Magnesium in PDB 4qv5: Ycp BETA5-M45I Mutant
Enzymatic activity of Ycp BETA5-M45I Mutant
All present enzymatic activity of Ycp BETA5-M45I Mutant:
3.4.25.1;
Protein crystallography data
The structure of Ycp BETA5-M45I Mutant, PDB code: 4qv5
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 /
2.70
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
134.400,
301.140,
144.120,
90.00,
112.72,
90.00
|
R / Rfree (%)
|
18.9 /
21.7
|
Other elements in 4qv5:
The structure of Ycp BETA5-M45I Mutant also contains other interesting chemical elements:
Magnesium Binding Sites:
The binding sites of Magnesium atom in the Ycp BETA5-M45I Mutant
(pdb code 4qv5). This binding sites where shown within
5.0 Angstroms radius around Magnesium atom.
In total 7 binding sites of Magnesium where determined in the
Ycp BETA5-M45I Mutant, PDB code: 4qv5:
Jump to Magnesium binding site number:
1;
2;
3;
4;
5;
6;
7;
Magnesium binding site 1 out
of 7 in 4qv5
Go back to
Magnesium Binding Sites List in 4qv5
Magnesium binding site 1 out
of 7 in the Ycp BETA5-M45I Mutant
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 1 of Ycp BETA5-M45I Mutant within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
G:Mg301
b:50.9
occ:1.00
|
O
|
G:MET125
|
2.2
|
51.4
|
1.0
|
OG1
|
G:THR8
|
2.6
|
43.8
|
1.0
|
O
|
G:ARG122
|
2.6
|
45.2
|
1.0
|
O
|
G:TYR119
|
2.8
|
39.5
|
1.0
|
CG2
|
G:THR8
|
3.2
|
46.9
|
1.0
|
O
|
G:ALA123
|
3.3
|
53.6
|
1.0
|
C
|
G:MET125
|
3.4
|
51.7
|
1.0
|
CB
|
G:THR8
|
3.4
|
46.0
|
1.0
|
C
|
G:ALA123
|
3.6
|
51.7
|
1.0
|
CA
|
G:ALA123
|
3.7
|
50.7
|
1.0
|
C
|
G:ARG122
|
3.7
|
47.9
|
1.0
|
C
|
G:TYR119
|
4.0
|
38.5
|
1.0
|
N
|
G:THR8
|
4.1
|
49.4
|
1.0
|
N
|
G:ALA123
|
4.1
|
49.4
|
1.0
|
CA
|
G:ARG126
|
4.2
|
45.1
|
1.0
|
N
|
G:ARG126
|
4.2
|
46.6
|
1.0
|
N
|
G:MET125
|
4.2
|
54.2
|
1.0
|
CA
|
G:MET125
|
4.4
|
55.5
|
1.0
|
CA
|
G:THR8
|
4.4
|
47.1
|
1.0
|
CD
|
G:PRO127
|
4.6
|
42.7
|
1.0
|
N
|
G:TYR124
|
4.6
|
53.6
|
1.0
|
O
|
G:HOH409
|
4.7
|
37.0
|
1.0
|
CA
|
G:TYR119
|
4.7
|
36.8
|
1.0
|
C
|
G:ARG126
|
4.9
|
44.3
|
1.0
|
C
|
G:TYR124
|
5.0
|
52.2
|
1.0
|
CA
|
G:ARG122
|
5.0
|
50.7
|
1.0
|
N
|
G:THR120
|
5.0
|
38.8
|
1.0
|
CB
|
G:ALA123
|
5.0
|
50.8
|
1.0
|
CB
|
G:MET125
|
5.0
|
59.5
|
1.0
|
|
Magnesium binding site 2 out
of 7 in 4qv5
Go back to
Magnesium Binding Sites List in 4qv5
Magnesium binding site 2 out
of 7 in the Ycp BETA5-M45I Mutant
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 2 of Ycp BETA5-M45I Mutant within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
H:Mg301
b:56.4
occ:1.00
|
OE1
|
H:GLN91
|
2.5
|
47.7
|
1.0
|
O
|
H:HOH407
|
2.6
|
44.8
|
1.0
|
OD1
|
N:ASP51
|
2.8
|
32.1
|
1.0
|
CD
|
H:GLN91
|
3.4
|
46.9
|
1.0
|
NE2
|
H:GLN91
|
3.6
|
48.1
|
1.0
|
OD2
|
N:ASP51
|
3.6
|
40.8
|
1.0
|
CG
|
N:ASP51
|
3.6
|
28.6
|
1.0
|
O
|
N:ASN92
|
3.9
|
51.6
|
1.0
|
CE1
|
H:PHE88
|
4.7
|
33.5
|
1.0
|
CG
|
H:GLN91
|
4.8
|
43.6
|
1.0
|
OG
|
N:SER48
|
4.9
|
40.2
|
1.0
|
CZ
|
H:PHE88
|
5.0
|
33.8
|
1.0
|
|
Magnesium binding site 3 out
of 7 in 4qv5
Go back to
Magnesium Binding Sites List in 4qv5
Magnesium binding site 3 out
of 7 in the Ycp BETA5-M45I Mutant
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 3 of Ycp BETA5-M45I Mutant within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
K:Mg301
b:48.8
occ:1.00
|
O
|
W:ASP204
|
2.2
|
58.9
|
1.0
|
O
|
K:ALA165
|
2.3
|
43.2
|
1.0
|
O
|
K:ASP168
|
2.3
|
42.6
|
1.0
|
O
|
K:SER171
|
2.7
|
46.8
|
1.0
|
C
|
W:ASP204
|
3.1
|
59.2
|
1.0
|
C
|
K:ASP168
|
3.3
|
40.3
|
1.0
|
C
|
K:ALA165
|
3.4
|
42.2
|
1.0
|
CA
|
W:ASP204
|
3.6
|
55.6
|
1.0
|
CA
|
K:ALA169
|
3.8
|
39.1
|
1.0
|
NH1
|
K:ARG19
|
3.8
|
52.9
|
1.0
|
C
|
K:SER171
|
3.9
|
44.0
|
1.0
|
O
|
K:HIS166
|
3.9
|
44.3
|
1.0
|
CB
|
W:ASP204
|
3.9
|
55.0
|
1.0
|
O
|
K:ALA169
|
3.9
|
42.9
|
1.0
|
N
|
K:ALA169
|
4.0
|
38.6
|
1.0
|
C
|
K:ALA169
|
4.0
|
41.2
|
1.0
|
OXT
|
W:ASP204
|
4.1
|
59.9
|
1.0
|
C
|
K:HIS166
|
4.2
|
42.6
|
1.0
|
CA
|
K:ALA165
|
4.3
|
42.8
|
1.0
|
N
|
K:SER171
|
4.4
|
40.0
|
1.0
|
N
|
K:HIS166
|
4.4
|
41.5
|
1.0
|
CZ
|
K:ARG19
|
4.5
|
51.3
|
1.0
|
N
|
K:ASP168
|
4.5
|
40.3
|
1.0
|
CA
|
K:ASP168
|
4.5
|
40.1
|
1.0
|
CA
|
K:HIS166
|
4.6
|
42.6
|
1.0
|
O
|
K:ALA164
|
4.6
|
41.4
|
1.0
|
CA
|
K:SER171
|
4.7
|
40.5
|
1.0
|
NH2
|
K:ARG19
|
4.7
|
53.2
|
1.0
|
C
|
K:ARG167
|
4.8
|
41.8
|
1.0
|
N
|
K:TYR170
|
4.8
|
41.9
|
1.0
|
N
|
K:GLY172
|
4.8
|
46.3
|
1.0
|
N
|
K:ARG167
|
4.9
|
41.8
|
1.0
|
CG
|
W:ASP204
|
4.9
|
53.8
|
1.0
|
CA
|
K:GLY172
|
4.9
|
46.5
|
1.0
|
|
Magnesium binding site 4 out
of 7 in 4qv5
Go back to
Magnesium Binding Sites List in 4qv5
Magnesium binding site 4 out
of 7 in the Ycp BETA5-M45I Mutant
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 4 of Ycp BETA5-M45I Mutant within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
K:Mg302
b:54.9
occ:1.00
|
O
|
K:ILE82
|
2.9
|
37.6
|
1.0
|
CB
|
K:ASN85
|
3.6
|
34.9
|
1.0
|
C
|
K:ILE82
|
3.7
|
36.0
|
1.0
|
CA
|
K:ILE82
|
3.8
|
35.8
|
1.0
|
N
|
K:LEU86
|
3.8
|
34.3
|
1.0
|
CG2
|
K:ILE82
|
4.0
|
35.3
|
1.0
|
C
|
K:ASN85
|
4.2
|
34.8
|
1.0
|
CA
|
K:LEU86
|
4.3
|
33.1
|
1.0
|
CB
|
K:LEU86
|
4.3
|
32.5
|
1.0
|
CB
|
K:ILE82
|
4.4
|
35.7
|
1.0
|
CA
|
K:ASN85
|
4.4
|
34.7
|
1.0
|
CH2
|
K:TRP58
|
4.5
|
35.5
|
1.0
|
O
|
K:LYS81
|
4.6
|
36.3
|
1.0
|
CG
|
K:ASN85
|
4.7
|
35.1
|
1.0
|
OD1
|
K:ASN85
|
4.8
|
38.4
|
1.0
|
CG1
|
K:ILE82
|
4.8
|
35.9
|
1.0
|
O
|
K:ASN85
|
4.9
|
34.8
|
1.0
|
N
|
K:ASN85
|
4.9
|
34.4
|
1.0
|
N
|
K:ILE82
|
5.0
|
36.5
|
1.0
|
|
Magnesium binding site 5 out
of 7 in 4qv5
Go back to
Magnesium Binding Sites List in 4qv5
Magnesium binding site 5 out
of 7 in the Ycp BETA5-M45I Mutant
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 5 of Ycp BETA5-M45I Mutant within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
N:Mg201
b:50.5
occ:1.00
|
O
|
N:ILE163
|
2.9
|
40.9
|
1.0
|
O
|
N:SER169
|
3.1
|
37.6
|
1.0
|
CD1
|
a:LEU34
|
3.5
|
45.0
|
1.0
|
O
|
N:ASP166
|
3.5
|
44.0
|
1.0
|
NH1
|
N:ARG19
|
3.6
|
41.6
|
1.0
|
C
|
N:ILE163
|
4.0
|
41.5
|
1.0
|
CG2
|
N:ILE163
|
4.0
|
40.7
|
1.0
|
CZ
|
N:ARG19
|
4.1
|
41.4
|
1.0
|
C
|
N:SER169
|
4.2
|
38.6
|
1.0
|
NH2
|
N:ARG19
|
4.2
|
43.0
|
1.0
|
C
|
N:ASP166
|
4.4
|
42.0
|
1.0
|
CA
|
N:GLY167
|
4.4
|
41.0
|
1.0
|
CA
|
N:GLY170
|
4.5
|
41.1
|
1.0
|
O
|
N:GLY167
|
4.6
|
37.2
|
1.0
|
CA
|
N:ILE163
|
4.7
|
41.0
|
1.0
|
CG
|
a:LEU34
|
4.8
|
45.1
|
1.0
|
N
|
N:GLY167
|
4.8
|
40.9
|
1.0
|
C
|
N:GLY167
|
4.8
|
40.0
|
1.0
|
N
|
N:GLY170
|
4.8
|
39.8
|
1.0
|
N
|
N:LYS164
|
5.0
|
43.8
|
1.0
|
O
|
N:LYS164
|
5.0
|
50.0
|
1.0
|
CB
|
N:ILE163
|
5.0
|
40.5
|
1.0
|
|
Magnesium binding site 6 out
of 7 in 4qv5
Go back to
Magnesium Binding Sites List in 4qv5
Magnesium binding site 6 out
of 7 in the Ycp BETA5-M45I Mutant
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 6 of Ycp BETA5-M45I Mutant within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
V:Mg301
b:55.0
occ:1.00
|
OXT
|
L:ASP222
|
2.0
|
68.1
|
1.0
|
O
|
V:ILE163
|
2.2
|
44.2
|
1.0
|
O
|
V:ASP166
|
2.2
|
43.5
|
1.0
|
O
|
V:SER169
|
2.2
|
42.3
|
1.0
|
C
|
L:ASP222
|
3.1
|
65.9
|
1.0
|
C
|
V:ASP166
|
3.2
|
43.3
|
1.0
|
C
|
V:ILE163
|
3.3
|
48.2
|
1.0
|
C
|
V:SER169
|
3.4
|
43.8
|
1.0
|
CA
|
L:ASP222
|
3.8
|
66.0
|
1.0
|
CA
|
V:LEU167
|
3.8
|
42.6
|
1.0
|
NH1
|
V:ARG19
|
3.8
|
59.0
|
1.0
|
O
|
V:GLY162
|
3.9
|
48.9
|
1.0
|
N
|
V:LEU167
|
3.9
|
43.0
|
1.0
|
CA
|
V:ILE163
|
4.1
|
49.0
|
1.0
|
O
|
L:ASP222
|
4.1
|
63.1
|
1.0
|
C
|
V:LEU167
|
4.2
|
42.6
|
1.0
|
O
|
V:TRP164
|
4.2
|
51.1
|
1.0
|
N
|
V:ASP166
|
4.2
|
44.0
|
1.0
|
N
|
V:SER169
|
4.2
|
43.3
|
1.0
|
N
|
V:TRP164
|
4.2
|
48.2
|
1.0
|
CB
|
L:ASP222
|
4.2
|
66.8
|
1.0
|
C
|
V:TRP164
|
4.3
|
49.6
|
1.0
|
O
|
V:LEU167
|
4.3
|
42.3
|
1.0
|
N
|
V:GLY170
|
4.3
|
45.6
|
1.0
|
CA
|
V:ASP166
|
4.3
|
43.7
|
1.0
|
CA
|
V:GLY170
|
4.3
|
48.1
|
1.0
|
CA
|
V:SER169
|
4.3
|
44.0
|
1.0
|
CA
|
V:TRP164
|
4.5
|
49.6
|
1.0
|
CZ
|
V:ARG19
|
4.5
|
57.9
|
1.0
|
NH2
|
V:ARG19
|
4.7
|
60.0
|
1.0
|
N
|
V:ASN165
|
4.7
|
47.5
|
1.0
|
CB
|
V:SER169
|
4.7
|
45.4
|
1.0
|
C
|
V:GLY162
|
4.8
|
49.6
|
1.0
|
N
|
V:GLY168
|
4.9
|
43.5
|
1.0
|
C
|
V:ASN165
|
4.9
|
45.5
|
1.0
|
N
|
V:ILE163
|
4.9
|
49.5
|
1.0
|
|
Magnesium binding site 7 out
of 7 in 4qv5
Go back to
Magnesium Binding Sites List in 4qv5
Magnesium binding site 7 out
of 7 in the Ycp BETA5-M45I Mutant
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 7 of Ycp BETA5-M45I Mutant within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
Y:Mg301
b:58.3
occ:1.00
|
O
|
Y:ASP168
|
2.3
|
44.6
|
1.0
|
O
|
I:ASP204
|
2.4
|
56.7
|
1.0
|
O
|
Y:ALA165
|
2.4
|
42.2
|
1.0
|
O
|
Y:SER171
|
3.1
|
42.5
|
1.0
|
C
|
I:ASP204
|
3.2
|
57.6
|
1.0
|
C
|
Y:ASP168
|
3.2
|
41.6
|
1.0
|
O
|
Y:HIS166
|
3.6
|
40.5
|
1.0
|
C
|
Y:ALA165
|
3.6
|
41.6
|
1.0
|
CA
|
Y:ALA169
|
3.6
|
41.6
|
1.0
|
CA
|
I:ASP204
|
3.7
|
54.8
|
1.0
|
N
|
Y:ALA169
|
3.8
|
41.6
|
1.0
|
C
|
Y:HIS166
|
4.0
|
40.7
|
1.0
|
C
|
Y:ALA169
|
4.0
|
43.0
|
1.0
|
O
|
Y:ALA169
|
4.1
|
44.1
|
1.0
|
OXT
|
I:ASP204
|
4.1
|
60.2
|
1.0
|
NH1
|
Y:ARG19
|
4.1
|
57.7
|
1.0
|
CB
|
I:ASP204
|
4.1
|
55.1
|
1.0
|
N
|
Y:ASP168
|
4.3
|
41.1
|
1.0
|
C
|
Y:SER171
|
4.3
|
44.0
|
1.0
|
CA
|
Y:ASP168
|
4.4
|
40.5
|
1.0
|
N
|
Y:HIS166
|
4.4
|
42.6
|
1.0
|
CA
|
Y:HIS166
|
4.5
|
42.1
|
1.0
|
C
|
Y:ARG167
|
4.5
|
40.7
|
1.0
|
CA
|
Y:ALA165
|
4.5
|
40.6
|
1.0
|
O
|
Y:ALA164
|
4.6
|
40.4
|
1.0
|
N
|
Y:ARG167
|
4.7
|
40.2
|
1.0
|
N
|
Y:SER171
|
4.7
|
42.8
|
1.0
|
O
|
Y:ARG167
|
4.7
|
41.2
|
1.0
|
CZ
|
Y:ARG19
|
4.8
|
55.0
|
1.0
|
N
|
Y:TYR170
|
4.9
|
42.5
|
1.0
|
CB
|
Y:ALA169
|
4.9
|
40.9
|
1.0
|
N
|
I:ASP204
|
5.0
|
52.6
|
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 02:16:01 2024
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