Sodium in PDB 6h6y: Gi.1 Human Norovirus Protruding Domain in Complex with Nano-7
Protein crystallography data
The structure of Gi.1 Human Norovirus Protruding Domain in Complex with Nano-7, PDB code: 6h6y
was solved by
T.Kilic,
K.Ruoff,
G.S.Hansman,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
|
Resolution Low / High (Å)
|
47.54 /
1.58
|
|
Space group
|
P 1 21 1
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
59.170,
140.900,
92.150,
90.00,
91.81,
90.00
|
|
R / Rfree (%)
|
15.5 /
17.5
|
Other elements in 6h6y:
The structure of Gi.1 Human Norovirus Protruding Domain in Complex with Nano-7 also contains other interesting chemical elements:
Sodium Binding Sites:
The binding sites of Sodium atom in the Gi.1 Human Norovirus Protruding Domain in Complex with Nano-7
(pdb code 6h6y). This binding sites where shown within
5.0 Angstroms radius around Sodium atom.
In total 10 binding sites of Sodium where determined in the
Gi.1 Human Norovirus Protruding Domain in Complex with Nano-7, PDB code: 6h6y:
Jump to Sodium binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
10;
Sodium binding site 1 out
of 10 in 6h6y
Go back to
Sodium Binding Sites List in 6h6y
Sodium binding site 1 out
of 10 in the Gi.1 Human Norovirus Protruding Domain in Complex with Nano-7
 Mono view
 Stereo pair view
|
|
A full contact list of Sodium with other atoms in the Na binding
site number 1 of Gi.1 Human Norovirus Protruding Domain in Complex with Nano-7 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na600
b:27.5
occ:1.00
|
O
|
A:GLY396
|
2.2
|
28.8
|
1.0
|
|
O
|
A:PHE352
|
2.3
|
19.6
|
1.0
|
|
O
|
A:HOH779
|
2.3
|
27.4
|
1.0
|
|
O
|
A:ASN394
|
2.4
|
21.9
|
1.0
|
|
O
|
A:HOH843
|
2.4
|
36.1
|
1.0
|
|
HD2
|
A:PHE352
|
3.3
|
22.9
|
1.0
|
|
ND2
|
A:ASN394
|
3.3
|
32.5
|
1.0
|
|
C
|
A:GLY396
|
3.4
|
28.6
|
1.0
|
|
HD22
|
A:ASN394
|
3.5
|
39.1
|
1.0
|
|
C
|
A:ASN394
|
3.5
|
19.4
|
1.0
|
|
CG
|
A:ASN394
|
3.5
|
32.5
|
1.0
|
|
HD21
|
A:ASN394
|
3.5
|
39.1
|
1.0
|
|
C
|
A:PHE352
|
3.5
|
18.5
|
1.0
|
|
HB3
|
A:PHE352
|
3.5
|
22.2
|
1.0
|
|
HB3
|
A:ASN394
|
3.6
|
30.4
|
1.0
|
|
HG12
|
A:VAL353
|
3.6
|
32.7
|
1.0
|
|
HA
|
A:VAL353
|
3.7
|
26.3
|
1.0
|
|
HA
|
A:SER397
|
3.8
|
45.6
|
1.0
|
|
OD1
|
A:ASN394
|
3.9
|
33.5
|
1.0
|
|
C
|
A:TYR395
|
3.9
|
20.7
|
1.0
|
|
N
|
A:GLY396
|
3.9
|
23.3
|
1.0
|
|
CB
|
A:ASN394
|
4.0
|
25.3
|
1.0
|
|
HG13
|
A:VAL353
|
4.0
|
32.7
|
1.0
|
|
O
|
A:PRO349
|
4.1
|
23.8
|
1.0
|
|
H
|
A:GLY396
|
4.1
|
28.0
|
1.0
|
|
O
|
A:TYR395
|
4.1
|
21.4
|
1.0
|
|
CD2
|
A:PHE352
|
4.2
|
19.0
|
1.0
|
|
HD2
|
A:PRO354
|
4.2
|
21.4
|
1.0
|
|
CA
|
A:GLY396
|
4.2
|
26.6
|
1.0
|
|
CG1
|
A:VAL353
|
4.2
|
27.2
|
1.0
|
|
CB
|
A:PHE352
|
4.3
|
18.5
|
1.0
|
|
CA
|
A:ASN394
|
4.4
|
19.0
|
1.0
|
|
N
|
A:TYR395
|
4.4
|
18.8
|
1.0
|
|
HA
|
A:TYR395
|
4.4
|
22.9
|
1.0
|
|
CA
|
A:PHE352
|
4.4
|
17.9
|
1.0
|
|
O
|
A:THR347
|
4.4
|
20.7
|
1.0
|
|
N
|
A:VAL353
|
4.4
|
19.0
|
1.0
|
|
N
|
A:SER397
|
4.4
|
31.6
|
1.0
|
|
CA
|
A:VAL353
|
4.5
|
21.9
|
1.0
|
|
CA
|
A:TYR395
|
4.5
|
19.2
|
1.0
|
|
H
|
A:PHE352
|
4.5
|
23.2
|
1.0
|
|
CA
|
A:SER397
|
4.6
|
38.0
|
1.0
|
|
HA2
|
A:GLY396
|
4.7
|
32.0
|
1.0
|
|
CG
|
A:PHE352
|
4.7
|
18.9
|
1.0
|
|
N
|
A:PHE352
|
4.8
|
19.3
|
1.0
|
|
HB2
|
A:ASN394
|
4.9
|
30.4
|
1.0
|
|
HG11
|
A:VAL353
|
5.0
|
32.7
|
1.0
|
|
HA
|
A:ASP350
|
5.0
|
30.4
|
1.0
|
|
Sodium binding site 2 out
of 10 in 6h6y
Go back to
Sodium Binding Sites List in 6h6y
Sodium binding site 2 out
of 10 in the Gi.1 Human Norovirus Protruding Domain in Complex with Nano-7
 Mono view
 Stereo pair view
|
|
A full contact list of Sodium with other atoms in the Na binding
site number 2 of Gi.1 Human Norovirus Protruding Domain in Complex with Nano-7 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Na600
b:20.8
occ:1.00
|
O
|
B:GLY396
|
2.2
|
24.4
|
1.0
|
|
O
|
B:PHE352
|
2.3
|
19.0
|
1.0
|
|
O
|
B:HOH738
|
2.4
|
21.3
|
1.0
|
|
O
|
B:ASN394
|
2.4
|
18.7
|
1.0
|
|
O
|
B:HOH786
|
2.5
|
27.8
|
1.0
|
|
HD2
|
B:PHE352
|
3.3
|
20.1
|
1.0
|
|
ND2
|
B:ASN394
|
3.3
|
26.9
|
1.0
|
|
HG12
|
B:VAL353
|
3.3
|
33.0
|
1.0
|
|
HD22
|
B:ASN394
|
3.3
|
32.3
|
1.0
|
|
C
|
B:GLY396
|
3.4
|
21.8
|
1.0
|
|
HD21
|
B:ASN394
|
3.5
|
32.3
|
1.0
|
|
C
|
B:PHE352
|
3.5
|
19.0
|
1.0
|
|
CG
|
B:ASN394
|
3.5
|
24.4
|
1.0
|
|
HB3
|
B:ASN394
|
3.5
|
24.7
|
1.0
|
|
C
|
B:ASN394
|
3.6
|
19.5
|
1.0
|
|
HB3
|
B:PHE352
|
3.6
|
22.2
|
1.0
|
|
HA
|
B:VAL353
|
3.6
|
21.9
|
1.0
|
|
HA
|
B:SER397
|
3.7
|
40.6
|
1.0
|
|
CB
|
B:ASN394
|
4.0
|
20.5
|
1.0
|
|
N
|
B:GLY396
|
4.0
|
19.5
|
1.0
|
|
C
|
B:TYR395
|
4.0
|
18.3
|
1.0
|
|
OD1
|
B:ASN394
|
4.1
|
29.6
|
1.0
|
|
O
|
B:PRO349
|
4.1
|
20.6
|
1.0
|
|
CD2
|
B:PHE352
|
4.1
|
16.8
|
1.0
|
|
O
|
B:TYR395
|
4.2
|
18.8
|
1.0
|
|
H
|
B:GLY396
|
4.2
|
23.4
|
1.0
|
|
HD2
|
B:PRO354
|
4.2
|
20.1
|
1.0
|
|
CG1
|
B:VAL353
|
4.2
|
27.4
|
1.0
|
|
CA
|
B:GLY396
|
4.3
|
21.9
|
1.0
|
|
CB
|
B:PHE352
|
4.3
|
18.4
|
1.0
|
|
N
|
B:VAL353
|
4.4
|
18.4
|
1.0
|
|
N
|
B:SER397
|
4.4
|
23.5
|
1.0
|
|
CA
|
B:VAL353
|
4.4
|
18.2
|
1.0
|
|
HG13
|
B:VAL353
|
4.4
|
33.0
|
1.0
|
|
CA
|
B:ASN394
|
4.4
|
18.6
|
1.0
|
|
CA
|
B:PHE352
|
4.4
|
18.4
|
1.0
|
|
N
|
B:TYR395
|
4.5
|
16.9
|
1.0
|
|
H
|
B:PHE352
|
4.5
|
21.9
|
1.0
|
|
CA
|
B:SER397
|
4.5
|
33.8
|
1.0
|
|
HA
|
B:TYR395
|
4.5
|
20.3
|
1.0
|
|
O
|
B:THR347
|
4.5
|
20.6
|
1.0
|
|
CA
|
B:TYR395
|
4.6
|
17.0
|
1.0
|
|
O
|
B:HOH823
|
4.7
|
31.5
|
1.0
|
|
HA2
|
B:GLY396
|
4.7
|
26.4
|
1.0
|
|
CG
|
B:PHE352
|
4.7
|
17.4
|
1.0
|
|
HA
|
B:ASP350
|
4.8
|
25.6
|
1.0
|
|
N
|
B:PHE352
|
4.8
|
18.2
|
1.0
|
|
HG11
|
B:VAL353
|
4.8
|
33.0
|
1.0
|
|
HB2
|
B:ASN394
|
4.9
|
24.7
|
1.0
|
|
CB
|
B:VAL353
|
4.9
|
21.9
|
1.0
|
|
O
|
B:HOH827
|
5.0
|
30.3
|
1.0
|
|
Sodium binding site 3 out
of 10 in 6h6y
Go back to
Sodium Binding Sites List in 6h6y
Sodium binding site 3 out
of 10 in the Gi.1 Human Norovirus Protruding Domain in Complex with Nano-7
 Mono view
 Stereo pair view
|
|
A full contact list of Sodium with other atoms in the Na binding
site number 3 of Gi.1 Human Norovirus Protruding Domain in Complex with Nano-7 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Na601
b:38.0
occ:1.00
|
O
|
B:VAL260
|
2.5
|
26.0
|
1.0
|
|
OG
|
B:SER256
|
2.5
|
22.1
|
1.0
|
|
O
|
B:PRO257
|
2.5
|
24.7
|
1.0
|
|
HG
|
B:SER256
|
2.6
|
26.6
|
1.0
|
|
HA
|
B:ASP258
|
3.3
|
38.8
|
1.0
|
|
HB
|
B:VAL260
|
3.3
|
25.5
|
1.0
|
|
C
|
B:PRO257
|
3.5
|
27.4
|
1.0
|
|
O
|
B:HOH837
|
3.5
|
32.7
|
1.0
|
|
H
|
B:VAL260
|
3.5
|
31.6
|
1.0
|
|
O
|
B:SER256
|
3.6
|
23.7
|
1.0
|
|
C
|
B:VAL260
|
3.6
|
24.3
|
1.0
|
|
CB
|
B:SER256
|
3.7
|
20.3
|
1.0
|
|
HB2
|
B:SER256
|
3.8
|
24.4
|
1.0
|
|
C
|
B:SER256
|
3.8
|
21.7
|
1.0
|
|
O
|
B:HOH885
|
3.9
|
41.6
|
1.0
|
|
CA
|
B:ASP258
|
4.0
|
32.4
|
1.0
|
|
O
|
B:ASP258
|
4.0
|
38.2
|
1.0
|
|
N
|
B:VAL260
|
4.1
|
26.3
|
1.0
|
|
C
|
B:ASP258
|
4.1
|
31.2
|
1.0
|
|
CB
|
B:VAL260
|
4.1
|
21.2
|
1.0
|
|
N
|
B:ASP258
|
4.2
|
33.2
|
1.0
|
|
CA
|
B:VAL260
|
4.2
|
23.4
|
1.0
|
|
O
|
B:HOH892
|
4.3
|
27.4
|
1.0
|
|
CA
|
B:SER256
|
4.3
|
20.7
|
1.0
|
|
N
|
B:PRO257
|
4.3
|
28.1
|
1.0
|
|
HG11
|
B:VAL260
|
4.4
|
23.9
|
1.0
|
|
HB3
|
B:SER256
|
4.4
|
24.4
|
1.0
|
|
HA
|
B:GLN261
|
4.5
|
27.2
|
1.0
|
|
HE21
|
B:GLN261
|
4.5
|
43.2
|
1.0
|
|
CA
|
B:PRO257
|
4.5
|
30.3
|
1.0
|
|
H
|
B:SER256
|
4.5
|
26.8
|
1.0
|
|
HE22
|
B:GLN261
|
4.6
|
43.2
|
1.0
|
|
O
|
B:HOH742
|
4.7
|
22.3
|
1.0
|
|
NE2
|
B:GLN261
|
4.7
|
36.0
|
1.0
|
|
N
|
B:GLN261
|
4.8
|
21.0
|
1.0
|
|
CG1
|
B:VAL260
|
4.8
|
19.9
|
1.0
|
|
N
|
B:SER256
|
4.8
|
22.3
|
1.0
|
|
N
|
B:ASN259
|
4.9
|
29.3
|
1.0
|
|
HA
|
B:PRO257
|
5.0
|
36.4
|
1.0
|
|
H
|
B:ASP258
|
5.0
|
39.8
|
1.0
|
|
Sodium binding site 4 out
of 10 in 6h6y
Go back to
Sodium Binding Sites List in 6h6y
Sodium binding site 4 out
of 10 in the Gi.1 Human Norovirus Protruding Domain in Complex with Nano-7
 Mono view
 Stereo pair view
|
|
A full contact list of Sodium with other atoms in the Na binding
site number 4 of Gi.1 Human Norovirus Protruding Domain in Complex with Nano-7 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Na602
b:29.4
occ:1.00
|
O
|
B:PHE309
|
2.3
|
17.7
|
1.0
|
|
O
|
B:HOH773
|
2.3
|
26.2
|
1.0
|
|
O
|
B:HOH829
|
2.4
|
32.5
|
1.0
|
|
O
|
B:HOH859
|
2.4
|
36.4
|
1.0
|
|
O
|
B:HOH855
|
2.5
|
36.7
|
1.0
|
|
O
|
B:HOH735
|
2.6
|
20.7
|
1.0
|
|
HD3
|
B:PRO311
|
3.4
|
22.9
|
1.0
|
|
C
|
B:PHE309
|
3.5
|
18.1
|
1.0
|
|
HD21
|
B:ASN300
|
3.7
|
60.1
|
1.0
|
|
H
|
B:PHE309
|
3.7
|
20.4
|
1.0
|
|
HB3
|
B:PHE309
|
3.8
|
19.7
|
1.0
|
|
HA
|
B:HIS310
|
4.0
|
21.9
|
1.0
|
|
O
|
B:LEU301
|
4.0
|
18.4
|
1.0
|
|
HD2
|
B:PHE309
|
4.0
|
19.7
|
1.0
|
|
N
|
B:PHE309
|
4.1
|
16.9
|
1.0
|
|
CA
|
B:PHE309
|
4.2
|
15.7
|
1.0
|
|
CD
|
B:PRO311
|
4.2
|
19.1
|
1.0
|
|
HD2
|
B:PRO311
|
4.3
|
22.9
|
1.0
|
|
HB3
|
B:PRO308
|
4.4
|
22.1
|
1.0
|
|
ND2
|
B:ASN300
|
4.4
|
50.0
|
1.0
|
|
OD1
|
B:ASN300
|
4.4
|
47.2
|
1.0
|
|
CB
|
B:PHE309
|
4.4
|
16.4
|
1.0
|
|
N
|
B:HIS310
|
4.5
|
17.1
|
1.0
|
|
CD2
|
B:PHE309
|
4.7
|
16.4
|
1.0
|
|
O
|
B:HOH800
|
4.7
|
29.2
|
1.0
|
|
CA
|
B:HIS310
|
4.7
|
18.3
|
1.0
|
|
HA3
|
B:GLY357
|
4.7
|
24.1
|
1.0
|
|
HA
|
B:PRO308
|
4.8
|
22.5
|
1.0
|
|
CG
|
B:ASN300
|
4.8
|
34.2
|
1.0
|
|
CG
|
B:PHE309
|
5.0
|
15.7
|
1.0
|
|
C
|
B:PRO308
|
5.0
|
16.6
|
1.0
|
|
Sodium binding site 5 out
of 10 in 6h6y
Go back to
Sodium Binding Sites List in 6h6y
Sodium binding site 5 out
of 10 in the Gi.1 Human Norovirus Protruding Domain in Complex with Nano-7
 Mono view
 Stereo pair view
|
|
A full contact list of Sodium with other atoms in the Na binding
site number 5 of Gi.1 Human Norovirus Protruding Domain in Complex with Nano-7 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Na600
b:24.1
occ:1.00
|
O
|
C:GLY396
|
2.1
|
24.6
|
1.0
|
|
O
|
C:HOH739
|
2.3
|
22.5
|
1.0
|
|
O
|
C:PHE352
|
2.3
|
18.8
|
1.0
|
|
O
|
C:ASN394
|
2.4
|
23.1
|
1.0
|
|
HD2
|
C:PHE352
|
3.2
|
23.1
|
1.0
|
|
ND2
|
C:ASN394
|
3.3
|
38.6
|
1.0
|
|
C
|
C:GLY396
|
3.3
|
20.9
|
1.0
|
|
CG
|
C:ASN394
|
3.4
|
30.2
|
1.0
|
|
C
|
C:ASN394
|
3.4
|
21.4
|
1.0
|
|
HB3
|
C:ASN394
|
3.4
|
24.6
|
1.0
|
|
HD22
|
C:ASN394
|
3.4
|
46.4
|
1.0
|
|
HD21
|
C:ASN394
|
3.5
|
46.4
|
1.0
|
|
C
|
C:PHE352
|
3.6
|
17.4
|
1.0
|
|
HB3
|
C:PHE352
|
3.7
|
23.6
|
1.0
|
|
HA
|
C:VAL353
|
3.7
|
22.1
|
1.0
|
|
HA
|
C:SER397
|
3.7
|
31.9
|
1.0
|
|
OD1
|
C:ASN394
|
3.8
|
33.1
|
1.0
|
|
CB
|
C:ASN394
|
3.8
|
20.5
|
1.0
|
|
N
|
C:GLY396
|
3.8
|
19.7
|
1.0
|
|
C
|
C:TYR395
|
3.9
|
18.7
|
1.0
|
|
H
|
C:GLY396
|
4.0
|
23.7
|
1.0
|
|
O
|
C:PRO349
|
4.0
|
22.2
|
1.0
|
|
CD2
|
C:PHE352
|
4.1
|
19.2
|
1.0
|
|
HD2
|
C:PRO354
|
4.1
|
21.4
|
1.0
|
|
O
|
C:TYR395
|
4.1
|
18.6
|
1.0
|
|
CA
|
C:GLY396
|
4.1
|
19.4
|
1.0
|
|
CA
|
C:ASN394
|
4.2
|
16.8
|
1.0
|
|
N
|
C:TYR395
|
4.3
|
21.0
|
1.0
|
|
N
|
C:SER397
|
4.3
|
24.0
|
1.0
|
|
HA
|
C:TYR395
|
4.3
|
22.4
|
1.0
|
|
CB
|
C:PHE352
|
4.4
|
19.7
|
1.0
|
|
CA
|
C:TYR395
|
4.4
|
18.7
|
1.0
|
|
O
|
C:THR347
|
4.4
|
20.9
|
1.0
|
|
CA
|
C:VAL353
|
4.5
|
18.4
|
1.0
|
|
N
|
C:VAL353
|
4.5
|
17.9
|
1.0
|
|
CA
|
C:SER397
|
4.5
|
26.5
|
1.0
|
|
CA
|
C:PHE352
|
4.5
|
17.6
|
1.0
|
|
HA
|
C:ASP350
|
4.5
|
28.4
|
1.0
|
|
HB
|
C:VAL353
|
4.5
|
27.1
|
1.0
|
|
H
|
C:PHE352
|
4.6
|
22.0
|
1.0
|
|
HA2
|
C:GLY396
|
4.6
|
23.3
|
1.0
|
|
HB2
|
C:ASN394
|
4.7
|
24.6
|
1.0
|
|
CG
|
C:PHE352
|
4.7
|
17.2
|
1.0
|
|
N
|
C:PHE352
|
4.9
|
18.4
|
1.0
|
|
HA
|
C:ASN394
|
4.9
|
20.0
|
1.0
|
|
HA3
|
C:GLY396
|
4.9
|
23.3
|
1.0
|
|
HE2
|
C:PHE352
|
5.0
|
25.6
|
1.0
|
|
HB3
|
C:SER397
|
5.0
|
33.2
|
1.0
|
|
CB
|
C:VAL353
|
5.0
|
22.6
|
1.0
|
|
Sodium binding site 6 out
of 10 in 6h6y
Go back to
Sodium Binding Sites List in 6h6y
Sodium binding site 6 out
of 10 in the Gi.1 Human Norovirus Protruding Domain in Complex with Nano-7
 Mono view
 Stereo pair view
|
|
A full contact list of Sodium with other atoms in the Na binding
site number 6 of Gi.1 Human Norovirus Protruding Domain in Complex with Nano-7 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Na601
b:37.2
occ:1.00
|
O
|
C:HOH886
|
2.2
|
47.0
|
1.0
|
|
O
|
C:PRO257
|
2.3
|
24.9
|
1.0
|
|
OG
|
C:SER256
|
2.5
|
23.8
|
1.0
|
|
O
|
C:VAL260
|
2.5
|
25.5
|
1.0
|
|
HG
|
C:SER256
|
2.5
|
28.6
|
1.0
|
|
H11
|
C:EDO603
|
2.8
|
51.7
|
1.0
|
|
HB
|
C:VAL260
|
3.3
|
23.6
|
1.0
|
|
HA
|
C:ASP258
|
3.3
|
47.0
|
1.0
|
|
C
|
C:PRO257
|
3.3
|
28.1
|
1.0
|
|
O
|
C:SER256
|
3.4
|
25.6
|
1.0
|
|
H
|
C:VAL260
|
3.4
|
32.4
|
1.0
|
|
O
|
C:HOH795
|
3.5
|
30.5
|
1.0
|
|
C
|
C:VAL260
|
3.5
|
21.6
|
1.0
|
|
CB
|
C:SER256
|
3.6
|
26.6
|
1.0
|
|
C
|
C:SER256
|
3.7
|
24.9
|
1.0
|
|
HB2
|
C:SER256
|
3.7
|
32.0
|
1.0
|
|
C1
|
C:EDO603
|
3.8
|
43.1
|
1.0
|
|
H22
|
C:EDO603
|
3.9
|
55.5
|
1.0
|
|
O2
|
C:EDO603
|
3.9
|
53.9
|
1.0
|
|
CA
|
C:ASP258
|
3.9
|
39.1
|
1.0
|
|
N
|
C:VAL260
|
3.9
|
27.0
|
1.0
|
|
O
|
C:ASP258
|
4.0
|
40.4
|
1.0
|
|
C
|
C:ASP258
|
4.0
|
36.9
|
1.0
|
|
N
|
C:ASP258
|
4.0
|
31.4
|
1.0
|
|
CA
|
C:VAL260
|
4.1
|
23.9
|
1.0
|
|
CB
|
C:VAL260
|
4.1
|
19.7
|
1.0
|
|
C2
|
C:EDO603
|
4.1
|
46.2
|
1.0
|
|
N
|
C:PRO257
|
4.2
|
28.4
|
1.0
|
|
CA
|
C:SER256
|
4.2
|
22.9
|
1.0
|
|
HG11
|
C:VAL260
|
4.3
|
22.9
|
1.0
|
|
CA
|
C:PRO257
|
4.3
|
29.3
|
1.0
|
|
HB3
|
C:SER256
|
4.4
|
32.0
|
1.0
|
|
HA
|
C:GLN261
|
4.4
|
28.6
|
1.0
|
|
H12
|
C:EDO603
|
4.4
|
51.7
|
1.0
|
|
HO2
|
C:EDO603
|
4.4
|
64.7
|
1.0
|
|
HE21
|
C:GLN261
|
4.5
|
40.0
|
1.0
|
|
H
|
C:SER256
|
4.5
|
25.6
|
1.0
|
|
HE22
|
C:GLN261
|
4.6
|
40.0
|
1.0
|
|
O
|
C:HOH884
|
4.6
|
37.5
|
1.0
|
|
NE2
|
C:GLN261
|
4.7
|
33.3
|
1.0
|
|
N
|
C:GLN261
|
4.7
|
20.3
|
1.0
|
|
O1
|
C:EDO603
|
4.7
|
32.8
|
1.0
|
|
N
|
C:ASN259
|
4.7
|
29.3
|
1.0
|
|
O
|
C:HOH727
|
4.7
|
20.7
|
1.0
|
|
CG1
|
C:VAL260
|
4.7
|
19.1
|
1.0
|
|
HO1
|
C:EDO603
|
4.8
|
39.4
|
1.0
|
|
N
|
C:SER256
|
4.8
|
21.4
|
1.0
|
|
HA
|
C:PRO257
|
4.8
|
35.2
|
1.0
|
|
H
|
C:ASP258
|
4.9
|
37.7
|
1.0
|
|
C
|
C:ASN259
|
5.0
|
37.1
|
1.0
|
|
Sodium binding site 7 out
of 10 in 6h6y
Go back to
Sodium Binding Sites List in 6h6y
Sodium binding site 7 out
of 10 in the Gi.1 Human Norovirus Protruding Domain in Complex with Nano-7
 Mono view
 Stereo pair view
|
|
A full contact list of Sodium with other atoms in the Na binding
site number 7 of Gi.1 Human Norovirus Protruding Domain in Complex with Nano-7 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Na602
b:26.7
occ:1.00
|
O
|
C:PHE309
|
2.3
|
17.8
|
1.0
|
|
O
|
C:HOH737
|
2.3
|
22.3
|
1.0
|
|
O
|
C:HOH834
|
2.4
|
33.3
|
1.0
|
|
O
|
C:HOH722
|
2.6
|
19.3
|
1.0
|
|
HD3
|
C:PRO311
|
3.3
|
21.8
|
1.0
|
|
C
|
C:PHE309
|
3.5
|
16.9
|
1.0
|
|
HD21
|
C:ASN300
|
3.6
|
52.0
|
1.0
|
|
H
|
C:PHE309
|
3.7
|
20.6
|
1.0
|
|
HB3
|
C:PHE309
|
3.8
|
19.1
|
1.0
|
|
HA
|
C:HIS310
|
3.9
|
19.7
|
1.0
|
|
O
|
C:LEU301
|
4.0
|
17.7
|
1.0
|
|
N
|
C:PHE309
|
4.1
|
17.1
|
1.0
|
|
HD2
|
C:PHE309
|
4.1
|
20.7
|
1.0
|
|
CD
|
C:PRO311
|
4.2
|
18.1
|
1.0
|
|
HD2
|
C:PRO311
|
4.2
|
21.8
|
1.0
|
|
CA
|
C:PHE309
|
4.2
|
15.2
|
1.0
|
|
O
|
C:HOH887
|
4.3
|
56.1
|
1.0
|
|
ND2
|
C:ASN300
|
4.3
|
43.4
|
1.0
|
|
OD1
|
C:ASN300
|
4.3
|
45.0
|
1.0
|
|
O
|
C:HOH791
|
4.4
|
29.2
|
1.0
|
|
HB3
|
C:PRO308
|
4.4
|
20.8
|
1.0
|
|
CB
|
C:PHE309
|
4.5
|
15.9
|
1.0
|
|
N
|
C:HIS310
|
4.5
|
16.2
|
1.0
|
|
CA
|
C:HIS310
|
4.7
|
16.4
|
1.0
|
|
O
|
C:HOH794
|
4.7
|
29.2
|
1.0
|
|
CD2
|
C:PHE309
|
4.8
|
17.2
|
1.0
|
|
CG
|
C:ASN300
|
4.8
|
34.7
|
1.0
|
|
HA3
|
C:GLY357
|
4.8
|
20.9
|
1.0
|
|
HA
|
C:PRO308
|
4.8
|
21.5
|
1.0
|
|
HD22
|
C:ASN300
|
5.0
|
52.0
|
1.0
|
|
C
|
C:PRO308
|
5.0
|
17.2
|
1.0
|
|
Sodium binding site 8 out
of 10 in 6h6y
Go back to
Sodium Binding Sites List in 6h6y
Sodium binding site 8 out
of 10 in the Gi.1 Human Norovirus Protruding Domain in Complex with Nano-7
 Mono view
 Stereo pair view
|
|
A full contact list of Sodium with other atoms in the Na binding
site number 8 of Gi.1 Human Norovirus Protruding Domain in Complex with Nano-7 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Na600
b:30.0
occ:1.00
|
O
|
D:GLY396
|
2.1
|
33.7
|
1.0
|
|
O
|
D:HOH788
|
2.3
|
28.6
|
1.0
|
|
O
|
D:ASN394
|
2.4
|
28.7
|
1.0
|
|
O
|
D:HOH875
|
2.5
|
36.1
|
1.0
|
|
O
|
D:PHE352
|
2.5
|
24.0
|
1.0
|
|
OD1
|
D:ASN394
|
3.1
|
40.0
|
1.0
|
|
C
|
D:GLY396
|
3.3
|
29.9
|
1.0
|
|
HD2
|
D:PHE352
|
3.4
|
27.7
|
1.0
|
|
CG
|
D:ASN394
|
3.4
|
34.8
|
1.0
|
|
C
|
D:ASN394
|
3.5
|
23.6
|
1.0
|
|
HB3
|
D:ASN394
|
3.6
|
27.9
|
1.0
|
|
C
|
D:PHE352
|
3.7
|
24.4
|
1.0
|
|
HG12
|
D:VAL353
|
3.7
|
38.4
|
1.0
|
|
HA
|
D:SER397
|
3.8
|
61.6
|
1.0
|
|
HB3
|
D:PHE352
|
3.8
|
29.1
|
1.0
|
|
HA
|
D:VAL353
|
3.8
|
23.9
|
1.0
|
|
N
|
D:GLY396
|
3.9
|
32.9
|
1.0
|
|
C
|
D:TYR395
|
3.9
|
30.4
|
1.0
|
|
CB
|
D:ASN394
|
3.9
|
23.2
|
1.0
|
|
ND2
|
D:ASN394
|
3.9
|
28.9
|
1.0
|
|
H
|
D:GLY396
|
4.0
|
39.5
|
1.0
|
|
HG13
|
D:VAL353
|
4.1
|
38.4
|
1.0
|
|
HD21
|
D:ASN394
|
4.1
|
34.7
|
1.0
|
|
O
|
D:PRO349
|
4.1
|
24.7
|
1.0
|
|
CA
|
D:GLY396
|
4.2
|
32.6
|
1.0
|
|
O
|
D:TYR395
|
4.2
|
23.2
|
1.0
|
|
CD2
|
D:PHE352
|
4.2
|
23.1
|
1.0
|
|
HD2
|
D:PRO354
|
4.3
|
23.8
|
1.0
|
|
CA
|
D:ASN394
|
4.3
|
20.6
|
1.0
|
|
N
|
D:SER397
|
4.3
|
37.5
|
1.0
|
|
CG1
|
D:VAL353
|
4.3
|
31.9
|
1.0
|
|
N
|
D:TYR395
|
4.4
|
20.9
|
1.0
|
|
HA
|
D:TYR395
|
4.5
|
28.1
|
1.0
|
|
HD22
|
D:ASN394
|
4.5
|
34.7
|
1.0
|
|
O
|
D:THR347
|
4.5
|
23.5
|
1.0
|
|
CA
|
D:TYR395
|
4.5
|
23.4
|
1.0
|
|
CA
|
D:SER397
|
4.5
|
51.4
|
1.0
|
|
CB
|
D:PHE352
|
4.5
|
24.2
|
1.0
|
|
CA
|
D:VAL353
|
4.6
|
19.9
|
1.0
|
|
N
|
D:VAL353
|
4.6
|
23.7
|
1.0
|
|
CA
|
D:PHE352
|
4.6
|
21.5
|
1.0
|
|
HA2
|
D:GLY396
|
4.6
|
39.1
|
1.0
|
|
H
|
D:PHE352
|
4.7
|
29.8
|
1.0
|
|
HA
|
D:ASP350
|
4.8
|
31.8
|
1.0
|
|
HB2
|
D:ASN394
|
4.8
|
27.9
|
1.0
|
|
CG
|
D:PHE352
|
4.9
|
22.3
|
1.0
|
|
HA3
|
D:GLY396
|
4.9
|
39.1
|
1.0
|
|
HA
|
D:ASN394
|
4.9
|
24.6
|
1.0
|
|
N
|
D:PHE352
|
5.0
|
24.8
|
1.0
|
|
O
|
D:HOH815
|
5.0
|
31.2
|
1.0
|
|
Sodium binding site 9 out
of 10 in 6h6y
Go back to
Sodium Binding Sites List in 6h6y
Sodium binding site 9 out
of 10 in the Gi.1 Human Norovirus Protruding Domain in Complex with Nano-7
 Mono view
 Stereo pair view
|
|
A full contact list of Sodium with other atoms in the Na binding
site number 9 of Gi.1 Human Norovirus Protruding Domain in Complex with Nano-7 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Na601
b:35.4
occ:1.00
|
O
|
D:HOH877
|
2.3
|
56.8
|
1.0
|
|
OG
|
D:SER256
|
2.4
|
24.5
|
1.0
|
|
O
|
D:VAL260
|
2.4
|
24.4
|
1.0
|
|
O
|
D:PRO257
|
2.5
|
28.1
|
1.0
|
|
H22
|
D:EDO603
|
2.9
|
39.2
|
1.0
|
|
HB
|
D:VAL260
|
3.4
|
25.5
|
1.0
|
|
HA
|
D:ASP258
|
3.4
|
40.4
|
1.0
|
|
C
|
D:PRO257
|
3.5
|
26.6
|
1.0
|
|
H
|
D:VAL260
|
3.5
|
32.8
|
1.0
|
|
H11
|
D:EDO603
|
3.5
|
48.2
|
1.0
|
|
O
|
D:HOH840
|
3.5
|
34.9
|
1.0
|
|
C
|
D:VAL260
|
3.6
|
23.6
|
1.0
|
|
O
|
D:SER256
|
3.6
|
27.0
|
1.0
|
|
CB
|
D:SER256
|
3.7
|
25.0
|
1.0
|
|
O1
|
D:EDO603
|
3.8
|
51.2
|
1.0
|
|
C
|
D:SER256
|
3.8
|
26.3
|
1.0
|
|
C2
|
D:EDO603
|
3.8
|
32.6
|
1.0
|
|
HB2
|
D:SER256
|
3.8
|
30.0
|
1.0
|
|
C1
|
D:EDO603
|
3.9
|
40.1
|
1.0
|
|
O
|
D:ASP258
|
4.0
|
38.4
|
1.0
|
|
CA
|
D:ASP258
|
4.0
|
33.7
|
1.0
|
|
N
|
D:VAL260
|
4.0
|
27.3
|
1.0
|
|
C
|
D:ASP258
|
4.1
|
29.9
|
1.0
|
|
CA
|
D:VAL260
|
4.1
|
24.5
|
1.0
|
|
CB
|
D:VAL260
|
4.1
|
21.2
|
1.0
|
|
N
|
D:ASP258
|
4.2
|
31.2
|
1.0
|
|
HE21
|
D:GLN261
|
4.2
|
37.7
|
1.0
|
|
HO1
|
D:EDO603
|
4.3
|
61.5
|
1.0
|
|
CA
|
D:SER256
|
4.3
|
24.8
|
1.0
|
|
N
|
D:PRO257
|
4.3
|
26.8
|
1.0
|
|
HG12
|
D:VAL260
|
4.3
|
26.2
|
1.0
|
|
HA
|
D:GLN261
|
4.4
|
24.6
|
1.0
|
|
HE22
|
D:GLN261
|
4.4
|
37.7
|
1.0
|
|
HB3
|
D:SER256
|
4.4
|
30.0
|
1.0
|
|
CA
|
D:PRO257
|
4.5
|
30.6
|
1.0
|
|
H
|
D:SER256
|
4.5
|
28.4
|
1.0
|
|
NE2
|
D:GLN261
|
4.5
|
31.4
|
1.0
|
|
H21
|
D:EDO603
|
4.5
|
39.2
|
1.0
|
|
O2
|
D:EDO603
|
4.6
|
26.6
|
1.0
|
|
O
|
D:HOH743
|
4.7
|
22.9
|
1.0
|
|
N
|
D:GLN261
|
4.7
|
21.1
|
1.0
|
|
HO2
|
D:EDO603
|
4.7
|
31.9
|
1.0
|
|
CG1
|
D:VAL260
|
4.8
|
21.8
|
1.0
|
|
N
|
D:SER256
|
4.8
|
23.7
|
1.0
|
|
N
|
D:ASN259
|
4.8
|
34.1
|
1.0
|
|
HA
|
D:PRO257
|
5.0
|
36.8
|
1.0
|
|
H12
|
D:EDO603
|
5.0
|
48.2
|
1.0
|
|
H
|
D:ASP258
|
5.0
|
37.4
|
1.0
|
|
Sodium binding site 10 out
of 10 in 6h6y
Go back to
Sodium Binding Sites List in 6h6y
Sodium binding site 10 out
of 10 in the Gi.1 Human Norovirus Protruding Domain in Complex with Nano-7
 Mono view
 Stereo pair view
|
|
A full contact list of Sodium with other atoms in the Na binding
site number 10 of Gi.1 Human Norovirus Protruding Domain in Complex with Nano-7 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Na602
b:32.1
occ:1.00
|
O
|
D:PHE309
|
2.3
|
19.7
|
1.0
|
|
O
|
D:HOH876
|
2.4
|
45.6
|
1.0
|
|
O
|
D:HOH828
|
2.5
|
32.4
|
1.0
|
|
O
|
D:HOH731
|
2.5
|
21.8
|
1.0
|
|
HD3
|
D:PRO311
|
3.4
|
29.6
|
1.0
|
|
C
|
D:PHE309
|
3.5
|
20.1
|
1.0
|
|
H
|
D:PHE309
|
3.6
|
22.0
|
1.0
|
|
HB3
|
D:PHE309
|
3.8
|
22.8
|
1.0
|
|
O
|
D:LEU301
|
4.0
|
20.6
|
1.0
|
|
HA
|
D:HIS310
|
4.0
|
22.8
|
1.0
|
|
N
|
D:PHE309
|
4.0
|
18.3
|
1.0
|
|
HD2
|
D:PHE309
|
4.1
|
25.3
|
1.0
|
|
CA
|
D:PHE309
|
4.2
|
18.9
|
1.0
|
|
HB3
|
D:PRO308
|
4.2
|
24.3
|
1.0
|
|
CD
|
D:PRO311
|
4.3
|
24.6
|
1.0
|
|
O
|
D:HOH827
|
4.3
|
31.6
|
1.0
|
|
HD2
|
D:PRO311
|
4.4
|
29.6
|
1.0
|
|
CB
|
D:PHE309
|
4.4
|
19.0
|
1.0
|
|
N
|
D:HIS310
|
4.5
|
18.7
|
1.0
|
|
HA
|
D:PRO308
|
4.7
|
22.3
|
1.0
|
|
CA
|
D:HIS310
|
4.7
|
19.0
|
1.0
|
|
O
|
D:HOH807
|
4.7
|
30.2
|
1.0
|
|
CD2
|
D:PHE309
|
4.8
|
21.1
|
1.0
|
|
HD1
|
D:HIS310
|
4.8
|
25.3
|
1.0
|
|
HA3
|
D:GLY357
|
4.9
|
30.6
|
1.0
|
|
C
|
D:PRO308
|
4.9
|
20.3
|
1.0
|
|
HG3
|
D:PRO311
|
5.0
|
32.3
|
1.0
|
|
Reference:
K.Ruoff,
T.Kilic,
J.Devant,
A.Koromyslova,
A.Ringel,
A.Hempelmann,
C.Geiss,
J.Graf,
M.Haas,
I.Roggenbach,
G.Hansman.
Structural Basis of Nanobodies Targeting the Prototype Norovirus. J. Virol. V. 93 2019.
ISSN: ESSN 1098-5514
PubMed: 30602609
DOI: 10.1128/JVI.02005-18
Page generated: Tue Oct 8 09:14:12 2024
|
