Sodium in PDB 8zpb: Cryo-Em Structure of Human Norepinephrine Transporter Net Bound with Norepinephrine in An Occluded State at A Resolution of 2.6 Angstrom
Other elements in 8zpb:
The structure of Cryo-Em Structure of Human Norepinephrine Transporter Net Bound with Norepinephrine in An Occluded State at A Resolution of 2.6 Angstrom also contains other interesting chemical elements:
Sodium Binding Sites:
The binding sites of Sodium atom in the Cryo-Em Structure of Human Norepinephrine Transporter Net Bound with Norepinephrine in An Occluded State at A Resolution of 2.6 Angstrom
(pdb code 8zpb). This binding sites where shown within
5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the
Cryo-Em Structure of Human Norepinephrine Transporter Net Bound with Norepinephrine in An Occluded State at A Resolution of 2.6 Angstrom, PDB code: 8zpb:
Jump to Sodium binding site number:
1;
2;
Sodium binding site 1 out
of 2 in 8zpb
Go back to
Sodium Binding Sites List in 8zpb
Sodium binding site 1 out
of 2 in the Cryo-Em Structure of Human Norepinephrine Transporter Net Bound with Norepinephrine in An Occluded State at A Resolution of 2.6 Angstrom
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 Human Norepinephrine Transporter Net Bound with Norepinephrine in An Occluded State at A Resolution of 2.6 Angstrom within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na702
b:34.3
occ:1.00
|
O
|
A:ALA73
|
2.0
|
23.2
|
1.0
|
OG
|
A:SER318
|
2.1
|
30.6
|
1.0
|
OD1
|
A:ASP75
|
2.1
|
27.8
|
1.0
|
OD1
|
A:ASN78
|
2.2
|
15.6
|
1.0
|
OD1
|
A:ASN350
|
2.4
|
18.6
|
1.0
|
O
|
A:SER318
|
2.4
|
28.2
|
1.0
|
HG
|
A:SER318
|
2.7
|
25.3
|
1.0
|
HA
|
A:SER318
|
2.9
|
24.2
|
1.0
|
C
|
A:SER318
|
3.0
|
22.5
|
1.0
|
H
|
A:ASP75
|
3.0
|
24.3
|
1.0
|
CB
|
A:SER318
|
3.1
|
21.2
|
1.0
|
CA
|
A:SER318
|
3.1
|
22.9
|
1.0
|
CG
|
A:ASN78
|
3.2
|
17.4
|
1.0
|
HD22
|
A:ASN78
|
3.2
|
24.9
|
1.0
|
HA
|
A:VAL74
|
3.2
|
26.3
|
1.0
|
C
|
A:ALA73
|
3.3
|
28.1
|
1.0
|
CG
|
A:ASP75
|
3.3
|
26.9
|
1.0
|
HB3
|
A:ALA77
|
3.5
|
23.9
|
1.0
|
CG
|
A:ASN350
|
3.5
|
31.4
|
1.0
|
ND2
|
A:ASN78
|
3.6
|
25.8
|
1.0
|
N
|
A:ASP75
|
3.6
|
17.8
|
1.0
|
HB2
|
A:SER318
|
3.7
|
24.3
|
1.0
|
HB3
|
A:SER318
|
3.7
|
23.5
|
1.0
|
HD22
|
A:ASN350
|
3.7
|
26.1
|
1.0
|
H
|
A:ASN78
|
3.9
|
25.5
|
1.0
|
CA
|
A:VAL74
|
3.9
|
22.8
|
1.0
|
HB3
|
A:ASP75
|
4.0
|
24.2
|
1.0
|
N
|
A:VAL74
|
4.0
|
24.6
|
1.0
|
N
|
A:LEU319
|
4.0
|
22.6
|
1.0
|
ND2
|
A:ASN350
|
4.1
|
31.4
|
1.0
|
CB
|
A:ASP75
|
4.1
|
25.5
|
1.0
|
HA
|
A:ALA73
|
4.2
|
24.4
|
1.0
|
OD2
|
A:ASP75
|
4.2
|
23.7
|
1.0
|
O
|
A:HOH830
|
4.2
|
26.3
|
1.0
|
C
|
A:VAL74
|
4.2
|
21.3
|
1.0
|
HA
|
A:LEU319
|
4.3
|
25.3
|
1.0
|
CA
|
A:ALA73
|
4.4
|
22.2
|
1.0
|
N
|
A:ASN78
|
4.4
|
28.0
|
1.0
|
CA
|
A:ASP75
|
4.4
|
16.5
|
1.0
|
HD21
|
A:ASN78
|
4.4
|
25.8
|
1.0
|
CB
|
A:ALA77
|
4.4
|
26.2
|
1.0
|
CB
|
A:ASN78
|
4.5
|
27.2
|
1.0
|
N
|
A:SER318
|
4.6
|
26.0
|
1.0
|
H
|
A:LEU319
|
4.6
|
24.6
|
1.0
|
CA
|
A:LEU319
|
4.7
|
25.6
|
1.0
|
CL
|
A:CL704
|
4.7
|
29.4
|
1.0
|
HB2
|
A:ASN350
|
4.8
|
25.9
|
1.0
|
HB1
|
A:ALA73
|
4.8
|
25.1
|
1.0
|
O
|
A:PHE72
|
4.8
|
25.5
|
1.0
|
CB
|
A:ASN350
|
4.8
|
28.6
|
1.0
|
HB1
|
A:ALA77
|
4.8
|
24.5
|
1.0
|
HG22
|
A:VAL74
|
4.8
|
25.5
|
1.0
|
HB2
|
A:ASN78
|
4.8
|
25.1
|
1.0
|
H
|
A:ALA77
|
4.8
|
25.0
|
1.0
|
HA
|
A:ASN78
|
4.9
|
24.5
|
1.0
|
O
|
A:ASP75
|
4.9
|
28.5
|
1.0
|
HB2
|
A:ALA77
|
4.9
|
24.8
|
1.0
|
H
|
A:VAL74
|
4.9
|
25.1
|
1.0
|
HNAA
|
A:LNR701
|
4.9
|
22.1
|
1.0
|
CA
|
A:ASN78
|
4.9
|
23.2
|
1.0
|
HD21
|
A:ASN350
|
4.9
|
25.8
|
1.0
|
C
|
A:ASP75
|
4.9
|
22.0
|
1.0
|
|
Sodium binding site 2 out
of 2 in 8zpb
Go back to
Sodium Binding Sites List in 8zpb
Sodium binding site 2 out
of 2 in the Cryo-Em Structure of Human Norepinephrine Transporter Net Bound with Norepinephrine in An Occluded State at A Resolution of 2.6 Angstrom
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 Human Norepinephrine Transporter Net Bound with Norepinephrine in An Occluded State at A Resolution of 2.6 Angstrom within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na703
b:22.6
occ:1.00
|
HG
|
A:SER419
|
2.0
|
25.8
|
1.0
|
O
|
A:GLY71
|
2.1
|
28.2
|
1.0
|
OD1
|
A:ASP418
|
2.1
|
29.6
|
1.0
|
O
|
A:LEU415
|
2.2
|
23.4
|
1.0
|
O
|
A:VAL74
|
2.3
|
29.3
|
1.0
|
HA
|
A:ASP75
|
2.4
|
23.6
|
1.0
|
OG
|
A:SER419
|
2.4
|
28.8
|
1.0
|
H
|
A:SER419
|
3.0
|
24.6
|
1.0
|
CG
|
A:ASP418
|
3.2
|
37.3
|
1.0
|
HA
|
A:LEU415
|
3.2
|
25.6
|
1.0
|
C
|
A:LEU415
|
3.2
|
25.9
|
1.0
|
CA
|
A:ASP75
|
3.2
|
16.5
|
1.0
|
C
|
A:GLY71
|
3.3
|
23.0
|
1.0
|
C
|
A:VAL74
|
3.3
|
21.3
|
1.0
|
O
|
A:HOH835
|
3.4
|
27.2
|
1.0
|
N
|
A:SER419
|
3.5
|
22.3
|
1.0
|
CB
|
A:SER419
|
3.5
|
19.7
|
1.0
|
HB2
|
A:SER419
|
3.6
|
23.9
|
1.0
|
HB3
|
A:ASP75
|
3.6
|
24.2
|
1.0
|
O
|
A:HOH801
|
3.6
|
32.8
|
1.0
|
N
|
A:ASP75
|
3.7
|
17.8
|
1.0
|
CA
|
A:LEU415
|
3.7
|
25.6
|
1.0
|
HB2
|
A:ASP75
|
3.8
|
24.4
|
1.0
|
CB
|
A:ASP75
|
3.8
|
25.5
|
1.0
|
OD2
|
A:ASP418
|
3.8
|
38.3
|
1.0
|
HA2
|
A:GLY71
|
3.8
|
26.3
|
1.0
|
HA
|
A:PHE72
|
3.8
|
23.9
|
1.0
|
CA
|
A:SER419
|
4.0
|
19.7
|
1.0
|
HH
|
A:TYR152
|
4.1
|
22.8
|
1.0
|
CA
|
A:GLY71
|
4.1
|
24.2
|
1.0
|
HD23
|
A:LEU415
|
4.1
|
24.6
|
1.0
|
HA
|
A:SER419
|
4.2
|
24.6
|
1.0
|
CB
|
A:ASP418
|
4.2
|
26.7
|
1.0
|
O
|
A:ALA414
|
4.2
|
21.1
|
1.0
|
HB2
|
A:ASP418
|
4.2
|
28.7
|
1.0
|
H
|
A:ASP418
|
4.2
|
28.0
|
1.0
|
HB3
|
A:LEU415
|
4.3
|
25.8
|
1.0
|
HB3
|
A:SER419
|
4.3
|
23.0
|
1.0
|
C
|
A:ASP418
|
4.3
|
22.9
|
1.0
|
N
|
A:PHE72
|
4.3
|
18.6
|
1.0
|
C
|
A:ASP75
|
4.4
|
22.0
|
1.0
|
O
|
A:PHE72
|
4.4
|
25.5
|
1.0
|
N
|
A:GLY416
|
4.4
|
28.6
|
1.0
|
CA
|
A:PHE72
|
4.4
|
18.9
|
1.0
|
HA3
|
A:GLY71
|
4.4
|
25.2
|
1.0
|
HA2
|
A:GLY416
|
4.4
|
24.2
|
1.0
|
H
|
A:LEU76
|
4.5
|
23.4
|
1.0
|
C
|
A:PHE72
|
4.5
|
23.9
|
1.0
|
HD22
|
A:LEU415
|
4.5
|
25.6
|
1.0
|
CB
|
A:LEU415
|
4.6
|
24.3
|
1.0
|
H
|
A:ASP75
|
4.6
|
24.3
|
1.0
|
CA
|
A:ASP418
|
4.6
|
26.1
|
1.0
|
N
|
A:ASP418
|
4.6
|
27.8
|
1.0
|
CA
|
A:VAL74
|
4.7
|
22.8
|
1.0
|
HG12
|
A:VAL74
|
4.7
|
26.3
|
1.0
|
OH
|
A:TYR152
|
4.7
|
20.6
|
1.0
|
CA
|
A:GLY416
|
4.8
|
24.8
|
1.0
|
N
|
A:LEU76
|
4.8
|
22.5
|
1.0
|
CD2
|
A:LEU415
|
4.8
|
23.3
|
1.0
|
C
|
A:GLY416
|
4.9
|
24.6
|
1.0
|
N
|
A:VAL74
|
4.9
|
24.6
|
1.0
|
N
|
A:LEU415
|
4.9
|
25.9
|
1.0
|
HB
|
A:VAL74
|
4.9
|
26.0
|
1.0
|
H
|
A:VAL74
|
4.9
|
25.1
|
1.0
|
|
Reference:
A.Song,
X.Wu.
Mechanistic Insights of Substrate Transport and Inhibitor Binding Revealed By High-Resolution Structures of Human Norepinephrine Transporter Cell Res. 2024.
ISSN: ISSN 1001-0602
DOI: 10.1038/S41422-024-01024-0
Page generated: Wed Oct 9 14:27:28 2024
|