Sodium in PDB 4oyf: Crystal Structure of Gltph R397A in Sodium-Bound State
Protein crystallography data
The structure of Crystal Structure of Gltph R397A in Sodium-Bound State, PDB code: 4oyf
was solved by
O.Boudker,
S.Oh,
G.Verdon,
R.Serio,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
12.00 /
3.41
|
Space group
|
P 31
|
Cell size a, b, c (Å), α, β, γ (°)
|
110.579,
110.579,
306.923,
90.00,
90.00,
120.00
|
R / Rfree (%)
|
28.4 /
29.3
|
Sodium Binding Sites:
The binding sites of Sodium atom in the Crystal Structure of Gltph R397A in Sodium-Bound State
(pdb code 4oyf). This binding sites where shown within
5.0 Angstroms radius around Sodium atom.
In total 6 binding sites of Sodium where determined in the
Crystal Structure of Gltph R397A in Sodium-Bound State, PDB code: 4oyf:
Jump to Sodium binding site number:
1;
2;
3;
4;
5;
6;
Sodium binding site 1 out
of 6 in 4oyf
Go back to
Sodium Binding Sites List in 4oyf
Sodium binding site 1 out
of 6 in the Crystal Structure of Gltph R397A in Sodium-Bound State
![](/pictures/NA/pdb/oy/4oyf-NA-sphere_01.jpg) Mono view
![](/pictures/NA/pdb/oy/4oyf-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 Gltph R397A in Sodium-Bound State within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na501
b:0.1
occ:1.00
|
OD2
|
A:ASP405
|
2.8
|
0.2
|
1.0
|
O
|
A:ASN310
|
2.8
|
0.9
|
1.0
|
O
|
A:GLY306
|
2.9
|
1.0
|
1.0
|
O
|
A:ASN401
|
3.5
|
0.3
|
1.0
|
OD1
|
A:ASP405
|
3.5
|
0.8
|
1.0
|
CG
|
A:ASP405
|
3.5
|
0.2
|
1.0
|
C
|
A:GLY306
|
3.7
|
0.1
|
1.0
|
CA
|
A:ALA307
|
3.8
|
0.8
|
1.0
|
C
|
A:ASN401
|
3.8
|
0.6
|
1.0
|
CB
|
A:ASN401
|
3.8
|
0.2
|
1.0
|
OG
|
A:SER278
|
4.0
|
0.2
|
1.0
|
C
|
A:ASN310
|
4.0
|
0.2
|
1.0
|
ND2
|
A:ASN310
|
4.1
|
0.8
|
1.0
|
CB
|
A:SER278
|
4.1
|
0.5
|
1.0
|
O
|
A:ALA307
|
4.1
|
0.5
|
1.0
|
N
|
A:ALA307
|
4.1
|
0.8
|
1.0
|
C
|
A:ALA307
|
4.1
|
0.9
|
1.0
|
CA
|
A:ASN401
|
4.3
|
0.7
|
1.0
|
N
|
A:VAL402
|
4.5
|
1.0
|
1.0
|
CG
|
A:ASN401
|
4.6
|
0.9
|
1.0
|
ND2
|
A:ASN401
|
4.6
|
1.0
|
1.0
|
CG
|
A:MET311
|
4.7
|
0.7
|
1.0
|
CB
|
A:ASN310
|
4.8
|
0.4
|
1.0
|
CA
|
A:VAL402
|
4.8
|
0.2
|
1.0
|
CA
|
A:GLY306
|
4.9
|
0.0
|
1.0
|
CA
|
A:ASN310
|
4.9
|
0.6
|
1.0
|
CG
|
A:ASN310
|
4.9
|
0.4
|
1.0
|
CA
|
A:MET311
|
4.9
|
0.9
|
1.0
|
N
|
A:MET311
|
5.0
|
0.3
|
1.0
|
CB
|
A:ASP405
|
5.0
|
0.3
|
1.0
|
|
Sodium binding site 2 out
of 6 in 4oyf
Go back to
Sodium Binding Sites List in 4oyf
Sodium binding site 2 out
of 6 in the Crystal Structure of Gltph R397A in Sodium-Bound State
![](/pictures/NA/pdb/oy/4oyf-NA-sphere_02.jpg) Mono view
![](/pictures/NA/pdb/oy/4oyf-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 Gltph R397A in Sodium-Bound State within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Na501
b:91.7
occ:1.00
|
OD2
|
B:ASP405
|
2.7
|
0.7
|
1.0
|
O
|
B:ASN310
|
3.0
|
0.5
|
1.0
|
O
|
B:GLY306
|
3.0
|
0.3
|
1.0
|
OD1
|
B:ASP405
|
3.4
|
0.7
|
1.0
|
CG
|
B:ASP405
|
3.4
|
0.4
|
1.0
|
O
|
B:ASN401
|
3.5
|
0.6
|
1.0
|
C
|
B:GLY306
|
3.8
|
0.6
|
1.0
|
C
|
B:ASN401
|
3.8
|
0.7
|
1.0
|
CA
|
B:ALA307
|
3.8
|
0.2
|
1.0
|
CB
|
B:ASN401
|
3.8
|
0.3
|
1.0
|
OG
|
B:SER278
|
3.9
|
0.4
|
1.0
|
CB
|
B:SER278
|
4.0
|
0.9
|
1.0
|
N
|
B:ALA307
|
4.1
|
0.4
|
1.0
|
ND2
|
B:ASN310
|
4.2
|
0.9
|
1.0
|
C
|
B:ASN310
|
4.2
|
0.9
|
1.0
|
O
|
B:ALA307
|
4.2
|
0.9
|
1.0
|
C
|
B:ALA307
|
4.2
|
0.6
|
1.0
|
CA
|
B:ASN401
|
4.3
|
0.6
|
1.0
|
N
|
B:VAL402
|
4.4
|
0.9
|
1.0
|
CG
|
B:ASN401
|
4.6
|
0.9
|
1.0
|
CA
|
B:VAL402
|
4.7
|
0.3
|
1.0
|
ND2
|
B:ASN401
|
4.7
|
0.3
|
1.0
|
CG
|
B:MET311
|
4.8
|
0.3
|
1.0
|
CB
|
B:ASN310
|
4.9
|
0.6
|
1.0
|
CA
|
B:GLY306
|
4.9
|
0.8
|
1.0
|
CB
|
B:ASP405
|
4.9
|
0.7
|
1.0
|
CB
|
B:ALA307
|
5.0
|
0.5
|
1.0
|
|
Sodium binding site 3 out
of 6 in 4oyf
Go back to
Sodium Binding Sites List in 4oyf
Sodium binding site 3 out
of 6 in the Crystal Structure of Gltph R397A in Sodium-Bound State
![](/pictures/NA/pdb/oy/4oyf-NA-sphere_03.jpg) Mono view
![](/pictures/NA/pdb/oy/4oyf-NA-sphere_03_stereo.jpg) Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 3 of Crystal Structure of Gltph R397A in Sodium-Bound State within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Na501
b:98.0
occ:1.00
|
O
|
C:ASN310
|
2.7
|
0.6
|
1.0
|
OD2
|
C:ASP405
|
2.8
|
0.1
|
1.0
|
O
|
C:GLY306
|
2.8
|
0.4
|
1.0
|
O
|
C:ASN401
|
3.5
|
0.8
|
1.0
|
OD1
|
C:ASP405
|
3.5
|
0.9
|
1.0
|
CG
|
C:ASP405
|
3.5
|
0.2
|
1.0
|
C
|
C:GLY306
|
3.7
|
0.8
|
1.0
|
CB
|
C:ASN401
|
3.8
|
0.5
|
1.0
|
C
|
C:ASN401
|
3.8
|
0.3
|
1.0
|
CA
|
C:ALA307
|
3.8
|
0.1
|
1.0
|
C
|
C:ASN310
|
3.9
|
0.4
|
1.0
|
OG
|
C:SER278
|
4.0
|
0.7
|
1.0
|
ND2
|
C:ASN310
|
4.0
|
0.2
|
1.0
|
CB
|
C:SER278
|
4.1
|
0.3
|
1.0
|
O
|
C:ALA307
|
4.1
|
0.5
|
1.0
|
N
|
C:ALA307
|
4.2
|
0.9
|
1.0
|
C
|
C:ALA307
|
4.2
|
0.9
|
1.0
|
CA
|
C:ASN401
|
4.3
|
0.9
|
1.0
|
N
|
C:VAL402
|
4.5
|
0.1
|
1.0
|
CG
|
C:ASN401
|
4.5
|
0.7
|
1.0
|
ND2
|
C:ASN401
|
4.5
|
0.8
|
1.0
|
CG
|
C:MET311
|
4.6
|
0.3
|
1.0
|
CB
|
C:ASN310
|
4.7
|
0.8
|
1.0
|
CA
|
C:ASN310
|
4.8
|
0.7
|
1.0
|
CA
|
C:VAL402
|
4.8
|
0.9
|
1.0
|
CA
|
C:MET311
|
4.8
|
0.8
|
1.0
|
CA
|
C:GLY306
|
4.8
|
0.6
|
1.0
|
N
|
C:MET311
|
4.9
|
0.2
|
1.0
|
CG
|
C:ASN310
|
4.9
|
0.6
|
1.0
|
CB
|
C:ASP405
|
5.0
|
0.4
|
1.0
|
|
Sodium binding site 4 out
of 6 in 4oyf
Go back to
Sodium Binding Sites List in 4oyf
Sodium binding site 4 out
of 6 in the Crystal Structure of Gltph R397A in Sodium-Bound State
![](/pictures/NA/pdb/oy/4oyf-NA-sphere_04.jpg) Mono view
![](/pictures/NA/pdb/oy/4oyf-NA-sphere_04_stereo.jpg) Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 4 of Crystal Structure of Gltph R397A in Sodium-Bound State within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Na501
b:0.6
occ:1.00
|
OD2
|
D:ASP405
|
2.7
|
0.8
|
1.0
|
O
|
D:ASN310
|
2.8
|
0.2
|
1.0
|
O
|
D:GLY306
|
2.9
|
0.1
|
1.0
|
O
|
D:ASN401
|
3.4
|
0.6
|
1.0
|
OD1
|
D:ASP405
|
3.4
|
0.8
|
1.0
|
CG
|
D:ASP405
|
3.5
|
0.1
|
1.0
|
C
|
D:GLY306
|
3.7
|
0.4
|
1.0
|
C
|
D:ASN401
|
3.8
|
0.0
|
1.0
|
CB
|
D:ASN401
|
3.8
|
1.0
|
1.0
|
CA
|
D:ALA307
|
3.9
|
0.4
|
1.0
|
C
|
D:ASN310
|
4.0
|
0.1
|
1.0
|
ND2
|
D:ASN310
|
4.0
|
0.2
|
1.0
|
OG
|
D:SER278
|
4.0
|
0.6
|
1.0
|
CB
|
D:SER278
|
4.1
|
0.3
|
1.0
|
N
|
D:ALA307
|
4.2
|
0.4
|
1.0
|
O
|
D:ALA307
|
4.2
|
0.6
|
1.0
|
C
|
D:ALA307
|
4.2
|
0.2
|
1.0
|
CA
|
D:ASN401
|
4.3
|
0.6
|
1.0
|
N
|
D:VAL402
|
4.4
|
0.8
|
1.0
|
CG
|
D:ASN401
|
4.5
|
0.1
|
1.0
|
ND2
|
D:ASN401
|
4.6
|
0.0
|
1.0
|
CG
|
D:MET311
|
4.7
|
0.5
|
1.0
|
CB
|
D:ASN310
|
4.8
|
0.8
|
1.0
|
CA
|
D:VAL402
|
4.8
|
0.6
|
1.0
|
CA
|
D:GLY306
|
4.8
|
0.5
|
1.0
|
CA
|
D:ASN310
|
4.9
|
0.6
|
1.0
|
CA
|
D:MET311
|
4.9
|
0.4
|
1.0
|
CG
|
D:ASN310
|
4.9
|
0.7
|
1.0
|
N
|
D:MET311
|
4.9
|
0.9
|
1.0
|
CB
|
D:ASP405
|
4.9
|
0.4
|
1.0
|
|
Sodium binding site 5 out
of 6 in 4oyf
Go back to
Sodium Binding Sites List in 4oyf
Sodium binding site 5 out
of 6 in the Crystal Structure of Gltph R397A in Sodium-Bound State
![](/pictures/NA/pdb/oy/4oyf-NA-sphere_05.jpg) Mono view
![](/pictures/NA/pdb/oy/4oyf-NA-sphere_05_stereo.jpg) Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 5 of Crystal Structure of Gltph R397A in Sodium-Bound State within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Na501
b:0.8
occ:1.00
|
OD2
|
E:ASP405
|
2.8
|
0.3
|
1.0
|
O
|
E:ASN310
|
2.8
|
0.1
|
1.0
|
O
|
E:GLY306
|
2.9
|
0.2
|
1.0
|
O
|
E:ASN401
|
3.4
|
0.2
|
1.0
|
OD1
|
E:ASP405
|
3.5
|
0.8
|
1.0
|
CG
|
E:ASP405
|
3.5
|
0.2
|
1.0
|
C
|
E:GLY306
|
3.7
|
0.3
|
1.0
|
C
|
E:ASN401
|
3.8
|
0.6
|
1.0
|
CA
|
E:ALA307
|
3.8
|
0.1
|
1.0
|
CB
|
E:ASN401
|
3.8
|
0.3
|
1.0
|
OG
|
E:SER278
|
4.0
|
0.5
|
1.0
|
ND2
|
E:ASN310
|
4.0
|
0.7
|
1.0
|
C
|
E:ASN310
|
4.0
|
0.3
|
1.0
|
CB
|
E:SER278
|
4.1
|
0.7
|
1.0
|
O
|
E:ALA307
|
4.1
|
0.8
|
1.0
|
N
|
E:ALA307
|
4.1
|
0.1
|
1.0
|
C
|
E:ALA307
|
4.2
|
0.3
|
1.0
|
CA
|
E:ASN401
|
4.3
|
0.7
|
1.0
|
N
|
E:VAL402
|
4.5
|
0.9
|
1.0
|
CG
|
E:ASN401
|
4.6
|
0.0
|
1.0
|
ND2
|
E:ASN401
|
4.7
|
0.1
|
1.0
|
CG
|
E:MET311
|
4.7
|
0.0
|
1.0
|
CB
|
E:ASN310
|
4.7
|
0.4
|
1.0
|
CA
|
E:VAL402
|
4.8
|
0.1
|
1.0
|
CA
|
E:GLY306
|
4.9
|
0.2
|
1.0
|
CA
|
E:ASN310
|
4.9
|
0.7
|
1.0
|
CG
|
E:ASN310
|
4.9
|
0.3
|
1.0
|
CA
|
E:MET311
|
4.9
|
0.1
|
1.0
|
CB
|
E:ASP405
|
5.0
|
0.2
|
1.0
|
N
|
E:MET311
|
5.0
|
0.5
|
1.0
|
|
Sodium binding site 6 out
of 6 in 4oyf
Go back to
Sodium Binding Sites List in 4oyf
Sodium binding site 6 out
of 6 in the Crystal Structure of Gltph R397A in Sodium-Bound State
![](/pictures/NA/pdb/oy/4oyf-NA-sphere_06.jpg) Mono view
![](/pictures/NA/pdb/oy/4oyf-NA-sphere_06_stereo.jpg) Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 6 of Crystal Structure of Gltph R397A in Sodium-Bound State within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Na501
b:92.2
occ:1.00
|
OD2
|
F:ASP405
|
2.7
|
0.6
|
1.0
|
O
|
F:ASN310
|
2.9
|
0.5
|
1.0
|
O
|
F:GLY306
|
3.0
|
0.2
|
1.0
|
OD1
|
F:ASP405
|
3.4
|
0.6
|
1.0
|
O
|
F:ASN401
|
3.4
|
0.6
|
1.0
|
CG
|
F:ASP405
|
3.4
|
0.3
|
1.0
|
C
|
F:ASN401
|
3.8
|
0.7
|
1.0
|
C
|
F:GLY306
|
3.8
|
0.5
|
1.0
|
CB
|
F:ASN401
|
3.8
|
0.2
|
1.0
|
CA
|
F:ALA307
|
3.8
|
0.0
|
1.0
|
OG
|
F:SER278
|
4.0
|
0.2
|
1.0
|
CB
|
F:SER278
|
4.1
|
0.7
|
1.0
|
ND2
|
F:ASN310
|
4.1
|
1.0
|
1.0
|
C
|
F:ASN310
|
4.1
|
1.0
|
1.0
|
N
|
F:ALA307
|
4.2
|
0.2
|
1.0
|
C
|
F:ALA307
|
4.3
|
0.5
|
1.0
|
O
|
F:ALA307
|
4.3
|
0.8
|
1.0
|
CA
|
F:ASN401
|
4.3
|
0.6
|
1.0
|
N
|
F:VAL402
|
4.4
|
0.8
|
1.0
|
CG
|
F:ASN401
|
4.6
|
0.9
|
1.0
|
ND2
|
F:ASN401
|
4.7
|
0.3
|
1.0
|
CA
|
F:VAL402
|
4.7
|
0.1
|
1.0
|
CG
|
F:MET311
|
4.8
|
0.2
|
1.0
|
CB
|
F:ASN310
|
4.8
|
0.6
|
1.0
|
CA
|
F:GLY306
|
4.9
|
0.7
|
1.0
|
CB
|
F:ASP405
|
4.9
|
0.6
|
1.0
|
CG
|
F:ASN310
|
5.0
|
0.1
|
1.0
|
CA
|
F:ASN310
|
5.0
|
0.9
|
1.0
|
CA
|
F:MET311
|
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: Tue Dec 15 06:57:33 2020
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