Sodium in PDB 7udq: Crystal Structure of COQ8A-CA157 Inhibitor Complex in Space Group P1
Protein crystallography data
The structure of Crystal Structure of COQ8A-CA157 Inhibitor Complex in Space Group P1, PDB code: 7udq
was solved by
C.A.Bingman,
N.Murray,
R.W.Smith,
D.J.Pagliarini,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
38.72 /
1.90
|
Space group
|
P 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
48.273,
54.859,
80.012,
109.79,
94.62,
92.11
|
R / Rfree (%)
|
19.2 /
23.9
|
Sodium Binding Sites:
The binding sites of Sodium atom in the Crystal Structure of COQ8A-CA157 Inhibitor Complex in Space Group P1
(pdb code 7udq). This binding sites where shown within
5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the
Crystal Structure of COQ8A-CA157 Inhibitor Complex in Space Group P1, PDB code: 7udq:
Jump to Sodium binding site number:
1;
2;
Sodium binding site 1 out
of 2 in 7udq
Go back to
Sodium Binding Sites List in 7udq
Sodium binding site 1 out
of 2 in the Crystal Structure of COQ8A-CA157 Inhibitor Complex in Space Group P1
![](/pictures/NA/pdb/ud/7udq-NA-sphere_01.jpg) Mono view
![](/pictures/NA/pdb/ud/7udq-NA-sphere_01_stereo.jpg) Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 1 of Crystal Structure of COQ8A-CA157 Inhibitor Complex in Space Group P1 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na702
b:69.2
occ:1.00
|
H
|
A:ILE341
|
2.1
|
51.2
|
1.0
|
HG12
|
A:ILE341
|
2.1
|
57.2
|
1.0
|
OE1
|
A:GLU405
|
2.2
|
66.2
|
1.0
|
OG
|
A:SER340
|
2.3
|
69.3
|
1.0
|
H
|
A:SER340
|
2.5
|
63.3
|
1.0
|
O
|
A:HOH814
|
2.7
|
42.8
|
1.0
|
N
|
A:ILE341
|
2.7
|
42.6
|
1.0
|
HG13
|
A:ILE341
|
2.7
|
57.2
|
1.0
|
CG1
|
A:ILE341
|
2.8
|
47.6
|
1.0
|
N
|
A:SER340
|
3.1
|
52.7
|
1.0
|
HB1
|
A:ALA339
|
3.1
|
63.8
|
1.0
|
HG23
|
A:ILE341
|
3.1
|
57.6
|
1.0
|
HB3
|
A:GLU405
|
3.2
|
54.6
|
1.0
|
CB
|
A:SER340
|
3.3
|
60.7
|
1.0
|
C
|
A:SER340
|
3.4
|
55.7
|
1.0
|
CA
|
A:SER340
|
3.4
|
58.2
|
1.0
|
CD
|
A:GLU405
|
3.5
|
60.5
|
1.0
|
CB
|
A:ILE341
|
3.6
|
49.9
|
1.0
|
HB2
|
A:SER340
|
3.6
|
72.9
|
1.0
|
HB3
|
A:ALA339
|
3.6
|
63.8
|
1.0
|
CA
|
A:ILE341
|
3.6
|
48.0
|
1.0
|
CB
|
A:ALA339
|
3.8
|
53.1
|
1.0
|
CG2
|
A:ILE341
|
3.8
|
48.0
|
1.0
|
H
|
A:GLY342
|
3.8
|
59.2
|
1.0
|
HB2
|
A:GLU405
|
3.9
|
54.6
|
1.0
|
CB
|
A:GLU405
|
3.9
|
45.5
|
1.0
|
HD11
|
A:ILE341
|
4.0
|
58.0
|
1.0
|
CD1
|
A:ILE341
|
4.0
|
48.3
|
1.0
|
C
|
A:ALA339
|
4.1
|
54.3
|
1.0
|
HB3
|
A:SER340
|
4.1
|
72.9
|
1.0
|
HG21
|
A:ILE341
|
4.2
|
57.6
|
1.0
|
CG
|
A:GLU405
|
4.3
|
53.5
|
1.0
|
N
|
A:GLY342
|
4.3
|
49.3
|
1.0
|
OE2
|
A:GLU405
|
4.3
|
66.5
|
1.0
|
C
|
A:ILE341
|
4.4
|
47.3
|
1.0
|
HA
|
A:SER340
|
4.4
|
69.9
|
1.0
|
HD13
|
A:ILE341
|
4.4
|
58.0
|
1.0
|
HA
|
A:ILE341
|
4.4
|
57.7
|
1.0
|
O
|
A:SER340
|
4.5
|
63.9
|
1.0
|
HB
|
A:ILE341
|
4.5
|
60.0
|
1.0
|
OH
|
A:TYR408
|
4.5
|
40.9
|
1.0
|
HB2
|
A:ALA339
|
4.5
|
63.8
|
1.0
|
CA
|
A:ALA339
|
4.6
|
62.6
|
1.0
|
HG22
|
A:ILE341
|
4.6
|
57.6
|
1.0
|
HE1
|
A:TYR408
|
4.7
|
47.1
|
1.0
|
HD12
|
A:ILE341
|
4.7
|
58.0
|
1.0
|
HG3
|
A:GLU405
|
4.9
|
64.2
|
1.0
|
HD23
|
A:LEU402
|
4.9
|
53.5
|
1.0
|
HH
|
A:TYR408
|
4.9
|
49.2
|
1.0
|
HG2
|
A:GLU405
|
4.9
|
64.2
|
1.0
|
O
|
A:ALA339
|
4.9
|
57.3
|
1.0
|
HA
|
A:ALA339
|
5.0
|
75.2
|
1.0
|
|
Sodium binding site 2 out
of 2 in 7udq
Go back to
Sodium Binding Sites List in 7udq
Sodium binding site 2 out
of 2 in the Crystal Structure of COQ8A-CA157 Inhibitor Complex in Space Group P1
![](/pictures/NA/pdb/ud/7udq-NA-sphere_02.jpg) Mono view
![](/pictures/NA/pdb/ud/7udq-NA-sphere_02_stereo.jpg) Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 2 of Crystal Structure of COQ8A-CA157 Inhibitor Complex in Space Group P1 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na703
b:59.5
occ:1.00
|
OD1
|
A:ASP420
|
2.2
|
68.9
|
1.0
|
O
|
A:HOH924
|
2.3
|
60.2
|
1.0
|
CG
|
A:ASP420
|
2.8
|
70.4
|
1.0
|
O
|
A:ARG416
|
2.8
|
43.3
|
1.0
|
OD2
|
A:ASP420
|
3.0
|
72.7
|
1.0
|
HB3
|
A:ARG419
|
3.1
|
51.2
|
1.0
|
HA
|
A:ARG416
|
3.4
|
46.6
|
1.0
|
HB3
|
A:ARG416
|
3.4
|
51.9
|
1.0
|
H
|
A:ASP420
|
3.5
|
54.3
|
1.0
|
HG2
|
A:ARG419
|
3.6
|
56.2
|
1.0
|
O
|
A:HOH803
|
3.7
|
64.8
|
1.0
|
C
|
A:ARG416
|
3.7
|
45.7
|
1.0
|
HD3
|
A:ARG419
|
3.7
|
58.0
|
1.0
|
N
|
A:ASP420
|
3.9
|
45.2
|
1.0
|
CA
|
A:ARG416
|
3.9
|
38.8
|
1.0
|
CB
|
A:ARG419
|
4.0
|
42.6
|
1.0
|
CB
|
A:ASP420
|
4.0
|
48.4
|
1.0
|
CB
|
A:ARG416
|
4.1
|
43.2
|
1.0
|
CG
|
A:ARG419
|
4.1
|
46.7
|
1.0
|
HE
|
A:ARG419
|
4.2
|
68.6
|
1.0
|
HA
|
A:ASP420
|
4.2
|
50.1
|
1.0
|
HB2
|
A:ASP420
|
4.3
|
58.2
|
1.0
|
CD
|
A:ARG419
|
4.3
|
48.3
|
1.0
|
CA
|
A:ASP420
|
4.3
|
41.7
|
1.0
|
HG2
|
A:ARG416
|
4.3
|
65.3
|
1.0
|
O
|
A:HOH879
|
4.5
|
46.2
|
1.0
|
C
|
A:ARG419
|
4.5
|
46.8
|
1.0
|
HB2
|
A:ARG419
|
4.7
|
51.2
|
1.0
|
NE
|
A:ARG419
|
4.7
|
57.1
|
1.0
|
CA
|
A:ARG419
|
4.8
|
40.4
|
1.0
|
CG
|
A:ARG416
|
4.8
|
54.4
|
1.0
|
HB3
|
A:ASP420
|
4.8
|
58.2
|
1.0
|
N
|
A:LYS417
|
4.9
|
40.7
|
1.0
|
HB2
|
A:ARG416
|
4.9
|
51.9
|
1.0
|
H
|
A:ARG419
|
4.9
|
46.6
|
1.0
|
HA
|
A:LYS417
|
4.9
|
44.1
|
1.0
|
HD3
|
A:ARG416
|
5.0
|
63.1
|
1.0
|
|
Reference:
N.H.Murray,
C.R.M.Asquith,
Z.Fang,
M.P.East,
N.Ptak,
R.W.Smith,
J.D.Vasta,
C.A.Zimprich,
C.R.Corona,
M.B.Robers,
G.L.Johnson,
C.A.Bingman,
D.J.Pagliarini.
Small-Molecule Inhibition of the Archetypal Ubib Protein COQ8. Nat.Chem.Biol. 2022.
ISSN: ESSN 1552-4469
PubMed: 36302899
DOI: 10.1038/S41589-022-01168-3
Page generated: Fri Apr 7 16:39:24 2023
|