Sodium in PDB 6wtx: Structure of Vcindy in Complex with Terephthalate
Protein crystallography data
The structure of Structure of Vcindy in Complex with Terephthalate, PDB code: 6wtx
was solved by
D.B.Sauer,
J.J.Marden,
D.N.Wang,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
47.80 /
3.92
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
108.458,
103.062,
174.447,
90.00,
95.85,
90.00
|
R / Rfree (%)
|
29 /
30.8
|
Sodium Binding Sites:
The binding sites of Sodium atom in the Structure of Vcindy in Complex with Terephthalate
(pdb code 6wtx). This binding sites where shown within
5.0 Angstroms radius around Sodium atom.
In total 8 binding sites of Sodium where determined in the
Structure of Vcindy in Complex with Terephthalate, PDB code: 6wtx:
Jump to Sodium binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
Sodium binding site 1 out
of 8 in 6wtx
Go back to
Sodium Binding Sites List in 6wtx
Sodium binding site 1 out
of 8 in the Structure of Vcindy in Complex with Terephthalate
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 1 of Structure of Vcindy in Complex with Terephthalate within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Na502
b:5.5
occ:1.00
|
H
|
C:ASN378
|
2.4
|
5.6
|
1.0
|
O
|
C:ALA376
|
2.4
|
5.5
|
1.0
|
O
|
C:ALA420
|
2.5
|
5.6
|
1.0
|
OD1
|
C:ASN378
|
2.5
|
5.6
|
1.0
|
O
|
C:THR373
|
2.5
|
5.5
|
1.0
|
N
|
C:ASN378
|
2.7
|
5.6
|
1.0
|
HA
|
C:ASN378
|
3.1
|
5.6
|
1.0
|
HA
|
C:SER377
|
3.2
|
5.6
|
1.0
|
CG
|
C:ASN378
|
3.2
|
5.6
|
1.0
|
OG1
|
C:THR373
|
3.3
|
5.5
|
1.0
|
C
|
C:SER377
|
3.3
|
5.7
|
1.0
|
CA
|
C:ASN378
|
3.3
|
5.6
|
1.0
|
C
|
C:ALA376
|
3.5
|
5.5
|
1.0
|
O12
|
C:UB7501
|
3.6
|
6.2
|
1.0
|
HB2
|
C:ALA414
|
3.6
|
5.6
|
1.0
|
C
|
C:ALA420
|
3.6
|
5.6
|
1.0
|
HG1
|
C:THR421
|
3.6
|
5.6
|
1.0
|
C
|
C:THR373
|
3.6
|
5.5
|
1.0
|
CA
|
C:SER377
|
3.6
|
5.7
|
1.0
|
HG1
|
C:THR373
|
3.7
|
5.6
|
1.0
|
HA
|
C:THR373
|
3.7
|
5.6
|
1.0
|
CB
|
C:ASN378
|
3.8
|
5.6
|
1.0
|
HA
|
C:ALA420
|
3.9
|
5.6
|
1.0
|
N
|
C:SER377
|
4.0
|
5.7
|
1.0
|
CA
|
C:THR373
|
4.1
|
5.5
|
1.0
|
HB2
|
C:ASN378
|
4.1
|
5.6
|
1.0
|
C10
|
C:UB7501
|
4.1
|
6.2
|
1.0
|
O
|
C:SER377
|
4.1
|
5.7
|
1.0
|
ND2
|
C:ASN378
|
4.1
|
5.6
|
1.0
|
H041
|
C:UB7501
|
4.2
|
5.6
|
1.0
|
CB
|
C:ALA414
|
4.2
|
5.7
|
1.0
|
HB1
|
C:ALA420
|
4.2
|
5.6
|
1.0
|
HB1
|
C:ALA414
|
4.2
|
5.6
|
1.0
|
OG1
|
C:THR421
|
4.2
|
5.7
|
1.0
|
HB3
|
C:ALA414
|
4.3
|
5.6
|
1.0
|
CB
|
C:THR373
|
4.3
|
5.5
|
1.0
|
CA
|
C:ALA420
|
4.3
|
5.6
|
1.0
|
HD21
|
C:ASN378
|
4.3
|
5.6
|
1.0
|
H
|
C:ALA376
|
4.4
|
5.6
|
1.0
|
O11
|
C:UB7501
|
4.5
|
6.2
|
1.0
|
HA
|
C:THR421
|
4.5
|
5.6
|
1.0
|
HB3
|
C:ASN378
|
4.6
|
5.6
|
1.0
|
N
|
C:THR421
|
4.6
|
5.7
|
1.0
|
O
|
C:ALA411
|
4.7
|
5.5
|
1.0
|
HG23
|
C:THR373
|
4.7
|
5.6
|
1.0
|
HA
|
C:GLU374
|
4.7
|
5.6
|
1.0
|
CA
|
C:ALA376
|
4.8
|
5.5
|
1.0
|
C
|
C:ASN378
|
4.8
|
5.6
|
1.0
|
CB
|
C:ALA420
|
4.8
|
5.6
|
1.0
|
N
|
C:GLU374
|
4.8
|
5.8
|
1.0
|
N
|
C:ALA376
|
4.8
|
5.5
|
1.0
|
HD22
|
C:ASN378
|
4.8
|
5.6
|
1.0
|
H
|
C:SER377
|
4.8
|
5.6
|
1.0
|
C04
|
C:UB7501
|
4.9
|
6.2
|
1.0
|
C03
|
C:UB7501
|
4.9
|
6.2
|
1.0
|
HB
|
C:THR373
|
5.0
|
5.6
|
1.0
|
CA
|
C:THR421
|
5.0
|
5.7
|
1.0
|
|
Sodium binding site 2 out
of 8 in 6wtx
Go back to
Sodium Binding Sites List in 6wtx
Sodium binding site 2 out
of 8 in the Structure of Vcindy in Complex with Terephthalate
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 2 of Structure of Vcindy in Complex with Terephthalate within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Na503
b:5.7
occ:1.00
|
HA2
|
C:GLY193
|
2.1
|
5.6
|
1.0
|
OD1
|
C:ASN151
|
2.2
|
5.6
|
1.0
|
OG
|
C:SER146
|
2.4
|
5.5
|
1.0
|
HA3
|
C:GLY193
|
2.5
|
5.6
|
1.0
|
CA
|
C:GLY193
|
2.7
|
5.6
|
1.0
|
O
|
C:SER146
|
2.7
|
5.5
|
1.0
|
HA2
|
C:GLY199
|
3.0
|
5.6
|
1.0
|
CG
|
C:ASN151
|
3.1
|
5.6
|
1.0
|
O
|
C:GLY199
|
3.1
|
5.6
|
1.0
|
HD21
|
C:ASN151
|
3.2
|
5.6
|
1.0
|
C
|
C:GLY199
|
3.3
|
5.6
|
1.0
|
HA3
|
C:GLY199
|
3.4
|
5.6
|
1.0
|
N
|
C:GLY193
|
3.4
|
5.6
|
1.0
|
O
|
C:SER150
|
3.4
|
5.6
|
1.0
|
CA
|
C:GLY199
|
3.4
|
5.6
|
1.0
|
ND2
|
C:ASN151
|
3.5
|
5.6
|
1.0
|
C
|
C:SER146
|
3.6
|
5.5
|
1.0
|
CB
|
C:SER146
|
3.7
|
5.5
|
1.0
|
C
|
C:SER150
|
3.7
|
5.6
|
1.0
|
H
|
C:GLY193
|
3.7
|
5.6
|
1.0
|
C
|
C:GLY193
|
3.9
|
5.6
|
1.0
|
HA
|
C:SER146
|
4.0
|
5.6
|
1.0
|
CA
|
C:SER146
|
4.0
|
5.5
|
1.0
|
C
|
C:GLY192
|
4.0
|
5.5
|
1.0
|
HB2
|
C:SER200
|
4.1
|
5.6
|
1.0
|
O
|
C:ALA189
|
4.1
|
5.7
|
1.0
|
HB3
|
C:SER146
|
4.1
|
5.6
|
1.0
|
N
|
C:SER200
|
4.1
|
5.5
|
1.0
|
N
|
C:ASN151
|
4.1
|
5.6
|
1.0
|
O
|
C:GLY192
|
4.1
|
5.5
|
1.0
|
HA
|
C:SER150
|
4.1
|
5.6
|
1.0
|
HA
|
C:ASN151
|
4.2
|
5.6
|
1.0
|
H
|
C:SER150
|
4.2
|
5.6
|
1.0
|
O
|
C:GLY193
|
4.2
|
5.6
|
1.0
|
HD22
|
C:ASN151
|
4.3
|
5.6
|
1.0
|
HB2
|
C:SER146
|
4.3
|
5.6
|
1.0
|
CB
|
C:ASN151
|
4.3
|
5.6
|
1.0
|
CA
|
C:SER150
|
4.4
|
5.6
|
1.0
|
CA
|
C:ASN151
|
4.5
|
5.6
|
1.0
|
H
|
C:SER200
|
4.5
|
5.6
|
1.0
|
H
|
C:ASN151
|
4.5
|
5.6
|
1.0
|
HA
|
C:MET147
|
4.5
|
5.6
|
1.0
|
N
|
C:MET147
|
4.6
|
5.8
|
1.0
|
N
|
C:SER150
|
4.6
|
5.6
|
1.0
|
HA
|
C:SER200
|
4.8
|
5.6
|
1.0
|
CA
|
C:SER200
|
4.8
|
5.5
|
1.0
|
N
|
C:GLY199
|
4.8
|
5.6
|
1.0
|
CB
|
C:SER200
|
4.9
|
5.5
|
1.0
|
HB2
|
C:ASN151
|
4.9
|
5.6
|
1.0
|
O09
|
C:UB7501
|
4.9
|
6.2
|
1.0
|
HB3
|
C:ASN151
|
4.9
|
5.6
|
1.0
|
CA
|
C:MET147
|
5.0
|
5.8
|
1.0
|
|
Sodium binding site 3 out
of 8 in 6wtx
Go back to
Sodium Binding Sites List in 6wtx
Sodium binding site 3 out
of 8 in the Structure of Vcindy in Complex with Terephthalate
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 3 of Structure of Vcindy in Complex with Terephthalate within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Na502
b:5.6
occ:1.00
|
H
|
D:ASN378
|
2.3
|
5.6
|
1.0
|
OD1
|
D:ASN378
|
2.3
|
5.6
|
1.0
|
N
|
D:ASN378
|
2.5
|
5.6
|
1.0
|
O
|
D:ALA376
|
2.6
|
5.6
|
1.0
|
O
|
D:ALA420
|
2.7
|
5.5
|
1.0
|
HA
|
D:ASN378
|
2.7
|
5.6
|
1.0
|
OG1
|
D:THR373
|
2.8
|
5.5
|
1.0
|
O
|
D:THR373
|
2.9
|
5.5
|
1.0
|
CG
|
D:ASN378
|
3.0
|
5.6
|
1.0
|
CA
|
D:ASN378
|
3.0
|
5.6
|
1.0
|
C
|
D:SER377
|
3.1
|
5.7
|
1.0
|
HG1
|
D:THR373
|
3.2
|
5.6
|
1.0
|
HA
|
D:SER377
|
3.2
|
5.6
|
1.0
|
CB
|
D:ASN378
|
3.5
|
5.6
|
1.0
|
HB2
|
D:ALA414
|
3.6
|
5.6
|
1.0
|
C
|
D:ALA376
|
3.6
|
5.6
|
1.0
|
CA
|
D:SER377
|
3.6
|
5.7
|
1.0
|
HA
|
D:THR373
|
3.6
|
5.6
|
1.0
|
C
|
D:ALA420
|
3.7
|
5.5
|
1.0
|
C
|
D:THR373
|
3.8
|
5.5
|
1.0
|
HB2
|
D:ASN378
|
3.9
|
5.6
|
1.0
|
O
|
D:SER377
|
3.9
|
5.7
|
1.0
|
CB
|
D:THR373
|
4.0
|
5.5
|
1.0
|
ND2
|
D:ASN378
|
4.0
|
5.6
|
1.0
|
CA
|
D:THR373
|
4.0
|
5.5
|
1.0
|
N
|
D:SER377
|
4.1
|
5.7
|
1.0
|
HA
|
D:ALA420
|
4.1
|
5.6
|
1.0
|
OG1
|
D:THR421
|
4.1
|
5.7
|
1.0
|
HD21
|
D:ASN378
|
4.2
|
5.6
|
1.0
|
CB
|
D:ALA414
|
4.3
|
5.7
|
1.0
|
HB3
|
D:ALA414
|
4.3
|
5.6
|
1.0
|
O12
|
D:UB7501
|
4.3
|
5.9
|
1.0
|
HB1
|
D:ALA420
|
4.3
|
5.6
|
1.0
|
HB3
|
D:ASN378
|
4.4
|
5.6
|
1.0
|
O
|
D:ALA411
|
4.4
|
5.5
|
1.0
|
HB1
|
D:ALA414
|
4.4
|
5.6
|
1.0
|
CA
|
D:ALA420
|
4.4
|
5.5
|
1.0
|
C
|
D:ASN378
|
4.5
|
5.6
|
1.0
|
HG1
|
D:THR421
|
4.5
|
5.6
|
1.0
|
HB
|
D:THR373
|
4.5
|
5.6
|
1.0
|
HA
|
D:THR421
|
4.6
|
5.6
|
1.0
|
HG23
|
D:THR373
|
4.6
|
5.6
|
1.0
|
HD22
|
D:ASN378
|
4.6
|
5.6
|
1.0
|
H
|
D:ALA376
|
4.7
|
5.6
|
1.0
|
H041
|
D:UB7501
|
4.7
|
5.6
|
1.0
|
N
|
D:THR421
|
4.7
|
5.7
|
1.0
|
C10
|
D:UB7501
|
4.8
|
5.9
|
1.0
|
CB
|
D:ALA420
|
4.9
|
5.5
|
1.0
|
O11
|
D:UB7501
|
4.9
|
5.9
|
1.0
|
CG2
|
D:THR373
|
4.9
|
5.5
|
1.0
|
H
|
D:SER377
|
4.9
|
5.6
|
1.0
|
CA
|
D:ALA376
|
5.0
|
5.6
|
1.0
|
|
Sodium binding site 4 out
of 8 in 6wtx
Go back to
Sodium Binding Sites List in 6wtx
Sodium binding site 4 out
of 8 in the Structure of Vcindy in Complex with Terephthalate
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 4 of Structure of Vcindy in Complex with Terephthalate within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Na503
b:5.8
occ:1.00
|
HA2
|
D:GLY199
|
2.0
|
5.6
|
1.0
|
O
|
D:SER146
|
2.1
|
5.5
|
1.0
|
O
|
D:GLY199
|
2.7
|
5.5
|
1.0
|
CA
|
D:GLY199
|
2.8
|
5.5
|
1.0
|
H
|
D:SER150
|
3.0
|
5.6
|
1.0
|
C
|
D:GLY199
|
3.0
|
5.5
|
1.0
|
O
|
D:SER150
|
3.0
|
5.6
|
1.0
|
HA3
|
D:GLY199
|
3.0
|
5.6
|
1.0
|
OG
|
D:SER146
|
3.1
|
5.5
|
1.0
|
HA2
|
D:GLY193
|
3.1
|
5.6
|
1.0
|
OD1
|
D:ASN151
|
3.2
|
5.5
|
1.0
|
HA
|
D:SER150
|
3.2
|
5.6
|
1.0
|
C
|
D:SER150
|
3.2
|
5.6
|
1.0
|
C
|
D:SER146
|
3.3
|
5.5
|
1.0
|
N
|
D:SER150
|
3.4
|
5.6
|
1.0
|
CA
|
D:SER150
|
3.5
|
5.6
|
1.0
|
HG
|
D:SER146
|
3.6
|
5.6
|
1.0
|
HA
|
D:SER146
|
3.7
|
5.6
|
1.0
|
CA
|
D:SER146
|
3.9
|
5.5
|
1.0
|
HA3
|
D:GLY193
|
3.9
|
5.6
|
1.0
|
CA
|
D:GLY193
|
3.9
|
5.6
|
1.0
|
CG
|
D:ASN151
|
4.0
|
5.5
|
1.0
|
N
|
D:ASN151
|
4.0
|
5.5
|
1.0
|
N
|
D:GLY199
|
4.0
|
5.5
|
1.0
|
H
|
D:ILE149
|
4.0
|
5.6
|
1.0
|
CB
|
D:SER146
|
4.1
|
5.5
|
1.0
|
N
|
D:SER200
|
4.2
|
5.5
|
1.0
|
HD21
|
D:ASN151
|
4.3
|
5.6
|
1.0
|
C
|
D:ILE149
|
4.3
|
5.6
|
1.0
|
H
|
D:GLY199
|
4.3
|
5.6
|
1.0
|
N
|
D:MET147
|
4.3
|
5.5
|
1.0
|
HA
|
D:MET147
|
4.4
|
5.6
|
1.0
|
N
|
D:ILE149
|
4.4
|
5.6
|
1.0
|
C
|
D:MET147
|
4.4
|
5.5
|
1.0
|
H
|
D:ASN151
|
4.4
|
5.6
|
1.0
|
HA
|
D:ASN151
|
4.5
|
5.6
|
1.0
|
ND2
|
D:ASN151
|
4.5
|
5.5
|
1.0
|
N
|
D:TRP148
|
4.5
|
5.5
|
1.0
|
H
|
D:TRP148
|
4.5
|
5.6
|
1.0
|
CA
|
D:MET147
|
4.6
|
5.5
|
1.0
|
H
|
D:SER200
|
4.7
|
5.6
|
1.0
|
HB2
|
D:SER146
|
4.7
|
5.6
|
1.0
|
HB3
|
D:SER146
|
4.7
|
5.6
|
1.0
|
N
|
D:GLY193
|
4.7
|
5.6
|
1.0
|
O
|
D:MET147
|
4.7
|
5.5
|
1.0
|
CA
|
D:ASN151
|
4.7
|
5.5
|
1.0
|
O
|
D:GLY192
|
4.9
|
5.5
|
1.0
|
O
|
D:VAL198
|
4.9
|
5.5
|
1.0
|
C
|
D:VAL198
|
4.9
|
5.5
|
1.0
|
C
|
D:TRP148
|
4.9
|
5.5
|
1.0
|
HG1
|
D:THR154
|
4.9
|
5.6
|
1.0
|
C
|
D:GLY193
|
5.0
|
5.6
|
1.0
|
HA
|
D:SER200
|
5.0
|
5.6
|
1.0
|
CB
|
D:SER150
|
5.0
|
5.6
|
1.0
|
CA
|
D:ILE149
|
5.0
|
5.6
|
1.0
|
CB
|
D:ASN151
|
5.0
|
5.5
|
1.0
|
O
|
D:GLY193
|
5.0
|
5.6
|
1.0
|
|
Sodium binding site 5 out
of 8 in 6wtx
Go back to
Sodium Binding Sites List in 6wtx
Sodium binding site 5 out
of 8 in the Structure of Vcindy in Complex with Terephthalate
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 5 of Structure of Vcindy in Complex with Terephthalate within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na501
b:5.6
occ:1.00
|
HA2
|
A:GLY193
|
2.3
|
5.6
|
1.0
|
OD1
|
A:ASN151
|
2.4
|
5.6
|
1.0
|
HA3
|
A:GLY193
|
2.5
|
5.6
|
1.0
|
OG
|
A:SER146
|
2.7
|
5.6
|
1.0
|
O
|
A:SER146
|
2.7
|
5.6
|
1.0
|
O
|
A:GLY199
|
2.8
|
5.6
|
1.0
|
CA
|
A:GLY193
|
2.8
|
5.6
|
1.0
|
HA2
|
A:GLY199
|
2.9
|
5.6
|
1.0
|
HG
|
A:SER146
|
3.0
|
5.6
|
1.0
|
C
|
A:GLY199
|
3.0
|
5.6
|
1.0
|
CG
|
A:ASN151
|
3.2
|
5.6
|
1.0
|
CA
|
A:GLY199
|
3.2
|
5.6
|
1.0
|
O
|
A:SER150
|
3.2
|
5.7
|
1.0
|
HA3
|
A:GLY199
|
3.2
|
5.6
|
1.0
|
HD21
|
A:ASN151
|
3.4
|
5.6
|
1.0
|
C
|
A:SER150
|
3.5
|
5.7
|
1.0
|
C
|
A:SER146
|
3.6
|
5.6
|
1.0
|
ND2
|
A:ASN151
|
3.6
|
5.6
|
1.0
|
N
|
A:GLY193
|
3.6
|
5.6
|
1.0
|
HA
|
A:SER150
|
3.8
|
5.6
|
1.0
|
N
|
A:SER200
|
3.9
|
5.4
|
1.0
|
CB
|
A:SER146
|
3.9
|
5.6
|
1.0
|
N
|
A:ASN151
|
3.9
|
5.6
|
1.0
|
H
|
A:GLY193
|
3.9
|
5.6
|
1.0
|
H
|
A:SER150
|
4.0
|
5.6
|
1.0
|
HB2
|
A:SER200
|
4.0
|
5.6
|
1.0
|
C
|
A:GLY193
|
4.0
|
5.6
|
1.0
|
HA
|
A:SER146
|
4.0
|
5.6
|
1.0
|
CA
|
A:SER150
|
4.1
|
5.7
|
1.0
|
CA
|
A:SER146
|
4.1
|
5.6
|
1.0
|
HA
|
A:ASN151
|
4.1
|
5.6
|
1.0
|
O
|
A:GLY193
|
4.2
|
5.6
|
1.0
|
O
|
A:ALA189
|
4.2
|
5.7
|
1.0
|
H
|
A:ASN151
|
4.3
|
5.6
|
1.0
|
N
|
A:SER150
|
4.3
|
5.7
|
1.0
|
H
|
A:SER200
|
4.3
|
5.6
|
1.0
|
CB
|
A:ASN151
|
4.4
|
5.6
|
1.0
|
HB3
|
A:SER146
|
4.4
|
5.6
|
1.0
|
C
|
A:GLY192
|
4.4
|
5.5
|
1.0
|
CA
|
A:ASN151
|
4.4
|
5.6
|
1.0
|
HD22
|
A:ASN151
|
4.4
|
5.6
|
1.0
|
O
|
A:GLY192
|
4.5
|
5.5
|
1.0
|
HB2
|
A:SER146
|
4.5
|
5.6
|
1.0
|
HA
|
A:SER200
|
4.5
|
5.6
|
1.0
|
HA
|
A:MET147
|
4.6
|
5.6
|
1.0
|
CA
|
A:SER200
|
4.6
|
5.4
|
1.0
|
N
|
A:MET147
|
4.6
|
5.7
|
1.0
|
N
|
A:GLY199
|
4.7
|
5.6
|
1.0
|
CB
|
A:SER200
|
4.7
|
5.4
|
1.0
|
O08
|
A:UB7503
|
4.8
|
5.9
|
1.0
|
HB2
|
A:ASN151
|
4.8
|
5.6
|
1.0
|
CA
|
A:MET147
|
5.0
|
5.7
|
1.0
|
H
|
A:GLY199
|
5.0
|
5.6
|
1.0
|
|
Sodium binding site 6 out
of 8 in 6wtx
Go back to
Sodium Binding Sites List in 6wtx
Sodium binding site 6 out
of 8 in the Structure of Vcindy in Complex with Terephthalate
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 6 of Structure of Vcindy in Complex with Terephthalate within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na502
b:5.5
occ:1.00
|
O
|
A:ALA420
|
2.2
|
5.7
|
1.0
|
O
|
A:ALA376
|
2.3
|
5.5
|
1.0
|
O
|
A:THR373
|
2.4
|
5.6
|
1.0
|
H
|
A:ASN378
|
2.7
|
5.6
|
1.0
|
HA
|
A:SER377
|
3.0
|
5.6
|
1.0
|
N
|
A:ASN378
|
3.1
|
5.4
|
1.0
|
C
|
A:ALA420
|
3.2
|
5.7
|
1.0
|
HA
|
A:ALA420
|
3.2
|
5.6
|
1.0
|
C
|
A:ALA376
|
3.2
|
5.5
|
1.0
|
OD1
|
A:ASN378
|
3.2
|
5.4
|
1.0
|
O11
|
A:UB7503
|
3.4
|
5.9
|
1.0
|
C
|
A:SER377
|
3.5
|
5.6
|
1.0
|
OG1
|
A:THR373
|
3.5
|
5.6
|
1.0
|
CA
|
A:SER377
|
3.5
|
5.6
|
1.0
|
C
|
A:THR373
|
3.5
|
5.6
|
1.0
|
CA
|
A:ALA420
|
3.7
|
5.7
|
1.0
|
HA
|
A:ASN378
|
3.7
|
5.6
|
1.0
|
N
|
A:SER377
|
3.7
|
5.6
|
1.0
|
HA
|
A:THR373
|
3.7
|
5.6
|
1.0
|
HB2
|
A:ALA414
|
3.8
|
5.6
|
1.0
|
HB1
|
A:ALA420
|
3.8
|
5.6
|
1.0
|
CG
|
A:ASN378
|
3.9
|
5.4
|
1.0
|
CA
|
A:ASN378
|
3.9
|
5.4
|
1.0
|
HG1
|
A:THR373
|
4.1
|
5.6
|
1.0
|
CA
|
A:THR373
|
4.1
|
5.6
|
1.0
|
H
|
A:ALA376
|
4.1
|
5.6
|
1.0
|
C10
|
A:UB7503
|
4.2
|
5.9
|
1.0
|
CB
|
A:ALA420
|
4.3
|
5.7
|
1.0
|
N
|
A:THR421
|
4.3
|
5.6
|
1.0
|
HB1
|
A:ALA414
|
4.4
|
5.6
|
1.0
|
O
|
A:SER377
|
4.4
|
5.6
|
1.0
|
CB
|
A:ALA414
|
4.4
|
5.8
|
1.0
|
CB
|
A:THR373
|
4.4
|
5.6
|
1.0
|
OG1
|
A:THR421
|
4.4
|
5.6
|
1.0
|
CB
|
A:ASN378
|
4.4
|
5.4
|
1.0
|
CA
|
A:ALA376
|
4.4
|
5.5
|
1.0
|
N
|
A:ALA376
|
4.4
|
5.5
|
1.0
|
HA
|
A:THR421
|
4.4
|
5.6
|
1.0
|
HB3
|
A:ALA414
|
4.5
|
5.6
|
1.0
|
H041
|
A:UB7503
|
4.5
|
5.6
|
1.0
|
HA
|
A:GLU374
|
4.5
|
5.6
|
1.0
|
H
|
A:SER377
|
4.6
|
5.6
|
1.0
|
O12
|
A:UB7503
|
4.6
|
5.9
|
1.0
|
N
|
A:GLU374
|
4.6
|
5.9
|
1.0
|
O
|
A:VAL419
|
4.6
|
5.8
|
1.0
|
HB2
|
A:ASN378
|
4.7
|
5.6
|
1.0
|
ND2
|
A:ASN378
|
4.7
|
5.4
|
1.0
|
HA
|
A:ALA376
|
4.8
|
5.6
|
1.0
|
HB3
|
A:ALA420
|
4.8
|
5.6
|
1.0
|
HG23
|
A:THR373
|
4.8
|
5.6
|
1.0
|
CA
|
A:THR421
|
4.8
|
5.6
|
1.0
|
HD21
|
A:ASN378
|
4.8
|
5.6
|
1.0
|
C
|
A:GLU374
|
4.8
|
5.9
|
1.0
|
CA
|
A:GLU374
|
4.9
|
5.9
|
1.0
|
O
|
A:GLU374
|
4.9
|
5.9
|
1.0
|
N
|
A:ALA420
|
4.9
|
5.7
|
1.0
|
HG1
|
A:THR421
|
5.0
|
5.6
|
1.0
|
CB
|
A:SER377
|
5.0
|
5.6
|
1.0
|
HB2
|
A:ALA420
|
5.0
|
5.6
|
1.0
|
|
Sodium binding site 7 out
of 8 in 6wtx
Go back to
Sodium Binding Sites List in 6wtx
Sodium binding site 7 out
of 8 in the Structure of Vcindy in Complex with Terephthalate
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 7 of Structure of Vcindy in Complex with Terephthalate within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Na502
b:5.6
occ:1.00
|
HD22
|
B:ASN378
|
2.2
|
5.6
|
1.0
|
O
|
B:ALA376
|
2.2
|
5.5
|
1.0
|
H
|
B:ASN378
|
2.5
|
5.6
|
1.0
|
N
|
B:ASN378
|
2.5
|
5.6
|
1.0
|
O
|
B:THR373
|
2.6
|
5.7
|
1.0
|
OG1
|
B:THR373
|
2.6
|
5.7
|
1.0
|
ND2
|
B:ASN378
|
2.6
|
5.6
|
1.0
|
HA
|
B:ASN378
|
2.7
|
5.6
|
1.0
|
O
|
B:ALA420
|
2.9
|
5.6
|
1.0
|
HD21
|
B:ASN378
|
2.9
|
5.6
|
1.0
|
C
|
B:SER377
|
3.0
|
5.7
|
1.0
|
HG1
|
B:THR373
|
3.1
|
5.6
|
1.0
|
CA
|
B:ASN378
|
3.1
|
5.6
|
1.0
|
HA
|
B:SER377
|
3.2
|
5.6
|
1.0
|
HA
|
B:THR373
|
3.3
|
5.6
|
1.0
|
C
|
B:ALA376
|
3.3
|
5.5
|
1.0
|
CG
|
B:ASN378
|
3.5
|
5.6
|
1.0
|
C
|
B:THR373
|
3.5
|
5.7
|
1.0
|
CA
|
B:SER377
|
3.5
|
5.7
|
1.0
|
HB2
|
B:ALA414
|
3.6
|
5.6
|
1.0
|
O
|
B:SER377
|
3.7
|
5.7
|
1.0
|
CA
|
B:THR373
|
3.7
|
5.7
|
1.0
|
CB
|
B:THR373
|
3.7
|
5.7
|
1.0
|
HG1
|
B:THR421
|
3.7
|
5.6
|
1.0
|
N
|
B:SER377
|
3.8
|
5.7
|
1.0
|
CB
|
B:ASN378
|
3.8
|
5.6
|
1.0
|
C
|
B:ALA420
|
3.9
|
5.6
|
1.0
|
HA
|
B:ALA420
|
4.1
|
5.6
|
1.0
|
HB1
|
B:ALA420
|
4.2
|
5.6
|
1.0
|
HB2
|
B:ASN378
|
4.3
|
5.6
|
1.0
|
HB
|
B:THR373
|
4.3
|
5.6
|
1.0
|
O
|
B:ALA411
|
4.3
|
5.4
|
1.0
|
OG1
|
B:THR421
|
4.4
|
5.5
|
1.0
|
H
|
B:ALA376
|
4.4
|
5.6
|
1.0
|
CB
|
B:ALA414
|
4.4
|
5.6
|
1.0
|
HG23
|
B:THR373
|
4.4
|
5.6
|
1.0
|
OD1
|
B:ASN378
|
4.4
|
5.6
|
1.0
|
C
|
B:ASN378
|
4.5
|
5.6
|
1.0
|
CA
|
B:ALA420
|
4.5
|
5.6
|
1.0
|
HB3
|
B:ALA414
|
4.5
|
5.6
|
1.0
|
O11
|
B:UB7501
|
4.5
|
5.8
|
1.0
|
HB1
|
B:ALA414
|
4.5
|
5.6
|
1.0
|
HB3
|
B:ASN378
|
4.6
|
5.6
|
1.0
|
CA
|
B:ALA376
|
4.6
|
5.5
|
1.0
|
HG
|
B:SER381
|
4.6
|
5.6
|
1.0
|
CG2
|
B:THR373
|
4.7
|
5.7
|
1.0
|
H
|
B:SER377
|
4.7
|
5.6
|
1.0
|
N
|
B:GLU374
|
4.8
|
5.6
|
1.0
|
N
|
B:ALA376
|
4.8
|
5.5
|
1.0
|
CB
|
B:ALA420
|
4.9
|
5.6
|
1.0
|
HB2
|
B:SER381
|
4.9
|
5.6
|
1.0
|
HA
|
B:THR421
|
4.9
|
5.6
|
1.0
|
N
|
B:THR421
|
4.9
|
5.5
|
1.0
|
OG
|
B:SER381
|
4.9
|
5.5
|
1.0
|
CB
|
B:SER377
|
5.0
|
5.7
|
1.0
|
HA
|
B:GLU374
|
5.0
|
5.6
|
1.0
|
|
Sodium binding site 8 out
of 8 in 6wtx
Go back to
Sodium Binding Sites List in 6wtx
Sodium binding site 8 out
of 8 in the Structure of Vcindy in Complex with Terephthalate
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 8 of Structure of Vcindy in Complex with Terephthalate within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Na503
b:5.8
occ:1.00
|
O
|
B:SER146
|
2.2
|
5.6
|
1.0
|
HA2
|
B:GLY199
|
2.5
|
5.6
|
1.0
|
O
|
B:SER150
|
2.6
|
5.6
|
1.0
|
OG
|
B:SER146
|
2.8
|
5.6
|
1.0
|
H
|
B:SER150
|
2.8
|
5.6
|
1.0
|
C
|
B:SER150
|
2.9
|
5.6
|
1.0
|
O
|
B:GLY199
|
3.0
|
5.6
|
1.0
|
OD1
|
B:ASN151
|
3.1
|
5.7
|
1.0
|
HA2
|
B:GLY193
|
3.1
|
5.6
|
1.0
|
HA
|
B:SER150
|
3.1
|
5.6
|
1.0
|
C
|
B:SER146
|
3.2
|
5.6
|
1.0
|
CA
|
B:GLY199
|
3.2
|
5.6
|
1.0
|
N
|
B:SER150
|
3.2
|
5.6
|
1.0
|
CA
|
B:SER150
|
3.2
|
5.6
|
1.0
|
C
|
B:GLY199
|
3.3
|
5.6
|
1.0
|
HA
|
B:SER146
|
3.3
|
5.6
|
1.0
|
HG
|
B:SER146
|
3.4
|
5.6
|
1.0
|
HA3
|
B:GLY199
|
3.4
|
5.6
|
1.0
|
CA
|
B:SER146
|
3.6
|
5.6
|
1.0
|
HA3
|
B:GLY193
|
3.7
|
5.6
|
1.0
|
N
|
B:ASN151
|
3.7
|
5.7
|
1.0
|
CB
|
B:SER146
|
3.8
|
5.6
|
1.0
|
CA
|
B:GLY193
|
3.8
|
5.6
|
1.0
|
CG
|
B:ASN151
|
3.9
|
5.7
|
1.0
|
H
|
B:ILE149
|
4.1
|
5.6
|
1.0
|
HA
|
B:ASN151
|
4.1
|
5.6
|
1.0
|
H
|
B:ASN151
|
4.2
|
5.6
|
1.0
|
C
|
B:ILE149
|
4.3
|
5.6
|
1.0
|
HB2
|
B:SER146
|
4.3
|
5.6
|
1.0
|
N
|
B:MET147
|
4.3
|
5.7
|
1.0
|
CA
|
B:ASN151
|
4.4
|
5.7
|
1.0
|
HB3
|
B:SER146
|
4.4
|
5.6
|
1.0
|
N
|
B:SER200
|
4.4
|
5.5
|
1.0
|
N
|
B:ILE149
|
4.5
|
5.6
|
1.0
|
HD21
|
B:ASN151
|
4.5
|
5.6
|
1.0
|
N
|
B:GLY199
|
4.5
|
5.6
|
1.0
|
N
|
B:GLY193
|
4.5
|
5.6
|
1.0
|
HA
|
B:MET147
|
4.6
|
5.6
|
1.0
|
ND2
|
B:ASN151
|
4.6
|
5.7
|
1.0
|
HG1
|
B:THR154
|
4.6
|
5.6
|
1.0
|
C
|
B:MET147
|
4.6
|
5.7
|
1.0
|
H
|
B:TRP148
|
4.6
|
5.6
|
1.0
|
N
|
B:TRP148
|
4.7
|
5.7
|
1.0
|
CB
|
B:SER150
|
4.8
|
5.6
|
1.0
|
CA
|
B:MET147
|
4.8
|
5.7
|
1.0
|
CB
|
B:ASN151
|
4.8
|
5.7
|
1.0
|
H
|
B:GLY199
|
4.8
|
5.6
|
1.0
|
O
|
B:GLY192
|
4.8
|
5.5
|
1.0
|
H
|
B:SER200
|
4.9
|
5.6
|
1.0
|
O09
|
B:UB7501
|
4.9
|
5.8
|
1.0
|
O
|
B:ALA189
|
4.9
|
5.6
|
1.0
|
H
|
B:GLY193
|
4.9
|
5.6
|
1.0
|
OG1
|
B:THR154
|
4.9
|
5.5
|
1.0
|
C
|
B:GLY192
|
4.9
|
5.5
|
1.0
|
C
|
B:GLY193
|
5.0
|
5.6
|
1.0
|
CA
|
B:ILE149
|
5.0
|
5.6
|
1.0
|
HB2
|
B:SER200
|
5.0
|
5.6
|
1.0
|
|
Reference:
D.B.Sauer,
N.Trebesch,
J.J.Marden,
N.Cocco,
J.Song,
A.Koide,
S.Koide,
E.Tajkhorshid,
D.N.Wang.
Structural Basis For the Reaction Cycle of Dass Dicarboxylate Transporters. Elife V. 9 2020.
ISSN: ESSN 2050-084X
PubMed: 32869741
DOI: 10.7554/ELIFE.61350
Page generated: Tue Oct 8 14:42:54 2024
|