Sodium in PDB 8tz5: Cryo-Em Structure of Bovine Concentrative Nucleoside Transporter 3 in Complex with N-Hydroxycytidine
Sodium Binding Sites:
The binding sites of Sodium atom in the Cryo-Em Structure of Bovine Concentrative Nucleoside Transporter 3 in Complex with N-Hydroxycytidine
(pdb code 8tz5). This binding sites where shown within
5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the
Cryo-Em Structure of Bovine Concentrative Nucleoside Transporter 3 in Complex with N-Hydroxycytidine, PDB code: 8tz5:
Jump to Sodium binding site number:
1;
2;
3;
Sodium binding site 1 out
of 3 in 8tz5
Go back to
Sodium Binding Sites List in 8tz5
Sodium binding site 1 out
of 3 in the Cryo-Em Structure of Bovine Concentrative Nucleoside Transporter 3 in Complex with N-Hydroxycytidine
 Mono view
 Stereo pair view
|
|
A full contact list of Sodium with other atoms in the Na binding
site number 1 of Cryo-Em Structure of Bovine Concentrative Nucleoside Transporter 3 in Complex with N-Hydroxycytidine within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na802
b:22.8
occ:1.00
|
O
|
A:ASN342
|
2.3
|
30.9
|
1.0
|
|
O
|
A:ILE345
|
2.3
|
27.3
|
1.0
|
|
OG1
|
A:THR376
|
2.5
|
22.8
|
1.0
|
|
OD1
|
A:ASN342
|
2.5
|
29.4
|
1.0
|
|
HA
|
A:ASN342
|
2.9
|
29.8
|
1.0
|
|
HG1
|
A:THR376
|
3.0
|
24.8
|
1.0
|
|
O
|
A:ILE377
|
3.0
|
25.1
|
1.0
|
|
HB3
|
A:ASN342
|
3.1
|
29.6
|
1.0
|
|
C
|
A:ASN342
|
3.1
|
28.5
|
1.0
|
|
CG
|
A:ASN342
|
3.3
|
24.4
|
1.0
|
|
HB
|
A:THR376
|
3.3
|
24.3
|
1.0
|
|
CA
|
A:ASN342
|
3.3
|
28.8
|
1.0
|
|
HA2
|
A:GLY346
|
3.3
|
30.7
|
1.0
|
|
CB
|
A:ASN342
|
3.4
|
24.2
|
1.0
|
|
CB
|
A:THR376
|
3.4
|
24.8
|
1.0
|
|
C
|
A:ILE345
|
3.5
|
28.1
|
1.0
|
|
C
|
A:ILE377
|
3.8
|
20.4
|
1.0
|
|
CA
|
A:GLY346
|
3.9
|
27.0
|
1.0
|
|
C
|
A:THR376
|
4.0
|
18.0
|
1.0
|
|
N
|
A:ILE377
|
4.0
|
23.7
|
1.0
|
|
C
|
A:GLY346
|
4.0
|
32.8
|
1.0
|
|
H
|
A:ILE345
|
4.2
|
31.2
|
1.0
|
|
N
|
A:GLY346
|
4.2
|
29.1
|
1.0
|
|
H
|
A:ILE377
|
4.2
|
23.8
|
1.0
|
|
HA2
|
A:GLY373
|
4.2
|
29.5
|
1.0
|
|
N
|
A:GLN347
|
4.3
|
32.2
|
1.0
|
|
CA
|
A:THR376
|
4.3
|
22.2
|
1.0
|
|
HB2
|
A:ASN342
|
4.3
|
28.6
|
1.0
|
|
O
|
A:THR376
|
4.3
|
25.4
|
1.0
|
|
CA
|
A:ILE377
|
4.4
|
19.1
|
1.0
|
|
O
|
A:GLY346
|
4.4
|
35.1
|
1.0
|
|
HA
|
A:ALA378
|
4.4
|
25.5
|
1.0
|
|
HA
|
A:ILE377
|
4.4
|
22.3
|
1.0
|
|
N
|
A:ILE343
|
4.4
|
22.7
|
1.0
|
|
H
|
A:GLN347
|
4.4
|
32.9
|
1.0
|
|
HG21
|
A:THR376
|
4.5
|
25.1
|
1.0
|
|
ND2
|
A:ASN342
|
4.5
|
27.3
|
1.0
|
|
N
|
A:ILE345
|
4.5
|
33.2
|
1.0
|
|
CG2
|
A:THR376
|
4.6
|
24.8
|
1.0
|
|
HA
|
A:GLN347
|
4.6
|
32.6
|
1.0
|
|
O
|
A:ALA372
|
4.6
|
26.7
|
1.0
|
|
H
|
A:THR376
|
4.6
|
25.2
|
1.0
|
|
N
|
A:ALA378
|
4.6
|
22.8
|
1.0
|
|
CA
|
A:ILE345
|
4.7
|
31.9
|
1.0
|
|
HB2
|
A:ALA378
|
4.7
|
25.6
|
1.0
|
|
N
|
A:ASN342
|
4.7
|
31.8
|
1.0
|
|
HB3
|
A:GLN347
|
4.8
|
33.1
|
1.0
|
|
HA
|
A:ILE343
|
4.8
|
25.9
|
1.0
|
|
O
|
A:GLY373
|
4.8
|
29.8
|
1.0
|
|
HA3
|
A:GLY346
|
4.8
|
30.6
|
1.0
|
|
HD22
|
A:ASN342
|
4.9
|
29.5
|
1.0
|
|
HB2
|
A:SER350
|
4.9
|
37.9
|
1.0
|
|
CA
|
A:ALA378
|
4.9
|
19.9
|
1.0
|
|
N
|
A:THR376
|
5.0
|
24.0
|
1.0
|
|
CA
|
A:GLN347
|
5.0
|
29.1
|
1.0
|
|
C
|
A:ILE343
|
5.0
|
27.9
|
1.0
|
|
Sodium binding site 2 out
of 3 in 8tz5
Go back to
Sodium Binding Sites List in 8tz5
Sodium binding site 2 out
of 3 in the Cryo-Em Structure of Bovine Concentrative Nucleoside Transporter 3 in Complex with N-Hydroxycytidine
 Mono view
 Stereo pair view
|
|
A full contact list of Sodium with other atoms in the Na binding
site number 2 of Cryo-Em Structure of Bovine Concentrative Nucleoside Transporter 3 in Complex with N-Hydroxycytidine within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Na802
b:22.8
occ:1.00
|
O
|
B:ASN342
|
2.3
|
30.9
|
1.0
|
|
O
|
B:ILE345
|
2.3
|
27.3
|
1.0
|
|
OG1
|
B:THR376
|
2.5
|
22.8
|
1.0
|
|
OD1
|
B:ASN342
|
2.5
|
29.4
|
1.0
|
|
HA
|
B:ASN342
|
2.9
|
29.8
|
1.0
|
|
HG1
|
B:THR376
|
3.0
|
24.8
|
1.0
|
|
O
|
B:ILE377
|
3.0
|
25.1
|
1.0
|
|
HB3
|
B:ASN342
|
3.1
|
29.6
|
1.0
|
|
C
|
B:ASN342
|
3.1
|
28.5
|
1.0
|
|
CG
|
B:ASN342
|
3.3
|
24.4
|
1.0
|
|
CA
|
B:ASN342
|
3.3
|
28.8
|
1.0
|
|
HB
|
B:THR376
|
3.3
|
24.3
|
1.0
|
|
HA2
|
B:GLY346
|
3.3
|
30.7
|
1.0
|
|
CB
|
B:ASN342
|
3.3
|
24.2
|
1.0
|
|
CB
|
B:THR376
|
3.4
|
24.8
|
1.0
|
|
C
|
B:ILE345
|
3.5
|
28.1
|
1.0
|
|
C
|
B:ILE377
|
3.8
|
20.4
|
1.0
|
|
CA
|
B:GLY346
|
3.9
|
27.0
|
1.0
|
|
C
|
B:THR376
|
4.0
|
18.0
|
1.0
|
|
N
|
B:ILE377
|
4.0
|
23.7
|
1.0
|
|
C
|
B:GLY346
|
4.0
|
32.8
|
1.0
|
|
H
|
B:ILE345
|
4.2
|
31.2
|
1.0
|
|
N
|
B:GLY346
|
4.2
|
29.1
|
1.0
|
|
H
|
B:ILE377
|
4.2
|
23.8
|
1.0
|
|
HA2
|
B:GLY373
|
4.2
|
29.5
|
1.0
|
|
N
|
B:GLN347
|
4.3
|
32.2
|
1.0
|
|
CA
|
B:THR376
|
4.3
|
22.2
|
1.0
|
|
HB2
|
B:ASN342
|
4.3
|
28.6
|
1.0
|
|
O
|
B:THR376
|
4.3
|
25.4
|
1.0
|
|
CA
|
B:ILE377
|
4.4
|
19.1
|
1.0
|
|
O
|
B:GLY346
|
4.4
|
35.1
|
1.0
|
|
HA
|
B:ALA378
|
4.4
|
25.5
|
1.0
|
|
HA
|
B:ILE377
|
4.4
|
22.3
|
1.0
|
|
N
|
B:ILE343
|
4.4
|
22.7
|
1.0
|
|
H
|
B:GLN347
|
4.4
|
32.9
|
1.0
|
|
HG21
|
B:THR376
|
4.5
|
25.1
|
1.0
|
|
ND2
|
B:ASN342
|
4.5
|
27.3
|
1.0
|
|
N
|
B:ILE345
|
4.5
|
33.2
|
1.0
|
|
CG2
|
B:THR376
|
4.6
|
24.8
|
1.0
|
|
HA
|
B:GLN347
|
4.6
|
32.6
|
1.0
|
|
O
|
B:ALA372
|
4.6
|
26.7
|
1.0
|
|
H
|
B:THR376
|
4.6
|
25.2
|
1.0
|
|
N
|
B:ALA378
|
4.6
|
22.8
|
1.0
|
|
CA
|
B:ILE345
|
4.7
|
31.9
|
1.0
|
|
HB2
|
B:ALA378
|
4.7
|
25.6
|
1.0
|
|
N
|
B:ASN342
|
4.7
|
31.8
|
1.0
|
|
HB3
|
B:GLN347
|
4.8
|
33.1
|
1.0
|
|
HA
|
B:ILE343
|
4.8
|
25.9
|
1.0
|
|
O
|
B:GLY373
|
4.8
|
29.8
|
1.0
|
|
HA3
|
B:GLY346
|
4.8
|
30.6
|
1.0
|
|
HD22
|
B:ASN342
|
4.9
|
29.5
|
1.0
|
|
HB2
|
B:SER350
|
4.9
|
37.9
|
1.0
|
|
CA
|
B:ALA378
|
4.9
|
19.9
|
1.0
|
|
N
|
B:THR376
|
5.0
|
24.0
|
1.0
|
|
CA
|
B:GLN347
|
5.0
|
29.1
|
1.0
|
|
C
|
B:ILE343
|
5.0
|
27.9
|
1.0
|
|
Sodium binding site 3 out
of 3 in 8tz5
Go back to
Sodium Binding Sites List in 8tz5
Sodium binding site 3 out
of 3 in the Cryo-Em Structure of Bovine Concentrative Nucleoside Transporter 3 in Complex with N-Hydroxycytidine
 Mono view
 Stereo pair view
|
|
A full contact list of Sodium with other atoms in the Na binding
site number 3 of Cryo-Em Structure of Bovine Concentrative Nucleoside Transporter 3 in Complex with N-Hydroxycytidine within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Na802
b:22.8
occ:1.00
|
O
|
C:ASN342
|
2.3
|
30.9
|
1.0
|
|
O
|
C:ILE345
|
2.3
|
27.3
|
1.0
|
|
OG1
|
C:THR376
|
2.5
|
22.8
|
1.0
|
|
OD1
|
C:ASN342
|
2.5
|
29.4
|
1.0
|
|
HA
|
C:ASN342
|
2.9
|
29.8
|
1.0
|
|
HG1
|
C:THR376
|
3.0
|
24.8
|
1.0
|
|
O
|
C:ILE377
|
3.0
|
25.1
|
1.0
|
|
HB3
|
C:ASN342
|
3.1
|
29.6
|
1.0
|
|
C
|
C:ASN342
|
3.1
|
28.5
|
1.0
|
|
CG
|
C:ASN342
|
3.3
|
24.4
|
1.0
|
|
CA
|
C:ASN342
|
3.3
|
28.8
|
1.0
|
|
HB
|
C:THR376
|
3.3
|
24.3
|
1.0
|
|
HA2
|
C:GLY346
|
3.3
|
30.7
|
1.0
|
|
CB
|
C:ASN342
|
3.4
|
24.2
|
1.0
|
|
CB
|
C:THR376
|
3.4
|
24.8
|
1.0
|
|
C
|
C:ILE345
|
3.5
|
28.1
|
1.0
|
|
C
|
C:ILE377
|
3.8
|
20.4
|
1.0
|
|
CA
|
C:GLY346
|
3.9
|
27.0
|
1.0
|
|
C
|
C:THR376
|
4.0
|
18.0
|
1.0
|
|
N
|
C:ILE377
|
4.0
|
23.7
|
1.0
|
|
C
|
C:GLY346
|
4.0
|
32.8
|
1.0
|
|
H
|
C:ILE345
|
4.2
|
31.2
|
1.0
|
|
N
|
C:GLY346
|
4.2
|
29.1
|
1.0
|
|
H
|
C:ILE377
|
4.2
|
23.8
|
1.0
|
|
HA2
|
C:GLY373
|
4.2
|
29.5
|
1.0
|
|
N
|
C:GLN347
|
4.3
|
32.2
|
1.0
|
|
CA
|
C:THR376
|
4.3
|
22.2
|
1.0
|
|
HB2
|
C:ASN342
|
4.3
|
28.6
|
1.0
|
|
O
|
C:THR376
|
4.3
|
25.4
|
1.0
|
|
CA
|
C:ILE377
|
4.4
|
19.1
|
1.0
|
|
O
|
C:GLY346
|
4.4
|
35.1
|
1.0
|
|
HA
|
C:ALA378
|
4.4
|
25.5
|
1.0
|
|
HA
|
C:ILE377
|
4.4
|
22.3
|
1.0
|
|
N
|
C:ILE343
|
4.4
|
22.7
|
1.0
|
|
H
|
C:GLN347
|
4.4
|
32.9
|
1.0
|
|
HG21
|
C:THR376
|
4.5
|
25.1
|
1.0
|
|
ND2
|
C:ASN342
|
4.5
|
27.3
|
1.0
|
|
N
|
C:ILE345
|
4.5
|
33.2
|
1.0
|
|
CG2
|
C:THR376
|
4.6
|
24.8
|
1.0
|
|
HA
|
C:GLN347
|
4.6
|
32.6
|
1.0
|
|
O
|
C:ALA372
|
4.6
|
26.7
|
1.0
|
|
H
|
C:THR376
|
4.6
|
25.2
|
1.0
|
|
N
|
C:ALA378
|
4.6
|
22.8
|
1.0
|
|
CA
|
C:ILE345
|
4.7
|
31.9
|
1.0
|
|
HB2
|
C:ALA378
|
4.7
|
25.6
|
1.0
|
|
N
|
C:ASN342
|
4.7
|
31.8
|
1.0
|
|
HB3
|
C:GLN347
|
4.8
|
33.1
|
1.0
|
|
HA
|
C:ILE343
|
4.8
|
25.9
|
1.0
|
|
O
|
C:GLY373
|
4.8
|
29.8
|
1.0
|
|
HA3
|
C:GLY346
|
4.8
|
30.6
|
1.0
|
|
HD22
|
C:ASN342
|
4.9
|
29.5
|
1.0
|
|
HB2
|
C:SER350
|
4.9
|
37.9
|
1.0
|
|
CA
|
C:ALA378
|
4.9
|
19.9
|
1.0
|
|
N
|
C:THR376
|
5.0
|
24.0
|
1.0
|
|
CA
|
C:GLN347
|
5.0
|
29.1
|
1.0
|
|
C
|
C:ILE343
|
5.0
|
27.9
|
1.0
|
|
Reference:
N.J.Wright,
F.Zhang,
Y.Suo,
L.Kong,
Y.Yin,
J.G.Fedor,
K.Sharma,
M.J.Borgnia,
W.Im,
S.Y.Lee.
Antiviral Drug Recognition and Elevator-Type Transport Motions of CNT3. Nat.Chem.Biol. 2024.
ISSN: ESSN 1552-4469
PubMed: 38418906
DOI: 10.1038/S41589-024-01559-8
Page generated: Wed Oct 9 13:45:15 2024
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