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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:

Chlorine (Cl) 4 atoms

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

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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

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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

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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

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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

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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

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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

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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

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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

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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 Dec 15 12:19:09 2020

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