7
|
85.6
|
1.0
|
N
|
Y:ALA169
|
3.8
|
61.3
|
1.0
|
C
|
Y:ALA169
|
4.0
|
66.8
|
1.0
|
C
|
Y:HIS166
|
4.0
|
67.3
|
1.0
|
C
|
Y:SER171
|
4.0
|
64.9
|
1.0
|
O
|
Y:ALA169
|
4.1
|
73.0
|
1.0
|
NH1
|
Y:ARG19
|
4.1
|
94.7
|
1.0
|
CB
|
I:ASP204
|
4.1
|
85.4
|
1.0
|
OXT
|
I:ASP204
|
4.2
|
75.9
|
1.0
|
N
|
Y:ASP168
|
4.3
|
64.7
|
1.0
|
CA
|
Y:ASP168
|
4.3
|
63.1
|
1.0
|
N
|
Y:SER171
|
4.4
|
61.4
|
1.0
|
N
|
Y:HIS166
|
4.4
|
69.6
|
1.0
|
CA
|
Y:HIS166
|
4.5
|
66.5
|
1.0
|
CA
|
Y:ALA165
|
4.5
|
66.4
|
1.0
|
C
|
Y:ARG167
|
4.5
|
66.7
|
1.0
|
O
|
Y:ALA164
|
4.6
|
64.9
|
1.0
|
N
|
Y:TYR170
|
4.7
|
64.3
|
1.0
|
N
|
Y:ARG167
|
4.7
|
66.7
|
1.0
|
O
|
Y:ARG167
|
4.8
|
63.4
|
1.0
|
CZ
|
Y:ARG19
|
4.8
|
87.7
|
1.0
|
CA
|
Y:SER171
|
4.8
|
61.5
|
1.0
|
CB
|
Y:ALA169
|
5.0
|
64.6
|
1.0
|
NH2
|
Y:ARG19
|
5.0
|
89.7
|
1.0
|
|
Reference:
E.M.Huber,
W.Heinemeyer,
M.Groll.
Bortezomib-Resistant Mutant Proteasomes: Structural and Biochemical Evaluation with Carfilzomib and Onx 0914. Structure 2015.
ISSN: ISSN 0969-2126
PubMed: 25599643
DOI: 10.1016/J.STR.2014.11.019
Page generated: Tue Aug 20 02:36:18 2024
|