Magnesium in PDB 4pl4: Crystal Structure of Murine IRE1 in Complex with OICR464 Inhibitor
Enzymatic activity of Crystal Structure of Murine IRE1 in Complex with OICR464 Inhibitor
All present enzymatic activity of Crystal Structure of Murine IRE1 in Complex with OICR464 Inhibitor:
2.7.11.1;
Protein crystallography data
The structure of Crystal Structure of Murine IRE1 in Complex with OICR464 Inhibitor, PDB code: 4pl4
was solved by
M.Sanches,
N.Duffy,
M.Talukdar,
N.Thevakumaran,
D.Chiovitti,
R.Al-Awar,
J.B.Patterson,
F.Sicheri,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
46.60 /
3.00
|
Space group
|
C 1 2 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
319.110,
62.310,
141.330,
90.00,
99.57,
90.00
|
R / Rfree (%)
|
21 /
27.6
|
Magnesium Binding Sites:
The binding sites of Magnesium atom in the Crystal Structure of Murine IRE1 in Complex with OICR464 Inhibitor
(pdb code 4pl4). This binding sites where shown within
5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the
Crystal Structure of Murine IRE1 in Complex with OICR464 Inhibitor, PDB code: 4pl4:
Jump to Magnesium binding site number:
1;
2;
3;
4;
Magnesium binding site 1 out
of 4 in 4pl4
Go back to
Magnesium Binding Sites List in 4pl4
Magnesium binding site 1 out
of 4 in the Crystal Structure of Murine IRE1 in Complex with OICR464 Inhibitor
 Mono view
 Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 1 of Crystal Structure of Murine IRE1 in Complex with OICR464 Inhibitor within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg1004
b:42.1
occ:1.00
|
OD2
|
A:ASP711
|
1.9
|
73.5
|
1.0
|
O2A
|
A:ADP1002
|
2.2
|
47.9
|
1.0
|
OD1
|
A:ASN693
|
2.4
|
49.3
|
1.0
|
O3B
|
A:ADP1002
|
2.4
|
47.3
|
1.0
|
O1B
|
A:ADP1002
|
2.4
|
79.6
|
1.0
|
PB
|
A:ADP1002
|
2.8
|
62.9
|
1.0
|
CG
|
A:ASP711
|
2.9
|
83.5
|
1.0
|
O3A
|
A:ADP1002
|
3.2
|
86.2
|
1.0
|
CG
|
A:ASN693
|
3.2
|
48.5
|
1.0
|
PA
|
A:ADP1002
|
3.2
|
62.9
|
1.0
|
CB
|
A:ASP711
|
3.3
|
79.7
|
1.0
|
ND2
|
A:ASN693
|
3.4
|
57.6
|
1.0
|
NZ
|
A:LYS599
|
3.4
|
76.9
|
1.0
|
OD1
|
A:ASP711
|
4.0
|
95.8
|
1.0
|
O5'
|
A:ADP1002
|
4.2
|
47.8
|
1.0
|
O2B
|
A:ADP1002
|
4.3
|
48.2
|
1.0
|
O1A
|
A:ADP1002
|
4.5
|
68.2
|
1.0
|
O
|
A:HIS692
|
4.6
|
77.7
|
1.0
|
CB
|
A:ASN693
|
4.7
|
47.4
|
1.0
|
CE
|
A:LYS599
|
4.7
|
63.9
|
1.0
|
CA
|
A:ASP711
|
4.8
|
79.6
|
1.0
|
OD2
|
A:ASP688
|
4.9
|
49.0
|
1.0
|
|
Magnesium binding site 2 out
of 4 in 4pl4
Go back to
Magnesium Binding Sites List in 4pl4
Magnesium binding site 2 out
of 4 in the Crystal Structure of Murine IRE1 in Complex with OICR464 Inhibitor
 Mono view
 Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 2 of Crystal Structure of Murine IRE1 in Complex with OICR464 Inhibitor within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg1002
b:53.9
occ:1.00
|
O3B
|
B:ADP1001
|
2.1
|
63.9
|
1.0
|
OD2
|
B:ASP711
|
2.2
|
99.7
|
1.0
|
O
|
B:HIS692
|
2.9
|
53.2
|
1.0
|
OD1
|
B:ASN693
|
3.1
|
77.6
|
1.0
|
O2A
|
B:ADP1001
|
3.1
|
62.5
|
1.0
|
CG
|
B:ASP711
|
3.2
|
84.6
|
1.0
|
O5'
|
B:ADP1001
|
3.4
|
54.9
|
1.0
|
PB
|
B:ADP1001
|
3.5
|
69.5
|
1.0
|
C8
|
B:ADP1001
|
3.5
|
72.6
|
1.0
|
OD1
|
B:ASP711
|
3.7
|
71.3
|
1.0
|
PA
|
B:ADP1001
|
3.8
|
77.1
|
1.0
|
C
|
B:HIS692
|
3.8
|
63.5
|
1.0
|
O2B
|
B:ADP1001
|
4.0
|
45.6
|
1.0
|
N7
|
B:ADP1001
|
4.1
|
52.6
|
1.0
|
O3A
|
B:ADP1001
|
4.1
|
0.8
|
1.0
|
C3'
|
B:ADP1001
|
4.2
|
62.4
|
1.0
|
CG
|
B:ASN693
|
4.2
|
75.6
|
1.0
|
CA
|
B:ASN693
|
4.4
|
61.5
|
1.0
|
CB
|
B:ASP711
|
4.4
|
71.5
|
1.0
|
CB
|
B:HIS692
|
4.4
|
66.9
|
1.0
|
N
|
B:ASN693
|
4.5
|
64.7
|
1.0
|
C5'
|
B:ADP1001
|
4.5
|
65.2
|
1.0
|
N9
|
B:ADP1001
|
4.5
|
58.1
|
1.0
|
O1B
|
B:ADP1001
|
4.6
|
74.6
|
1.0
|
C2'
|
B:ADP1001
|
4.6
|
44.2
|
1.0
|
CA
|
B:HIS692
|
4.7
|
74.3
|
1.0
|
C4'
|
B:ADP1001
|
4.8
|
65.5
|
1.0
|
CD2
|
B:LEU695
|
4.8
|
54.6
|
1.0
|
NZ
|
B:LYS599
|
4.9
|
89.9
|
1.0
|
O4'
|
B:ADP1001
|
4.9
|
50.0
|
1.0
|
CB
|
B:ASN693
|
4.9
|
61.3
|
1.0
|
C1'
|
B:ADP1001
|
5.0
|
38.4
|
1.0
|
|
Magnesium binding site 3 out
of 4 in 4pl4
Go back to
Magnesium Binding Sites List in 4pl4
Magnesium binding site 3 out
of 4 in the Crystal Structure of Murine IRE1 in Complex with OICR464 Inhibitor
 Mono view
 Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 3 of Crystal Structure of Murine IRE1 in Complex with OICR464 Inhibitor within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mg1002
b:98.5
occ:1.00
|
O2A
|
C:ADP1001
|
1.9
|
61.3
|
1.0
|
O3B
|
C:ADP1001
|
1.9
|
74.7
|
1.0
|
OD1
|
C:ASN693
|
2.2
|
67.1
|
1.0
|
PA
|
C:ADP1001
|
3.0
|
70.6
|
1.0
|
PB
|
C:ADP1001
|
3.0
|
65.2
|
1.0
|
O5'
|
C:ADP1001
|
3.2
|
58.3
|
1.0
|
OD1
|
C:ASP711
|
3.3
|
96.3
|
1.0
|
O1B
|
C:ADP1001
|
3.3
|
60.7
|
1.0
|
CG
|
C:ASN693
|
3.3
|
79.8
|
1.0
|
OD2
|
C:ASP711
|
3.3
|
0.1
|
1.0
|
O3A
|
C:ADP1001
|
3.4
|
0.7
|
1.0
|
CG
|
C:ASP711
|
3.5
|
99.5
|
1.0
|
O
|
C:HIS692
|
3.8
|
56.8
|
1.0
|
C8
|
C:ADP1001
|
4.0
|
61.9
|
1.0
|
ND2
|
C:ASN693
|
4.1
|
95.4
|
1.0
|
C
|
C:HIS692
|
4.2
|
57.0
|
1.0
|
O2B
|
C:ADP1001
|
4.3
|
50.2
|
1.0
|
CA
|
C:ASN693
|
4.3
|
58.2
|
1.0
|
C5'
|
C:ADP1001
|
4.3
|
61.2
|
1.0
|
C3'
|
C:ADP1001
|
4.4
|
86.1
|
1.0
|
O1A
|
C:ADP1001
|
4.4
|
78.7
|
1.0
|
CB
|
C:ASN693
|
4.4
|
65.7
|
1.0
|
N
|
C:ASN693
|
4.4
|
59.4
|
1.0
|
CB
|
C:ASP711
|
4.6
|
86.3
|
1.0
|
N7
|
C:ADP1001
|
4.7
|
35.0
|
1.0
|
CB
|
C:HIS692
|
4.8
|
56.1
|
1.0
|
C2'
|
C:ADP1001
|
4.9
|
71.5
|
1.0
|
C4'
|
C:ADP1001
|
4.9
|
70.7
|
1.0
|
OG
|
C:SER710
|
4.9
|
73.0
|
1.0
|
N9
|
C:ADP1001
|
4.9
|
61.1
|
1.0
|
|
Magnesium binding site 4 out
of 4 in 4pl4
Go back to
Magnesium Binding Sites List in 4pl4
Magnesium binding site 4 out
of 4 in the Crystal Structure of Murine IRE1 in Complex with OICR464 Inhibitor
 Mono view
 Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 4 of Crystal Structure of Murine IRE1 in Complex with OICR464 Inhibitor within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Mg1002
b:65.6
occ:1.00
|
OD2
|
D:ASP711
|
2.0
|
84.6
|
1.0
|
O3A
|
D:ADP1001
|
2.6
|
30.7
|
1.0
|
O1B
|
D:ADP1001
|
2.6
|
99.1
|
1.0
|
O1A
|
D:ADP1001
|
2.7
|
98.9
|
1.0
|
CG
|
D:ASP711
|
3.0
|
82.7
|
1.0
|
PA
|
D:ADP1001
|
3.0
|
0.8
|
1.0
|
ND2
|
D:ASN693
|
3.1
|
81.2
|
1.0
|
PB
|
D:ADP1001
|
3.3
|
97.1
|
1.0
|
O2A
|
D:ADP1001
|
3.4
|
0.4
|
1.0
|
O
|
D:HIS692
|
3.5
|
61.0
|
1.0
|
CA
|
D:ASN693
|
3.7
|
79.8
|
1.0
|
OD1
|
D:ASP711
|
3.7
|
79.7
|
1.0
|
CB
|
D:ASP711
|
3.8
|
82.5
|
1.0
|
CB
|
D:ASN693
|
3.8
|
89.7
|
1.0
|
CG
|
D:ASN693
|
3.9
|
89.0
|
1.0
|
C
|
D:HIS692
|
4.0
|
72.4
|
1.0
|
N
|
D:ASN693
|
4.1
|
78.1
|
1.0
|
O3B
|
D:ADP1001
|
4.2
|
0.5
|
1.0
|
O2B
|
D:ADP1001
|
4.4
|
77.1
|
1.0
|
O5'
|
D:ADP1001
|
4.5
|
37.9
|
1.0
|
NZ
|
D:LYS690
|
4.7
|
85.8
|
1.0
|
CB
|
D:HIS692
|
4.7
|
96.8
|
1.0
|
CE
|
D:LYS690
|
4.9
|
60.4
|
1.0
|
NZ
|
D:LYS599
|
4.9
|
0.7
|
1.0
|
OD1
|
D:ASN693
|
5.0
|
93.3
|
1.0
|
CA
|
D:HIS692
|
5.0
|
91.4
|
1.0
|
|
Reference:
M.Sanches,
N.M.Duffy,
M.Talukdar,
N.Thevakumaran,
D.Chiovitti,
M.D.Canny,
K.Lee,
I.Kurinov,
D.Uehling,
R.Al-Awar,
G.Poda,
M.Prakesch,
B.Wilson,
V.Tam,
C.Schweitzer,
A.Toro,
J.L.Lucas,
D.Vuga,
L.Lehmann,
D.Durocher,
Q.Zeng,
J.B.Patterson,
F.Sicheri.
Structure and Mechanism of Action of the Hydroxy-Aryl-Aldehyde Class of IRE1 Endoribonuclease Inhibitors. Nat Commun V. 5 4202 2014.
ISSN: ESSN 2041-1723
PubMed: 25164867
DOI: 10.1038/NCOMMS5202
Page generated: Tue Aug 20 01:34:58 2024
|