Sodium in PDB 5cfy: Crystal Structure of Gltph R397A in Complex with Na+ and L-Asp
Protein crystallography data
The structure of Crystal Structure of Gltph R397A in Complex with Na+ and L-Asp, PDB code: 5cfy
was solved by
O.Boudker,
S.Oh,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
|
Resolution Low / High (Å)
|
15.00 /
3.50
|
|
Space group
|
P 31
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
116.958,
116.958,
313.517,
90.00,
90.00,
120.00
|
|
R / Rfree (%)
|
24.9 /
29.4
|
Sodium Binding Sites:
Pages:
>>> Page 1 <<<
Page 2, Binding sites: 11 -
12;
Binding sites:
The binding sites of Sodium atom in the Crystal Structure of Gltph R397A in Complex with Na+ and L-Asp
(pdb code 5cfy). This binding sites where shown within
5.0 Angstroms radius around Sodium atom.
In total 12 binding sites of Sodium where determined in the
Crystal Structure of Gltph R397A in Complex with Na+ and L-Asp, PDB code: 5cfy:
Jump to Sodium binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
10;
Sodium binding site 1 out
of 12 in 5cfy
Go back to
Sodium Binding Sites List in 5cfy
Sodium binding site 1 out
of 12 in the Crystal Structure of Gltph R397A in Complex with Na+ and L-Asp
 Mono view
 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 Complex with Na+ and L-Asp within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na502
b:0.6
occ:1.00
|
O
|
A:THR352
|
2.0
|
0.7
|
1.0
|
|
O
|
A:SER349
|
2.5
|
0.1
|
1.0
|
|
O
|
A:THR308
|
2.8
|
0.5
|
1.0
|
|
SD
|
A:MET311
|
2.9
|
0.2
|
1.0
|
|
C
|
A:THR352
|
2.9
|
0.4
|
1.0
|
|
N
|
A:THR352
|
3.1
|
0.7
|
1.0
|
|
CA
|
A:THR352
|
3.4
|
0.9
|
1.0
|
|
C
|
A:ILE350
|
3.4
|
1.0
|
1.0
|
|
O
|
A:ILE350
|
3.5
|
0.9
|
1.0
|
|
C
|
A:GLY351
|
3.5
|
0.7
|
1.0
|
|
C
|
A:SER349
|
3.5
|
0.9
|
1.0
|
|
C
|
A:THR308
|
3.6
|
0.9
|
1.0
|
|
N
|
A:GLY351
|
3.6
|
0.8
|
1.0
|
|
CG
|
A:MET311
|
3.8
|
0.7
|
1.0
|
|
CE
|
A:MET311
|
3.8
|
0.8
|
1.0
|
|
CB
|
A:THR352
|
3.8
|
0.1
|
1.0
|
|
CA
|
A:ILE350
|
3.9
|
0.3
|
1.0
|
|
CA
|
A:GLY351
|
4.0
|
0.6
|
1.0
|
|
N
|
A:ALA353
|
4.1
|
0.7
|
1.0
|
|
N
|
A:ILE350
|
4.1
|
0.3
|
1.0
|
|
O
|
A:GLY351
|
4.1
|
0.1
|
1.0
|
|
CA
|
A:THR308
|
4.1
|
0.2
|
1.0
|
|
CA
|
A:ALA353
|
4.5
|
0.3
|
1.0
|
|
CB
|
A:MET311
|
4.6
|
0.9
|
1.0
|
|
N
|
A:ILE309
|
4.6
|
0.8
|
1.0
|
|
CB
|
A:THR308
|
4.6
|
0.5
|
1.0
|
|
CG2
|
A:THR352
|
4.7
|
0.8
|
1.0
|
|
C
|
A:ALA353
|
4.7
|
0.0
|
1.0
|
|
CA
|
A:SER349
|
4.7
|
0.9
|
1.0
|
|
O
|
A:ALA353
|
4.8
|
0.3
|
1.0
|
|
CA
|
A:ILE309
|
4.9
|
0.8
|
1.0
|
|
OG1
|
A:THR352
|
4.9
|
0.6
|
1.0
|
|
Sodium binding site 2 out
of 12 in 5cfy
Go back to
Sodium Binding Sites List in 5cfy
Sodium binding site 2 out
of 12 in the Crystal Structure of Gltph R397A in Complex with Na+ and L-Asp
 Mono view
 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 Complex with Na+ and L-Asp within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na503
b:0.9
occ:1.00
|
O
|
A:GLY306
|
2.6
|
0.3
|
1.0
|
|
O
|
A:ASN310
|
2.7
|
0.9
|
1.0
|
|
OD2
|
A:ASP405
|
3.0
|
0.8
|
1.0
|
|
OG
|
A:SER278
|
3.3
|
0.8
|
1.0
|
|
O
|
A:ALA307
|
3.4
|
0.8
|
1.0
|
|
CA
|
A:ALA307
|
3.5
|
0.8
|
1.0
|
|
C
|
A:ALA307
|
3.5
|
0.6
|
1.0
|
|
C
|
A:GLY306
|
3.5
|
0.9
|
1.0
|
|
O
|
A:ASN401
|
3.5
|
0.7
|
1.0
|
|
C
|
A:ASN310
|
3.7
|
0.6
|
1.0
|
|
CB
|
A:ASN401
|
3.8
|
0.8
|
1.0
|
|
CG
|
A:MET311
|
3.8
|
0.7
|
1.0
|
|
C
|
A:ASN401
|
3.8
|
0.4
|
1.0
|
|
N
|
A:ALA307
|
3.8
|
0.4
|
1.0
|
|
CG
|
A:ASP405
|
3.9
|
0.8
|
1.0
|
|
OD1
|
A:ASP405
|
4.0
|
0.9
|
1.0
|
|
CB
|
A:SER278
|
4.0
|
0.9
|
1.0
|
|
N
|
A:THR308
|
4.2
|
0.5
|
1.0
|
|
CA
|
A:ASN401
|
4.3
|
0.7
|
1.0
|
|
CE
|
A:MET311
|
4.3
|
0.8
|
1.0
|
|
N
|
A:VAL402
|
4.4
|
0.5
|
1.0
|
|
N
|
A:MET311
|
4.5
|
0.2
|
1.0
|
|
CA
|
A:MET311
|
4.5
|
0.1
|
1.0
|
|
N
|
A:ASN310
|
4.6
|
0.6
|
1.0
|
|
O
|
A:THR308
|
4.6
|
0.5
|
1.0
|
|
CA
|
A:ASN310
|
4.6
|
0.0
|
1.0
|
|
CB
|
A:MET311
|
4.8
|
0.9
|
1.0
|
|
CA
|
A:VAL402
|
4.8
|
0.5
|
1.0
|
|
CA
|
A:GLY306
|
4.8
|
0.4
|
1.0
|
|
C
|
A:THR308
|
4.8
|
0.9
|
1.0
|
|
CB
|
A:ALA307
|
4.8
|
0.4
|
1.0
|
|
CA
|
A:THR308
|
4.8
|
0.2
|
1.0
|
|
CG
|
A:ASN401
|
4.9
|
0.9
|
1.0
|
|
SD
|
A:MET311
|
5.0
|
0.2
|
1.0
|
|
Sodium binding site 3 out
of 12 in 5cfy
Go back to
Sodium Binding Sites List in 5cfy
Sodium binding site 3 out
of 12 in the Crystal Structure of Gltph R397A in Complex with Na+ and L-Asp
 Mono view
 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 Complex with Na+ and L-Asp within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Na502
b:0.6
occ:1.00
|
O
|
B:THR308
|
2.2
|
0.8
|
1.0
|
|
O
|
B:THR352
|
2.3
|
0.1
|
1.0
|
|
O
|
B:SER349
|
2.5
|
0.3
|
1.0
|
|
C
|
B:THR308
|
3.2
|
0.9
|
1.0
|
|
SD
|
B:MET311
|
3.2
|
0.8
|
1.0
|
|
C
|
B:THR352
|
3.2
|
0.1
|
1.0
|
|
N
|
B:THR352
|
3.5
|
0.9
|
1.0
|
|
C
|
B:ILE350
|
3.5
|
0.5
|
1.0
|
|
O
|
B:ILE350
|
3.6
|
0.2
|
1.0
|
|
C
|
B:SER349
|
3.6
|
0.7
|
1.0
|
|
CA
|
B:THR352
|
3.7
|
0.0
|
1.0
|
|
C
|
B:GLY351
|
3.8
|
0.9
|
1.0
|
|
CG
|
B:MET311
|
3.8
|
0.7
|
1.0
|
|
N
|
B:GLY351
|
3.8
|
0.5
|
1.0
|
|
CE
|
B:MET311
|
3.8
|
0.2
|
1.0
|
|
CA
|
B:THR308
|
3.9
|
0.9
|
1.0
|
|
CB
|
B:THR352
|
3.9
|
0.9
|
1.0
|
|
CA
|
B:ILE350
|
3.9
|
0.1
|
1.0
|
|
O
|
B:GLY351
|
4.1
|
0.2
|
1.0
|
|
N
|
B:ILE309
|
4.2
|
0.4
|
1.0
|
|
N
|
B:ILE350
|
4.2
|
0.7
|
1.0
|
|
CA
|
B:GLY351
|
4.2
|
1.0
|
1.0
|
|
N
|
B:ALA353
|
4.3
|
0.1
|
1.0
|
|
CB
|
B:THR308
|
4.4
|
0.3
|
1.0
|
|
CA
|
B:ILE309
|
4.5
|
0.2
|
1.0
|
|
CA
|
B:ALA353
|
4.6
|
0.3
|
1.0
|
|
CB
|
B:MET311
|
4.6
|
0.1
|
1.0
|
|
C
|
B:ALA353
|
4.6
|
0.8
|
1.0
|
|
C
|
B:ILE309
|
4.7
|
0.0
|
1.0
|
|
O
|
B:ALA353
|
4.7
|
0.5
|
1.0
|
|
CG2
|
B:THR352
|
4.8
|
0.2
|
1.0
|
|
CA
|
B:SER349
|
4.8
|
0.6
|
1.0
|
|
OG1
|
B:THR308
|
4.9
|
0.8
|
1.0
|
|
O
|
B:ILE309
|
4.9
|
0.0
|
1.0
|
|
OG1
|
B:THR352
|
5.0
|
0.5
|
1.0
|
|
Sodium binding site 4 out
of 12 in 5cfy
Go back to
Sodium Binding Sites List in 5cfy
Sodium binding site 4 out
of 12 in the Crystal Structure of Gltph R397A in Complex with Na+ and L-Asp
 Mono view
 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 Complex with Na+ and L-Asp within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Na503
b:0.8
occ:1.00
|
O
|
B:GLY306
|
2.4
|
0.8
|
1.0
|
|
OD2
|
B:ASP405
|
2.6
|
0.7
|
1.0
|
|
O
|
B:ASN401
|
2.8
|
0.0
|
1.0
|
|
O
|
B:ASN310
|
2.9
|
0.3
|
1.0
|
|
OD1
|
B:ASP405
|
3.2
|
0.7
|
1.0
|
|
CG
|
B:ASP405
|
3.3
|
0.7
|
1.0
|
|
C
|
B:GLY306
|
3.4
|
0.0
|
1.0
|
|
C
|
B:ASN401
|
3.5
|
0.1
|
1.0
|
|
OG
|
B:SER278
|
3.5
|
0.4
|
1.0
|
|
CA
|
B:ALA307
|
3.6
|
0.9
|
1.0
|
|
CB
|
B:ASN401
|
3.7
|
0.9
|
1.0
|
|
C
|
B:ALA307
|
3.7
|
0.2
|
1.0
|
|
C
|
B:ASN310
|
3.7
|
0.5
|
1.0
|
|
O
|
B:ALA307
|
3.8
|
0.0
|
1.0
|
|
N
|
B:ALA307
|
3.8
|
0.9
|
1.0
|
|
CG
|
B:MET311
|
4.0
|
0.7
|
1.0
|
|
CA
|
B:ASN401
|
4.1
|
0.2
|
1.0
|
|
CB
|
B:SER278
|
4.2
|
0.9
|
1.0
|
|
N
|
B:VAL402
|
4.3
|
0.1
|
1.0
|
|
N
|
B:THR308
|
4.4
|
0.9
|
1.0
|
|
N
|
B:MET311
|
4.5
|
0.1
|
1.0
|
|
N
|
B:ASN310
|
4.5
|
0.9
|
1.0
|
|
CA
|
B:ASN310
|
4.6
|
0.3
|
1.0
|
|
CE
|
B:MET311
|
4.6
|
0.2
|
1.0
|
|
CA
|
B:MET311
|
4.6
|
0.9
|
1.0
|
|
CA
|
B:VAL402
|
4.6
|
0.5
|
1.0
|
|
CA
|
B:GLY306
|
4.7
|
0.4
|
1.0
|
|
CG2
|
B:VAL402
|
4.7
|
0.1
|
1.0
|
|
CG
|
B:ASN401
|
4.7
|
0.2
|
1.0
|
|
O
|
B:HOH601
|
4.8
|
0.3
|
1.0
|
|
CB
|
B:ASP405
|
4.8
|
0.5
|
1.0
|
|
CB
|
B:ALA307
|
4.9
|
0.5
|
1.0
|
|
CB
|
B:ASN310
|
4.9
|
0.7
|
1.0
|
|
CB
|
B:MET311
|
5.0
|
0.1
|
1.0
|
|
Sodium binding site 5 out
of 12 in 5cfy
Go back to
Sodium Binding Sites List in 5cfy
Sodium binding site 5 out
of 12 in the Crystal Structure of Gltph R397A in Complex with Na+ and L-Asp
 Mono view
 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 Complex with Na+ and L-Asp within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Na502
b:0.7
occ:1.00
|
O
|
C:THR352
|
2.0
|
0.1
|
1.0
|
|
O
|
C:SER349
|
2.4
|
0.2
|
1.0
|
|
O
|
C:THR308
|
2.8
|
0.4
|
1.0
|
|
SD
|
C:MET311
|
2.9
|
0.6
|
1.0
|
|
C
|
C:THR352
|
2.9
|
1.0
|
1.0
|
|
N
|
C:THR352
|
3.1
|
0.2
|
1.0
|
|
CA
|
C:THR352
|
3.3
|
0.8
|
1.0
|
|
C
|
C:SER349
|
3.5
|
0.7
|
1.0
|
|
C
|
C:GLY351
|
3.6
|
0.5
|
1.0
|
|
C
|
C:ILE350
|
3.6
|
0.4
|
1.0
|
|
CB
|
C:THR352
|
3.6
|
0.2
|
1.0
|
|
O
|
C:ILE350
|
3.7
|
0.4
|
1.0
|
|
C
|
C:THR308
|
3.7
|
0.3
|
1.0
|
|
N
|
C:GLY351
|
3.7
|
1.0
|
1.0
|
|
CE
|
C:MET311
|
3.7
|
0.8
|
1.0
|
|
CG
|
C:MET311
|
3.9
|
0.8
|
1.0
|
|
N
|
C:ALA353
|
4.0
|
0.8
|
1.0
|
|
CA
|
C:ILE350
|
4.1
|
0.4
|
1.0
|
|
CA
|
C:GLY351
|
4.1
|
0.0
|
1.0
|
|
O
|
C:GLY351
|
4.1
|
0.3
|
1.0
|
|
CA
|
C:THR308
|
4.2
|
0.0
|
1.0
|
|
N
|
C:ILE350
|
4.2
|
0.6
|
1.0
|
|
CA
|
C:ALA353
|
4.3
|
0.7
|
1.0
|
|
C
|
C:ALA353
|
4.4
|
1.0
|
1.0
|
|
O
|
C:ALA353
|
4.4
|
0.9
|
1.0
|
|
CG2
|
C:THR352
|
4.5
|
0.5
|
1.0
|
|
CB
|
C:THR308
|
4.5
|
0.1
|
1.0
|
|
CA
|
C:SER349
|
4.6
|
0.3
|
1.0
|
|
CB
|
C:MET311
|
4.6
|
0.5
|
1.0
|
|
N
|
C:ILE309
|
4.7
|
0.7
|
1.0
|
|
OG1
|
C:THR352
|
4.7
|
0.1
|
1.0
|
|
CA
|
C:ILE309
|
4.9
|
0.6
|
1.0
|
|
Sodium binding site 6 out
of 12 in 5cfy
Go back to
Sodium Binding Sites List in 5cfy
Sodium binding site 6 out
of 12 in the Crystal Structure of Gltph R397A in Complex with Na+ and L-Asp
 Mono view
 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 Complex with Na+ and L-Asp within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Na503
b:0.3
occ:1.00
|
O
|
C:GLY306
|
2.7
|
0.8
|
1.0
|
|
OG
|
C:SER278
|
3.0
|
0.8
|
1.0
|
|
OD2
|
C:ASP405
|
3.1
|
0.5
|
1.0
|
|
O
|
C:ASN310
|
3.1
|
0.4
|
1.0
|
|
O
|
C:ASN401
|
3.1
|
0.9
|
1.0
|
|
O
|
C:ALA307
|
3.5
|
0.9
|
1.0
|
|
CA
|
C:ALA307
|
3.5
|
0.4
|
1.0
|
|
C
|
C:ASN401
|
3.5
|
1.0
|
1.0
|
|
C
|
C:ALA307
|
3.6
|
0.6
|
1.0
|
|
C
|
C:GLY306
|
3.6
|
0.8
|
1.0
|
|
CB
|
C:ASN401
|
3.6
|
0.0
|
1.0
|
|
CG
|
C:ASP405
|
3.8
|
0.8
|
1.0
|
|
CB
|
C:SER278
|
3.8
|
0.0
|
1.0
|
|
OD1
|
C:ASP405
|
3.8
|
0.8
|
1.0
|
|
N
|
C:ALA307
|
3.9
|
0.5
|
1.0
|
|
C
|
C:ASN310
|
3.9
|
0.8
|
1.0
|
|
CG
|
C:MET311
|
4.0
|
0.8
|
1.0
|
|
CA
|
C:ASN401
|
4.1
|
0.2
|
1.0
|
|
N
|
C:VAL402
|
4.2
|
0.2
|
1.0
|
|
N
|
C:THR308
|
4.4
|
0.7
|
1.0
|
|
CA
|
C:VAL402
|
4.5
|
0.4
|
1.0
|
|
CE
|
C:MET311
|
4.6
|
0.8
|
1.0
|
|
CG2
|
C:VAL402
|
4.6
|
0.0
|
1.0
|
|
N
|
C:MET311
|
4.7
|
0.5
|
1.0
|
|
CA
|
C:MET311
|
4.7
|
0.5
|
1.0
|
|
O
|
C:HOH601
|
4.7
|
0.2
|
1.0
|
|
CG
|
C:ASN401
|
4.8
|
0.2
|
1.0
|
|
CB
|
C:ALA307
|
4.8
|
0.5
|
1.0
|
|
N
|
C:ASN310
|
4.8
|
0.2
|
1.0
|
|
CA
|
C:ASN310
|
4.9
|
0.5
|
1.0
|
|
CA
|
C:GLY306
|
4.9
|
0.1
|
1.0
|
|
O
|
C:THR308
|
4.9
|
0.4
|
1.0
|
|
Sodium binding site 7 out
of 12 in 5cfy
Go back to
Sodium Binding Sites List in 5cfy
Sodium binding site 7 out
of 12 in the Crystal Structure of Gltph R397A in Complex with Na+ and L-Asp
 Mono view
 Stereo pair view
|
|
A full contact list of Sodium with other atoms in the Na binding
site number 7 of Crystal Structure of Gltph R397A in Complex with Na+ and L-Asp within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Na502
b:0.8
occ:1.00
|
O
|
D:THR352
|
2.1
|
0.7
|
1.0
|
|
O
|
D:SER349
|
2.4
|
0.6
|
1.0
|
|
O
|
D:THR308
|
2.7
|
0.9
|
1.0
|
|
SD
|
D:MET311
|
2.9
|
0.9
|
1.0
|
|
C
|
D:THR352
|
3.0
|
0.8
|
1.0
|
|
N
|
D:THR352
|
3.2
|
0.2
|
1.0
|
|
CA
|
D:THR352
|
3.5
|
0.3
|
1.0
|
|
C
|
D:SER349
|
3.5
|
0.9
|
1.0
|
|
C
|
D:ILE350
|
3.5
|
0.7
|
1.0
|
|
C
|
D:THR308
|
3.5
|
0.3
|
1.0
|
|
O
|
D:ILE350
|
3.5
|
0.2
|
1.0
|
|
CB
|
D:THR352
|
3.6
|
0.4
|
1.0
|
|
C
|
D:GLY351
|
3.7
|
0.7
|
1.0
|
|
N
|
D:GLY351
|
3.7
|
0.5
|
1.0
|
|
CE
|
D:MET311
|
3.8
|
0.7
|
1.0
|
|
CG
|
D:MET311
|
3.9
|
0.4
|
1.0
|
|
CA
|
D:ILE350
|
4.0
|
0.2
|
1.0
|
|
N
|
D:ALA353
|
4.1
|
0.9
|
1.0
|
|
CA
|
D:THR308
|
4.1
|
0.3
|
1.0
|
|
N
|
D:ILE350
|
4.2
|
0.7
|
1.0
|
|
CA
|
D:GLY351
|
4.2
|
0.6
|
1.0
|
|
O
|
D:GLY351
|
4.2
|
0.7
|
1.0
|
|
CA
|
D:ALA353
|
4.4
|
0.7
|
1.0
|
|
O
|
D:ALA353
|
4.5
|
0.9
|
1.0
|
|
C
|
D:ALA353
|
4.5
|
0.6
|
1.0
|
|
CG2
|
D:THR352
|
4.5
|
0.6
|
1.0
|
|
N
|
D:ILE309
|
4.5
|
0.1
|
1.0
|
|
CB
|
D:MET311
|
4.6
|
0.7
|
1.0
|
|
CB
|
D:THR308
|
4.6
|
0.8
|
1.0
|
|
CA
|
D:SER349
|
4.6
|
0.8
|
1.0
|
|
OG1
|
D:THR352
|
4.7
|
0.8
|
1.0
|
|
CA
|
D:ILE309
|
4.8
|
0.0
|
1.0
|
|
Sodium binding site 8 out
of 12 in 5cfy
Go back to
Sodium Binding Sites List in 5cfy
Sodium binding site 8 out
of 12 in the Crystal Structure of Gltph R397A in Complex with Na+ and L-Asp
 Mono view
 Stereo pair view
|
|
A full contact list of Sodium with other atoms in the Na binding
site number 8 of Crystal Structure of Gltph R397A in Complex with Na+ and L-Asp within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Na503
b:1.0
occ:1.00
|
O
|
D:GLY306
|
2.6
|
0.8
|
1.0
|
|
O
|
D:ASN310
|
3.0
|
0.5
|
1.0
|
|
O
|
D:ASN401
|
3.0
|
0.9
|
1.0
|
|
OD2
|
D:ASP405
|
3.0
|
1.0
|
1.0
|
|
OG
|
D:SER278
|
3.1
|
0.5
|
1.0
|
|
CA
|
D:ALA307
|
3.4
|
0.1
|
1.0
|
|
C
|
D:ASN401
|
3.5
|
0.7
|
1.0
|
|
C
|
D:GLY306
|
3.5
|
0.9
|
1.0
|
|
C
|
D:ALA307
|
3.6
|
0.2
|
1.0
|
|
O
|
D:ALA307
|
3.6
|
0.5
|
1.0
|
|
CB
|
D:ASN401
|
3.7
|
0.0
|
1.0
|
|
OD1
|
D:ASP405
|
3.7
|
0.3
|
1.0
|
|
CG
|
D:ASP405
|
3.7
|
0.7
|
1.0
|
|
C
|
D:ASN310
|
3.9
|
0.8
|
1.0
|
|
N
|
D:ALA307
|
3.9
|
1.0
|
1.0
|
|
CB
|
D:SER278
|
3.9
|
0.8
|
1.0
|
|
CG
|
D:MET311
|
4.0
|
0.4
|
1.0
|
|
CA
|
D:ASN401
|
4.1
|
0.2
|
1.0
|
|
N
|
D:VAL402
|
4.2
|
0.2
|
1.0
|
|
N
|
D:THR308
|
4.3
|
0.7
|
1.0
|
|
CE
|
D:MET311
|
4.5
|
0.7
|
1.0
|
|
N
|
D:MET311
|
4.6
|
0.8
|
1.0
|
|
CA
|
D:VAL402
|
4.6
|
0.4
|
1.0
|
|
CA
|
D:MET311
|
4.6
|
0.2
|
1.0
|
|
CB
|
D:ALA307
|
4.7
|
0.1
|
1.0
|
|
CG
|
D:ASN401
|
4.8
|
0.1
|
1.0
|
|
CA
|
D:ASN310
|
4.8
|
0.1
|
1.0
|
|
N
|
D:ASN310
|
4.8
|
0.6
|
1.0
|
|
CG2
|
D:VAL402
|
4.8
|
0.6
|
1.0
|
|
O
|
D:HOH601
|
4.8
|
0.2
|
1.0
|
|
CA
|
D:GLY306
|
4.8
|
0.5
|
1.0
|
|
O
|
D:THR308
|
4.9
|
0.9
|
1.0
|
|
CB
|
D:MET311
|
4.9
|
0.7
|
1.0
|
|
Sodium binding site 9 out
of 12 in 5cfy
Go back to
Sodium Binding Sites List in 5cfy
Sodium binding site 9 out
of 12 in the Crystal Structure of Gltph R397A in Complex with Na+ and L-Asp
 Mono view
 Stereo pair view
|
|
A full contact list of Sodium with other atoms in the Na binding
site number 9 of Crystal Structure of Gltph R397A in Complex with Na+ and L-Asp within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Na502
b:0.3
occ:1.00
|
O
|
E:THR352
|
2.1
|
0.4
|
1.0
|
|
O
|
E:SER349
|
2.5
|
0.3
|
1.0
|
|
O
|
E:THR308
|
2.6
|
0.1
|
1.0
|
|
C
|
E:THR352
|
3.0
|
0.7
|
1.0
|
|
SD
|
E:MET311
|
3.0
|
0.2
|
1.0
|
|
N
|
E:THR352
|
3.1
|
1.0
|
1.0
|
|
O
|
E:ILE350
|
3.3
|
0.7
|
1.0
|
|
C
|
E:ILE350
|
3.4
|
0.1
|
1.0
|
|
C
|
E:THR308
|
3.5
|
0.2
|
1.0
|
|
CA
|
E:THR352
|
3.5
|
0.4
|
1.0
|
|
C
|
E:SER349
|
3.5
|
0.7
|
1.0
|
|
C
|
E:GLY351
|
3.6
|
0.5
|
1.0
|
|
N
|
E:GLY351
|
3.6
|
0.2
|
1.0
|
|
CG
|
E:MET311
|
3.8
|
0.1
|
1.0
|
|
CE
|
E:MET311
|
3.8
|
0.4
|
1.0
|
|
CB
|
E:THR352
|
3.9
|
0.0
|
1.0
|
|
CA
|
E:ILE350
|
3.9
|
0.8
|
1.0
|
|
CA
|
E:THR308
|
4.0
|
0.1
|
1.0
|
|
CA
|
E:GLY351
|
4.1
|
0.7
|
1.0
|
|
N
|
E:ILE350
|
4.1
|
0.9
|
1.0
|
|
O
|
E:GLY351
|
4.1
|
0.4
|
1.0
|
|
N
|
E:ALA353
|
4.1
|
0.8
|
1.0
|
|
N
|
E:ILE309
|
4.5
|
0.3
|
1.0
|
|
CB
|
E:MET311
|
4.5
|
0.8
|
1.0
|
|
CB
|
E:THR308
|
4.6
|
0.4
|
1.0
|
|
CA
|
E:ALA353
|
4.6
|
0.0
|
1.0
|
|
CA
|
E:SER349
|
4.6
|
0.0
|
1.0
|
|
CG2
|
E:THR352
|
4.7
|
0.1
|
1.0
|
|
C
|
E:ALA353
|
4.8
|
1.0
|
1.0
|
|
CA
|
E:ILE309
|
4.8
|
0.7
|
1.0
|
|
O
|
E:ALA353
|
4.9
|
0.0
|
1.0
|
|
Sodium binding site 10 out
of 12 in 5cfy
Go back to
Sodium Binding Sites List in 5cfy
Sodium binding site 10 out
of 12 in the Crystal Structure of Gltph R397A in Complex with Na+ and L-Asp
 Mono view
 Stereo pair view
|
|
A full contact list of Sodium with other atoms in the Na binding
site number 10 of Crystal Structure of Gltph R397A in Complex with Na+ and L-Asp within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Na503
b:0.9
occ:1.00
|
O
|
E:GLY306
|
2.6
|
0.6
|
1.0
|
|
OD2
|
E:ASP405
|
2.8
|
0.9
|
1.0
|
|
O
|
E:ASN310
|
2.9
|
0.5
|
1.0
|
|
OG
|
E:SER278
|
3.3
|
0.5
|
1.0
|
|
O
|
E:ASN401
|
3.4
|
0.6
|
1.0
|
|
C
|
E:GLY306
|
3.5
|
0.2
|
1.0
|
|
CA
|
E:ALA307
|
3.5
|
0.1
|
1.0
|
|
C
|
E:ALA307
|
3.6
|
0.5
|
1.0
|
|
C
|
E:ASN401
|
3.7
|
0.9
|
1.0
|
|
CB
|
E:ASN401
|
3.7
|
0.4
|
1.0
|
|
CG
|
E:ASP405
|
3.7
|
0.7
|
1.0
|
|
O
|
E:ALA307
|
3.8
|
0.7
|
1.0
|
|
OD1
|
E:ASP405
|
3.9
|
0.2
|
1.0
|
|
N
|
E:ALA307
|
3.9
|
0.7
|
1.0
|
|
C
|
E:ASN310
|
3.9
|
0.2
|
1.0
|
|
CB
|
E:SER278
|
4.0
|
0.8
|
1.0
|
|
CG
|
E:MET311
|
4.0
|
0.1
|
1.0
|
|
CA
|
E:ASN401
|
4.2
|
0.0
|
1.0
|
|
N
|
E:VAL402
|
4.3
|
0.5
|
1.0
|
|
N
|
E:THR308
|
4.3
|
0.1
|
1.0
|
|
CE
|
E:MET311
|
4.5
|
0.4
|
1.0
|
|
CA
|
E:VAL402
|
4.6
|
0.9
|
1.0
|
|
CA
|
E:MET311
|
4.7
|
0.6
|
1.0
|
|
N
|
E:MET311
|
4.7
|
0.1
|
1.0
|
|
CA
|
E:GLY306
|
4.8
|
0.6
|
1.0
|
|
N
|
E:ASN310
|
4.8
|
0.4
|
1.0
|
|
O
|
E:HOH601
|
4.8
|
0.2
|
1.0
|
|
CB
|
E:ALA307
|
4.9
|
0.7
|
1.0
|
|
CG
|
E:ASN401
|
4.9
|
0.5
|
1.0
|
|
CA
|
E:ASN310
|
4.9
|
0.9
|
1.0
|
|
O
|
E:THR308
|
4.9
|
0.1
|
1.0
|
|
CG2
|
E:VAL402
|
4.9
|
0.9
|
1.0
|
|
CB
|
E:MET311
|
4.9
|
0.8
|
1.0
|
|
CA
|
E:THR308
|
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 10:42:27 2020
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