Thallium in PDB 4p1a: Thallium-Bound Inward-Facing State of the Glutamate Transporter Homologue Gltph
Protein crystallography data
The structure of Thallium-Bound Inward-Facing State of the Glutamate Transporter Homologue Gltph, PDB code: 4p1a
was solved by
G.Verdon,
O.Boudker,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
15.00 /
3.75
|
Space group
|
C 2 2 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
106.979,
196.564,
206.499,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
23 /
25.7
|
Other elements in 4p1a:
The structure of Thallium-Bound Inward-Facing State of the Glutamate Transporter Homologue Gltph also contains other interesting chemical elements:
Thallium Binding Sites:
The binding sites of Thallium atom in the Thallium-Bound Inward-Facing State of the Glutamate Transporter Homologue Gltph
(pdb code 4p1a). This binding sites where shown within
5.0 Angstroms radius around Thallium atom.
In total 6 binding sites of Thallium where determined in the
Thallium-Bound Inward-Facing State of the Glutamate Transporter Homologue Gltph, PDB code: 4p1a:
Jump to Thallium binding site number:
1;
2;
3;
4;
5;
6;
Thallium binding site 1 out
of 6 in 4p1a
Go back to
Thallium Binding Sites List in 4p1a
Thallium binding site 1 out
of 6 in the Thallium-Bound Inward-Facing State of the Glutamate Transporter Homologue Gltph
Mono view
Stereo pair view
|
A full contact list of Thallium with other atoms in the Tl binding
site number 1 of Thallium-Bound Inward-Facing State of the Glutamate Transporter Homologue Gltph within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Tl501
b:0.1
occ:0.80
|
O
|
A:THR308
|
2.7
|
1.0
|
1.0
|
O
|
A:SER349
|
2.8
|
0.3
|
1.0
|
O
|
A:ASN310
|
3.4
|
0.7
|
1.0
|
N
|
A:GLY351
|
3.4
|
0.8
|
1.0
|
N
|
A:THR352
|
3.5
|
0.7
|
1.0
|
C
|
A:SER349
|
3.6
|
0.5
|
1.0
|
N
|
A:ALA353
|
3.6
|
0.7
|
1.0
|
CA
|
A:ILE350
|
3.6
|
0.4
|
1.0
|
C
|
A:ILE309
|
3.7
|
0.1
|
1.0
|
O
|
A:ILE309
|
3.7
|
0.9
|
1.0
|
C
|
A:THR308
|
3.8
|
0.6
|
1.0
|
CA
|
A:ILE309
|
3.9
|
0.9
|
1.0
|
CA
|
A:ALA353
|
3.9
|
0.1
|
1.0
|
C
|
A:ILE350
|
3.9
|
0.2
|
1.0
|
N
|
A:ILE350
|
3.9
|
0.6
|
1.0
|
C
|
A:ASN310
|
4.0
|
0.3
|
1.0
|
C
|
A:THR352
|
4.0
|
0.5
|
1.0
|
OG
|
A:SER349
|
4.0
|
0.8
|
1.0
|
CB
|
A:ALA353
|
4.1
|
1.0
|
1.0
|
CA
|
A:THR352
|
4.3
|
0.9
|
1.0
|
N
|
A:ASN310
|
4.3
|
0.4
|
1.0
|
CG
|
A:MET311
|
4.3
|
0.3
|
1.0
|
N
|
A:ILE309
|
4.3
|
0.2
|
1.0
|
C
|
A:GLY351
|
4.4
|
0.1
|
1.0
|
CA
|
A:GLY351
|
4.4
|
0.9
|
1.0
|
CA
|
A:MET311
|
4.5
|
0.6
|
1.0
|
OG1
|
A:THR352
|
4.5
|
0.6
|
1.0
|
N
|
A:MET311
|
4.6
|
0.0
|
1.0
|
CB
|
A:SER349
|
4.7
|
0.2
|
1.0
|
O
|
A:THR352
|
4.7
|
0.5
|
1.0
|
CA
|
A:SER349
|
4.8
|
0.0
|
1.0
|
CA
|
A:ASN310
|
4.8
|
0.1
|
1.0
|
CB
|
A:ILE350
|
4.8
|
0.1
|
1.0
|
CB
|
A:THR352
|
4.9
|
0.8
|
1.0
|
CB
|
A:MET311
|
5.0
|
0.8
|
1.0
|
OG1
|
A:THR314
|
5.0
|
0.2
|
1.0
|
|
Thallium binding site 2 out
of 6 in 4p1a
Go back to
Thallium Binding Sites List in 4p1a
Thallium binding site 2 out
of 6 in the Thallium-Bound Inward-Facing State of the Glutamate Transporter Homologue Gltph
Mono view
Stereo pair view
|
A full contact list of Thallium with other atoms in the Tl binding
site number 2 of Thallium-Bound Inward-Facing State of the Glutamate Transporter Homologue Gltph within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Tl502
b:0.2
occ:0.80
|
O
|
A:VAL355
|
2.9
|
0.8
|
1.0
|
OD2
|
A:ASP394
|
2.9
|
0.9
|
1.0
|
O
|
A:ARG276
|
2.9
|
0.5
|
1.0
|
OG1
|
A:THR398
|
2.9
|
0.5
|
1.0
|
O
|
A:PRO356
|
3.2
|
0.7
|
1.0
|
NH2
|
A:ARG397
|
3.4
|
0.0
|
1.0
|
O
|
A:ALA353
|
3.6
|
1.0
|
1.0
|
CZ
|
A:ARG397
|
3.7
|
0.2
|
1.0
|
NH1
|
A:ARG397
|
3.8
|
0.3
|
1.0
|
CA
|
A:GLY354
|
3.9
|
0.6
|
1.0
|
CG
|
A:ASP394
|
4.0
|
0.8
|
1.0
|
C
|
A:VAL355
|
4.0
|
0.5
|
1.0
|
C
|
A:ARG276
|
4.1
|
0.6
|
1.0
|
C
|
A:PRO356
|
4.1
|
0.7
|
1.0
|
CB
|
A:THR398
|
4.1
|
0.8
|
1.0
|
CG2
|
A:THR398
|
4.3
|
0.6
|
1.0
|
O
|
A:ASP394
|
4.3
|
0.5
|
1.0
|
CA
|
A:PRO356
|
4.4
|
0.1
|
1.0
|
NE
|
A:ARG397
|
4.5
|
0.2
|
1.0
|
OD1
|
A:ASP394
|
4.5
|
0.0
|
1.0
|
C
|
A:ALA353
|
4.6
|
0.5
|
1.0
|
CA
|
A:THR398
|
4.7
|
0.8
|
1.0
|
N
|
A:PRO356
|
4.7
|
0.1
|
1.0
|
N
|
A:THR398
|
4.7
|
0.7
|
1.0
|
CA
|
A:ARG276
|
4.7
|
0.5
|
1.0
|
N
|
A:GLY354
|
4.8
|
0.3
|
1.0
|
N
|
A:ALA358
|
4.9
|
0.4
|
1.0
|
CB
|
A:ARG276
|
4.9
|
0.4
|
1.0
|
CG1
|
A:VAL355
|
4.9
|
1.0
|
1.0
|
|
Thallium binding site 3 out
of 6 in 4p1a
Go back to
Thallium Binding Sites List in 4p1a
Thallium binding site 3 out
of 6 in the Thallium-Bound Inward-Facing State of the Glutamate Transporter Homologue Gltph
Mono view
Stereo pair view
|
A full contact list of Thallium with other atoms in the Tl binding
site number 3 of Thallium-Bound Inward-Facing State of the Glutamate Transporter Homologue Gltph within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Tl501
b:1.0
occ:0.80
|
O
|
B:THR308
|
2.8
|
0.6
|
1.0
|
O
|
B:SER349
|
3.1
|
0.9
|
1.0
|
O
|
B:ASN310
|
3.5
|
0.7
|
1.0
|
N
|
B:GLY351
|
3.6
|
0.6
|
1.0
|
CA
|
B:ILE350
|
3.7
|
0.3
|
1.0
|
C
|
B:ILE309
|
3.7
|
0.1
|
1.0
|
O
|
B:ILE309
|
3.7
|
0.3
|
1.0
|
N
|
B:ALA353
|
3.7
|
0.1
|
1.0
|
C
|
B:SER349
|
3.7
|
0.3
|
1.0
|
N
|
B:THR352
|
3.7
|
0.3
|
1.0
|
CA
|
B:ILE309
|
3.9
|
0.5
|
1.0
|
C
|
B:ASN310
|
3.9
|
1.0
|
1.0
|
C
|
B:THR308
|
3.9
|
0.5
|
1.0
|
CA
|
B:ALA353
|
4.0
|
0.4
|
1.0
|
OG
|
B:SER349
|
4.0
|
0.3
|
1.0
|
N
|
B:ILE350
|
4.0
|
0.2
|
1.0
|
CB
|
B:ALA353
|
4.0
|
1.0
|
1.0
|
C
|
B:ILE350
|
4.1
|
0.6
|
1.0
|
CG
|
B:MET311
|
4.1
|
0.4
|
1.0
|
N
|
B:ASN310
|
4.2
|
0.1
|
1.0
|
C
|
B:THR352
|
4.2
|
0.1
|
1.0
|
CA
|
B:MET311
|
4.2
|
0.2
|
1.0
|
N
|
B:MET311
|
4.4
|
0.4
|
1.0
|
N
|
B:ILE309
|
4.4
|
0.5
|
1.0
|
CA
|
B:THR352
|
4.5
|
0.5
|
1.0
|
C
|
B:GLY351
|
4.6
|
0.0
|
1.0
|
CA
|
B:GLY351
|
4.6
|
0.6
|
1.0
|
CA
|
B:ASN310
|
4.6
|
0.8
|
1.0
|
CB
|
B:SER349
|
4.7
|
0.9
|
1.0
|
CB
|
B:MET311
|
4.7
|
0.9
|
1.0
|
OG1
|
B:THR352
|
4.7
|
0.6
|
1.0
|
CB
|
B:ILE350
|
4.8
|
0.8
|
1.0
|
CA
|
B:SER349
|
4.8
|
0.9
|
1.0
|
OG1
|
B:THR314
|
4.9
|
0.2
|
1.0
|
O
|
B:THR352
|
4.9
|
0.5
|
1.0
|
|
Thallium binding site 4 out
of 6 in 4p1a
Go back to
Thallium Binding Sites List in 4p1a
Thallium binding site 4 out
of 6 in the Thallium-Bound Inward-Facing State of the Glutamate Transporter Homologue Gltph
Mono view
Stereo pair view
|
A full contact list of Thallium with other atoms in the Tl binding
site number 4 of Thallium-Bound Inward-Facing State of the Glutamate Transporter Homologue Gltph within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Tl502
b:0.8
occ:0.80
|
OD2
|
B:ASP394
|
2.7
|
0.2
|
1.0
|
OG1
|
B:THR398
|
2.9
|
0.3
|
1.0
|
O
|
B:ARG276
|
3.0
|
0.9
|
1.0
|
O
|
B:VAL355
|
3.0
|
0.3
|
1.0
|
O
|
B:PRO356
|
3.1
|
0.2
|
1.0
|
NH2
|
B:ARG397
|
3.4
|
0.7
|
1.0
|
CZ
|
B:ARG397
|
3.6
|
0.2
|
1.0
|
NH1
|
B:ARG397
|
3.7
|
0.3
|
1.0
|
O
|
B:ALA353
|
3.8
|
0.8
|
1.0
|
CG
|
B:ASP394
|
3.9
|
1.0
|
1.0
|
CB
|
B:THR398
|
4.1
|
0.1
|
1.0
|
C
|
B:PRO356
|
4.1
|
0.8
|
1.0
|
CA
|
B:GLY354
|
4.1
|
0.3
|
1.0
|
C
|
B:ARG276
|
4.1
|
0.7
|
1.0
|
O
|
B:ASP394
|
4.2
|
0.0
|
1.0
|
C
|
B:VAL355
|
4.2
|
0.6
|
1.0
|
CG2
|
B:THR398
|
4.3
|
0.1
|
1.0
|
NE
|
B:ARG397
|
4.4
|
0.6
|
1.0
|
OD1
|
B:ASP394
|
4.4
|
0.3
|
1.0
|
CA
|
B:PRO356
|
4.5
|
0.1
|
1.0
|
CA
|
B:THR398
|
4.6
|
0.4
|
1.0
|
N
|
B:THR398
|
4.6
|
0.8
|
1.0
|
CA
|
B:ARG276
|
4.8
|
0.2
|
1.0
|
C
|
B:ALA353
|
4.8
|
0.2
|
1.0
|
N
|
B:PRO356
|
4.8
|
0.1
|
1.0
|
CB
|
B:ARG276
|
4.8
|
1.0
|
1.0
|
N
|
B:ALA358
|
4.9
|
0.1
|
1.0
|
CB
|
B:ASP394
|
5.0
|
0.7
|
1.0
|
N
|
B:GLY354
|
5.0
|
0.3
|
1.0
|
|
Thallium binding site 5 out
of 6 in 4p1a
Go back to
Thallium Binding Sites List in 4p1a
Thallium binding site 5 out
of 6 in the Thallium-Bound Inward-Facing State of the Glutamate Transporter Homologue Gltph
Mono view
Stereo pair view
|
A full contact list of Thallium with other atoms in the Tl binding
site number 5 of Thallium-Bound Inward-Facing State of the Glutamate Transporter Homologue Gltph within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Tl501
b:0.4
occ:0.50
|
O
|
C:SER349
|
2.9
|
0.9
|
1.0
|
O
|
C:ASN310
|
3.1
|
0.7
|
1.0
|
O
|
C:THR308
|
3.2
|
1.0
|
1.0
|
C
|
C:SER349
|
3.6
|
0.7
|
1.0
|
N
|
C:ALA353
|
3.7
|
0.6
|
1.0
|
OG
|
C:SER349
|
3.7
|
0.4
|
1.0
|
O
|
C:ILE309
|
3.7
|
0.8
|
1.0
|
C
|
C:ASN310
|
3.7
|
0.8
|
1.0
|
CA
|
C:ALA353
|
3.8
|
0.0
|
1.0
|
C
|
C:ILE309
|
3.9
|
0.6
|
1.0
|
CA
|
C:ILE350
|
3.9
|
0.2
|
1.0
|
N
|
C:THR352
|
3.9
|
0.3
|
1.0
|
CA
|
C:MET311
|
4.0
|
0.1
|
1.0
|
N
|
C:GLY351
|
4.0
|
0.2
|
1.0
|
CB
|
C:ALA353
|
4.0
|
0.5
|
1.0
|
CG
|
C:MET311
|
4.1
|
0.4
|
1.0
|
N
|
C:ILE350
|
4.1
|
0.1
|
1.0
|
C
|
C:THR352
|
4.1
|
0.7
|
1.0
|
N
|
C:MET311
|
4.2
|
0.8
|
1.0
|
CA
|
C:ILE309
|
4.3
|
0.9
|
1.0
|
C
|
C:THR308
|
4.3
|
0.3
|
1.0
|
N
|
C:ASN310
|
4.4
|
0.5
|
1.0
|
OG1
|
C:THR314
|
4.4
|
0.3
|
1.0
|
C
|
C:ILE350
|
4.4
|
1.0
|
1.0
|
CB
|
C:SER349
|
4.5
|
0.9
|
1.0
|
CA
|
C:THR352
|
4.5
|
1.0
|
1.0
|
CB
|
C:MET311
|
4.6
|
0.7
|
1.0
|
OG1
|
C:THR352
|
4.6
|
0.9
|
1.0
|
CA
|
C:ASN310
|
4.7
|
0.3
|
1.0
|
CA
|
C:SER349
|
4.7
|
0.2
|
1.0
|
O
|
C:THR352
|
4.8
|
0.3
|
1.0
|
N
|
C:ILE309
|
4.8
|
0.9
|
1.0
|
C
|
C:GLY351
|
4.9
|
0.4
|
1.0
|
CA
|
C:GLY351
|
5.0
|
0.2
|
1.0
|
|
Thallium binding site 6 out
of 6 in 4p1a
Go back to
Thallium Binding Sites List in 4p1a
Thallium binding site 6 out
of 6 in the Thallium-Bound Inward-Facing State of the Glutamate Transporter Homologue Gltph
Mono view
Stereo pair view
|
A full contact list of Thallium with other atoms in the Tl binding
site number 6 of Thallium-Bound Inward-Facing State of the Glutamate Transporter Homologue Gltph within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Tl502
b:0.9
occ:0.50
|
OD2
|
C:ASP394
|
2.3
|
0.1
|
1.0
|
OG1
|
C:THR398
|
2.7
|
0.6
|
1.0
|
O
|
C:PRO356
|
3.0
|
1.0
|
1.0
|
O
|
C:ARG276
|
3.2
|
0.3
|
1.0
|
NH2
|
C:ARG397
|
3.2
|
0.7
|
1.0
|
O
|
C:VAL355
|
3.4
|
0.1
|
1.0
|
CG
|
C:ASP394
|
3.4
|
0.9
|
1.0
|
CZ
|
C:ARG397
|
3.4
|
0.2
|
1.0
|
NH1
|
C:ARG397
|
3.6
|
0.1
|
1.0
|
O
|
C:ASP394
|
3.7
|
0.7
|
1.0
|
CB
|
C:THR398
|
4.0
|
0.2
|
1.0
|
OD1
|
C:ASP394
|
4.0
|
0.6
|
1.0
|
O
|
C:ALA353
|
4.1
|
0.1
|
1.0
|
C
|
C:PRO356
|
4.1
|
0.7
|
1.0
|
NE
|
C:ARG397
|
4.1
|
0.7
|
1.0
|
C
|
C:ARG276
|
4.3
|
0.0
|
1.0
|
N
|
C:THR398
|
4.3
|
0.1
|
1.0
|
CG2
|
C:THR398
|
4.4
|
0.7
|
1.0
|
CA
|
C:THR398
|
4.5
|
0.0
|
1.0
|
CB
|
C:ASP394
|
4.5
|
0.1
|
1.0
|
C
|
C:VAL355
|
4.6
|
1.0
|
1.0
|
CA
|
C:GLY354
|
4.6
|
0.5
|
1.0
|
C
|
C:ASP394
|
4.7
|
1.0
|
1.0
|
CB
|
C:ARG397
|
4.7
|
0.5
|
1.0
|
CA
|
C:PRO356
|
4.7
|
0.1
|
1.0
|
CB
|
C:ARG276
|
4.7
|
0.1
|
1.0
|
CA
|
C:ARG276
|
4.8
|
0.5
|
1.0
|
CA
|
C:ASP394
|
4.8
|
0.5
|
1.0
|
N
|
C:ALA358
|
4.9
|
0.7
|
1.0
|
CD
|
C:ARG397
|
5.0
|
0.1
|
1.0
|
|
Reference:
G.Verdon,
S.Oh,
R.N.Serio,
O.Boudker.
Coupled Ion Binding and Structural Transitions Along the Transport Cycle of Glutamate Transporters. Elife V. 3 02283 2014.
ISSN: ESSN 2050-084X
PubMed: 24842876
DOI: 10.7554/ELIFE.02283
Page generated: Wed Dec 16 02:28:46 2020
|