Sodium in PDB 6okz: Structure of Vcindy Bound to Fumarate
Protein crystallography data
The structure of Structure of Vcindy Bound to Fumarate, PDB code: 6okz
was solved by
D.B.Sauer,
J.Marden,
D.N.Wang,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
|
Resolution Low / High (Å)
|
47.90 /
3.29
|
|
Space group
|
P 1 21 1
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
105.795,
102.063,
171.173,
90.00,
98.94,
90.00
|
|
R / Rfree (%)
|
24.7 /
28.6
|
Sodium Binding Sites:
The binding sites of Sodium atom in the Structure of Vcindy Bound to Fumarate
(pdb code 6okz). This binding sites where shown within
5.0 Angstroms radius around Sodium atom.
In total 7 binding sites of Sodium where determined in the
Structure of Vcindy Bound to Fumarate, PDB code: 6okz:
Jump to Sodium binding site number:
1;
2;
3;
4;
5;
6;
7;
Sodium binding site 1 out
of 7 in 6okz
Go back to
Sodium Binding Sites List in 6okz
Sodium binding site 1 out
of 7 in the Structure of Vcindy Bound to Fumarate
 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 Bound to Fumarate within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Na501
b:0.8
occ:1.00
|
O
|
C:ALA376
|
2.4
|
0.0
|
1.0
|
|
O
|
C:ALA420
|
2.4
|
0.8
|
1.0
|
|
O
|
C:THR373
|
2.6
|
0.5
|
1.0
|
|
OD1
|
C:ASN378
|
2.9
|
0.6
|
1.0
|
|
N
|
C:ASN378
|
2.9
|
0.8
|
1.0
|
|
OG1
|
C:THR373
|
3.1
|
89.2
|
1.0
|
|
C
|
C:SER377
|
3.2
|
0.6
|
1.0
|
|
C
|
C:ALA420
|
3.4
|
0.3
|
1.0
|
|
C
|
C:ALA376
|
3.4
|
0.9
|
1.0
|
|
CA
|
C:ASN378
|
3.6
|
0.6
|
1.0
|
|
CA
|
C:SER377
|
3.6
|
0.4
|
1.0
|
|
CG
|
C:ASN378
|
3.6
|
0.2
|
1.0
|
|
C
|
C:THR373
|
3.7
|
0.9
|
1.0
|
|
O
|
C:SER377
|
3.8
|
0.3
|
1.0
|
|
CB
|
C:ALA414
|
3.9
|
95.3
|
1.0
|
|
N
|
C:SER377
|
4.0
|
0.4
|
1.0
|
|
CA
|
C:ALA420
|
4.0
|
0.6
|
1.0
|
|
CB
|
C:ASN378
|
4.1
|
0.0
|
1.0
|
|
OG1
|
C:THR421
|
4.1
|
0.7
|
1.0
|
|
CA
|
C:THR373
|
4.1
|
0.8
|
1.0
|
|
CB
|
C:THR373
|
4.2
|
99.6
|
1.0
|
|
O8
|
C:FUM503
|
4.4
|
0.9
|
1.0
|
|
N
|
C:THR421
|
4.4
|
1.0
|
1.0
|
|
ND2
|
C:ASN378
|
4.5
|
0.3
|
1.0
|
|
CB
|
C:ALA420
|
4.5
|
0.3
|
1.0
|
|
O
|
C:ALA411
|
4.7
|
0.7
|
1.0
|
|
CA
|
C:ALA376
|
4.7
|
0.4
|
1.0
|
|
N
|
C:ALA376
|
4.8
|
0.3
|
1.0
|
|
CA
|
C:THR421
|
4.8
|
0.4
|
1.0
|
|
N
|
C:GLU374
|
4.9
|
0.7
|
1.0
|
|
C
|
C:ASN378
|
4.9
|
0.7
|
1.0
|
|
O7
|
C:FUM503
|
5.0
|
0.7
|
1.0
|
|
CB
|
C:SER377
|
5.0
|
0.7
|
1.0
|
|
Sodium binding site 2 out
of 7 in 6okz
Go back to
Sodium Binding Sites List in 6okz
Sodium binding site 2 out
of 7 in the Structure of Vcindy Bound to Fumarate
 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 Bound to Fumarate within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Na502
b:0.4
occ:1.00
|
O
|
C:SER146
|
2.2
|
0.9
|
1.0
|
|
O
|
C:GLY199
|
2.2
|
0.1
|
1.0
|
|
OD1
|
C:ASN151
|
2.3
|
0.4
|
1.0
|
|
OG
|
C:SER146
|
2.3
|
97.7
|
1.0
|
|
O
|
C:SER150
|
2.3
|
0.1
|
1.0
|
|
C
|
C:SER150
|
2.7
|
0.1
|
1.0
|
|
C
|
C:GLY199
|
3.0
|
0.7
|
1.0
|
|
C
|
C:SER146
|
3.1
|
0.2
|
1.0
|
|
CG
|
C:ASN151
|
3.1
|
0.7
|
1.0
|
|
CA
|
C:GLY199
|
3.3
|
92.7
|
1.0
|
|
CA
|
C:SER146
|
3.3
|
0.4
|
1.0
|
|
CB
|
C:SER146
|
3.3
|
99.7
|
1.0
|
|
CA
|
C:SER150
|
3.3
|
0.6
|
1.0
|
|
N
|
C:ASN151
|
3.4
|
0.4
|
1.0
|
|
CA
|
C:GLY193
|
3.5
|
0.1
|
1.0
|
|
N
|
C:SER150
|
3.7
|
97.2
|
1.0
|
|
ND2
|
C:ASN151
|
3.8
|
0.0
|
1.0
|
|
CA
|
C:ASN151
|
4.0
|
0.9
|
1.0
|
|
N
|
C:SER200
|
4.1
|
81.7
|
1.0
|
|
N
|
C:GLY193
|
4.1
|
0.3
|
1.0
|
|
CB
|
C:ASN151
|
4.1
|
0.2
|
1.0
|
|
N
|
C:MET147
|
4.3
|
0.5
|
1.0
|
|
O
|
C:ALA189
|
4.4
|
0.3
|
1.0
|
|
N
|
C:GLY199
|
4.6
|
99.6
|
1.0
|
|
CA
|
C:SER200
|
4.7
|
88.5
|
1.0
|
|
OG1
|
C:THR154
|
4.7
|
0.5
|
1.0
|
|
C
|
C:ILE149
|
4.8
|
0.8
|
1.0
|
|
CB
|
C:SER150
|
4.8
|
96.0
|
1.0
|
|
N
|
C:SER146
|
4.8
|
0.7
|
1.0
|
|
C
|
C:GLY193
|
4.8
|
0.3
|
1.0
|
|
CA
|
C:MET147
|
4.9
|
0.3
|
1.0
|
|
C
|
C:GLY192
|
5.0
|
0.8
|
1.0
|
|
Sodium binding site 3 out
of 7 in 6okz
Go back to
Sodium Binding Sites List in 6okz
Sodium binding site 3 out
of 7 in the Structure of Vcindy Bound to Fumarate
 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 Bound to Fumarate within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Na501
b:0.6
occ:1.00
|
O
|
D:ALA376
|
2.3
|
0.1
|
1.0
|
|
OD1
|
D:ASN378
|
2.4
|
98.6
|
1.0
|
|
O
|
D:ALA420
|
2.5
|
0.1
|
1.0
|
|
N
|
D:ASN378
|
2.6
|
0.9
|
1.0
|
|
OG1
|
D:THR373
|
2.6
|
74.4
|
1.0
|
|
O
|
D:THR373
|
2.7
|
0.6
|
1.0
|
|
C
|
D:SER377
|
2.9
|
99.7
|
1.0
|
|
CA
|
D:ASN378
|
3.0
|
0.9
|
1.0
|
|
CG
|
D:ASN378
|
3.2
|
91.8
|
1.0
|
|
O
|
D:SER377
|
3.4
|
0.0
|
1.0
|
|
C
|
D:ALA420
|
3.4
|
0.1
|
1.0
|
|
C
|
D:ALA376
|
3.4
|
0.3
|
1.0
|
|
CA
|
D:SER377
|
3.5
|
0.4
|
1.0
|
|
C
|
D:THR373
|
3.6
|
0.7
|
1.0
|
|
CB
|
D:ASN378
|
3.6
|
0.4
|
1.0
|
|
CB
|
D:THR373
|
3.8
|
74.0
|
1.0
|
|
CA
|
D:THR373
|
3.8
|
0.7
|
1.0
|
|
CA
|
D:ALA420
|
3.9
|
0.2
|
1.0
|
|
N
|
D:SER377
|
3.9
|
0.8
|
1.0
|
|
ND2
|
D:ASN378
|
4.3
|
0.3
|
1.0
|
|
CB
|
D:ALA420
|
4.3
|
1.0
|
1.0
|
|
C
|
D:ASN378
|
4.4
|
97.4
|
1.0
|
|
OG1
|
D:THR421
|
4.4
|
0.0
|
1.0
|
|
CB
|
D:ALA414
|
4.4
|
85.4
|
1.0
|
|
O
|
D:ALA411
|
4.5
|
0.1
|
1.0
|
|
N
|
D:THR421
|
4.6
|
0.6
|
1.0
|
|
CA
|
D:ALA376
|
4.7
|
0.5
|
1.0
|
|
CG2
|
D:THR373
|
4.8
|
71.9
|
1.0
|
|
N
|
D:ALA376
|
4.8
|
0.7
|
1.0
|
|
N
|
D:GLU374
|
4.8
|
0.2
|
1.0
|
|
OG
|
D:SER381
|
4.8
|
81.4
|
1.0
|
|
CB
|
D:SER377
|
4.9
|
93.0
|
1.0
|
|
O
|
D:ASN378
|
5.0
|
96.6
|
1.0
|
|
Sodium binding site 4 out
of 7 in 6okz
Go back to
Sodium Binding Sites List in 6okz
Sodium binding site 4 out
of 7 in the Structure of Vcindy Bound to Fumarate
 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 Bound to Fumarate within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Na502
b:0.5
occ:1.00
|
O
|
D:SER146
|
2.4
|
87.1
|
1.0
|
|
OD1
|
D:ASN151
|
2.4
|
0.5
|
1.0
|
|
OG
|
D:SER146
|
2.4
|
98.1
|
1.0
|
|
O
|
D:GLY199
|
2.5
|
0.5
|
1.0
|
|
O
|
D:SER150
|
2.6
|
0.2
|
1.0
|
|
C
|
D:GLY199
|
2.8
|
90.5
|
1.0
|
|
CA
|
D:GLY199
|
2.9
|
77.9
|
1.0
|
|
C
|
D:SER150
|
3.0
|
0.1
|
1.0
|
|
CA
|
D:GLY193
|
3.2
|
95.3
|
1.0
|
|
CG
|
D:ASN151
|
3.2
|
1.0
|
1.0
|
|
C
|
D:SER146
|
3.3
|
85.7
|
1.0
|
|
CA
|
D:SER150
|
3.5
|
0.7
|
1.0
|
|
CB
|
D:SER146
|
3.6
|
0.9
|
1.0
|
|
N
|
D:ASN151
|
3.7
|
0.9
|
1.0
|
|
CA
|
D:SER146
|
3.7
|
0.3
|
1.0
|
|
N
|
D:GLY193
|
3.8
|
95.3
|
1.0
|
|
ND2
|
D:ASN151
|
3.8
|
0.5
|
1.0
|
|
N
|
D:SER150
|
3.9
|
91.8
|
1.0
|
|
N
|
D:SER200
|
4.0
|
81.7
|
1.0
|
|
CA
|
D:ASN151
|
4.2
|
99.0
|
1.0
|
|
N
|
D:GLY199
|
4.3
|
87.8
|
1.0
|
|
CB
|
D:ASN151
|
4.3
|
96.3
|
1.0
|
|
C
|
D:GLY193
|
4.5
|
91.8
|
1.0
|
|
C
|
D:GLY192
|
4.5
|
95.9
|
1.0
|
|
N
|
D:MET147
|
4.5
|
75.5
|
1.0
|
|
O
|
D:ALA189
|
4.5
|
0.1
|
1.0
|
|
O
|
D:GLY192
|
4.7
|
94.5
|
1.0
|
|
O
|
D:GLY193
|
4.7
|
0.1
|
1.0
|
|
CA
|
D:SER200
|
4.8
|
69.8
|
1.0
|
|
C
|
D:ILE149
|
4.8
|
99.0
|
1.0
|
|
CA
|
D:MET147
|
4.9
|
88.3
|
1.0
|
|
CB
|
D:SER150
|
5.0
|
89.8
|
1.0
|
|
C
|
D:MET147
|
5.0
|
93.6
|
1.0
|
|
Sodium binding site 5 out
of 7 in 6okz
Go back to
Sodium Binding Sites List in 6okz
Sodium binding site 5 out
of 7 in the Structure of Vcindy Bound to Fumarate
 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 Bound to Fumarate within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na501
b:0.7
occ:1.00
|
O
|
A:ALA376
|
2.3
|
0.7
|
1.0
|
|
O
|
A:THR373
|
2.4
|
0.6
|
1.0
|
|
OG1
|
A:THR373
|
2.6
|
0.6
|
1.0
|
|
OD1
|
A:ASN378
|
2.6
|
0.1
|
1.0
|
|
O
|
A:ALA420
|
2.8
|
0.9
|
1.0
|
|
N
|
A:ASN378
|
2.9
|
1.0
|
1.0
|
|
C
|
A:SER377
|
3.1
|
0.6
|
1.0
|
|
CA
|
A:ASN378
|
3.3
|
0.3
|
1.0
|
|
C
|
A:THR373
|
3.4
|
0.8
|
1.0
|
|
CG
|
A:ASN378
|
3.5
|
0.7
|
1.0
|
|
C
|
A:ALA376
|
3.5
|
0.9
|
1.0
|
|
O
|
A:SER377
|
3.6
|
0.7
|
1.0
|
|
CA
|
A:THR373
|
3.6
|
1.0
|
1.0
|
|
CB
|
A:THR373
|
3.7
|
0.3
|
1.0
|
|
CA
|
A:SER377
|
3.7
|
0.8
|
1.0
|
|
C
|
A:ALA420
|
3.8
|
0.0
|
1.0
|
|
CB
|
A:ASN378
|
3.9
|
0.8
|
1.0
|
|
N
|
A:SER377
|
4.1
|
0.3
|
1.0
|
|
OG1
|
A:THR421
|
4.3
|
0.9
|
1.0
|
|
CA
|
A:ALA420
|
4.4
|
0.3
|
1.0
|
|
CB
|
A:ALA414
|
4.5
|
0.8
|
1.0
|
|
ND2
|
A:ASN378
|
4.5
|
0.7
|
1.0
|
|
N
|
A:GLU374
|
4.6
|
0.9
|
1.0
|
|
O
|
A:ALA411
|
4.6
|
0.6
|
1.0
|
|
C
|
A:ASN378
|
4.6
|
0.6
|
1.0
|
|
CG2
|
A:THR373
|
4.7
|
0.7
|
1.0
|
|
N
|
A:ALA376
|
4.7
|
0.1
|
1.0
|
|
CA
|
A:ALA376
|
4.7
|
0.8
|
1.0
|
|
OG
|
A:SER381
|
4.7
|
0.4
|
1.0
|
|
CB
|
A:ALA420
|
4.7
|
0.8
|
1.0
|
|
N
|
A:THR421
|
4.8
|
0.4
|
1.0
|
|
Sodium binding site 6 out
of 7 in 6okz
Go back to
Sodium Binding Sites List in 6okz
Sodium binding site 6 out
of 7 in the Structure of Vcindy Bound to Fumarate
 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 Bound to Fumarate within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na502
b:0.5
occ:1.00
|
O
|
A:SER146
|
2.2
|
0.3
|
1.0
|
|
CA
|
A:GLY199
|
2.5
|
1.0
|
1.0
|
|
CA
|
A:GLY193
|
2.5
|
0.9
|
1.0
|
|
O
|
A:GLY199
|
2.6
|
0.4
|
1.0
|
|
C
|
A:GLY199
|
2.7
|
0.1
|
1.0
|
|
OG
|
A:SER146
|
3.0
|
0.7
|
1.0
|
|
ND2
|
A:ASN151
|
3.1
|
0.6
|
1.0
|
|
O
|
A:SER150
|
3.2
|
0.4
|
1.0
|
|
C
|
A:SER146
|
3.3
|
0.5
|
1.0
|
|
N
|
A:GLY193
|
3.5
|
0.8
|
1.0
|
|
C
|
A:GLY193
|
3.6
|
0.8
|
1.0
|
|
O
|
A:GLY193
|
3.7
|
0.6
|
1.0
|
|
C
|
A:SER150
|
3.7
|
0.8
|
1.0
|
|
N
|
A:SER200
|
3.7
|
90.3
|
1.0
|
|
N
|
A:GLY199
|
3.9
|
98.2
|
1.0
|
|
CB
|
A:SER146
|
4.0
|
0.6
|
1.0
|
|
CA
|
A:SER146
|
4.1
|
0.4
|
1.0
|
|
CG
|
A:ASN151
|
4.1
|
0.0
|
1.0
|
|
CA
|
A:SER150
|
4.1
|
0.5
|
1.0
|
|
N
|
A:SER150
|
4.2
|
0.8
|
1.0
|
|
N
|
A:MET147
|
4.2
|
0.2
|
1.0
|
|
C
|
A:GLY192
|
4.2
|
0.1
|
1.0
|
|
O
|
A:GLY192
|
4.4
|
0.8
|
1.0
|
|
C
|
A:MET147
|
4.4
|
0.7
|
1.0
|
|
CA
|
A:MET147
|
4.4
|
0.6
|
1.0
|
|
OD1
|
A:ASN151
|
4.4
|
0.0
|
1.0
|
|
O
|
A:VAL198
|
4.5
|
1.0
|
1.0
|
|
N
|
A:ASN151
|
4.5
|
0.0
|
1.0
|
|
O
|
A:MET147
|
4.6
|
0.0
|
1.0
|
|
C
|
A:VAL198
|
4.7
|
0.9
|
1.0
|
|
CA
|
A:SER200
|
4.7
|
93.7
|
1.0
|
|
N
|
A:TRP148
|
4.8
|
0.3
|
1.0
|
|
N
|
A:ILE194
|
4.8
|
0.5
|
1.0
|
|
CB
|
A:SER200
|
5.0
|
0.4
|
1.0
|
|
Sodium binding site 7 out
of 7 in 6okz
Go back to
Sodium Binding Sites List in 6okz
Sodium binding site 7 out
of 7 in the Structure of Vcindy Bound to Fumarate
 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 Bound to Fumarate within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Na501
b:81.0
occ:1.00
|
O
|
B:ALA376
|
2.3
|
85.2
|
1.0
|
|
OG1
|
B:THR373
|
2.4
|
98.3
|
1.0
|
|
OD1
|
B:ASN378
|
2.6
|
0.7
|
1.0
|
|
O
|
B:THR373
|
2.6
|
0.9
|
1.0
|
|
N
|
B:ASN378
|
2.8
|
0.2
|
1.0
|
|
O
|
B:ALA420
|
2.9
|
0.8
|
1.0
|
|
C
|
B:SER377
|
3.0
|
90.6
|
1.0
|
|
CA
|
B:ASN378
|
3.0
|
0.3
|
1.0
|
|
O
|
B:SER377
|
3.2
|
98.1
|
1.0
|
|
CG
|
B:ASN378
|
3.4
|
0.1
|
1.0
|
|
C
|
B:THR373
|
3.5
|
96.5
|
1.0
|
|
C
|
B:ALA376
|
3.5
|
93.1
|
1.0
|
|
CB
|
B:THR373
|
3.6
|
93.0
|
1.0
|
|
CA
|
B:THR373
|
3.6
|
93.7
|
1.0
|
|
CA
|
B:SER377
|
3.8
|
1.0
|
1.0
|
|
CB
|
B:ASN378
|
3.8
|
0.2
|
1.0
|
|
C
|
B:ALA420
|
3.8
|
0.6
|
1.0
|
|
N
|
B:SER377
|
4.1
|
98.5
|
1.0
|
|
O3
|
B:FUM502
|
4.2
|
0.7
|
1.0
|
|
O
|
B:ALA411
|
4.2
|
0.5
|
1.0
|
|
C
|
B:ASN378
|
4.3
|
95.9
|
1.0
|
|
OG1
|
B:THR421
|
4.3
|
0.6
|
1.0
|
|
CA
|
B:ALA420
|
4.4
|
89.5
|
1.0
|
|
ND2
|
B:ASN378
|
4.6
|
0.8
|
1.0
|
|
OG
|
B:SER381
|
4.6
|
75.2
|
1.0
|
|
CB
|
B:ALA414
|
4.6
|
83.0
|
1.0
|
|
CG2
|
B:THR373
|
4.6
|
88.4
|
1.0
|
|
CB
|
B:ALA420
|
4.7
|
80.1
|
1.0
|
|
O
|
B:ASN378
|
4.7
|
92.2
|
1.0
|
|
CA
|
B:ALA376
|
4.7
|
0.3
|
1.0
|
|
N
|
B:GLU374
|
4.7
|
99.2
|
1.0
|
|
N
|
B:ALA376
|
4.8
|
89.1
|
1.0
|
|
N
|
B:THR421
|
4.9
|
0.2
|
1.0
|
|
Reference:
D.B.Sauer,
J.Marden,
D.N.Wang.
Dynamics of Protomer Conformational States Regulate the Transport Cycle of the Homodimeric Dicarboxylate Transporter Vcindy To Be Published.
Page generated: Tue Oct 8 12:32:05 2024
|
