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Sodium in PDB 5or7: Atomic Structure of the Murine Norovirus Protruding Domain and SCD300LF Receptor Complex

Protein crystallography data

The structure of Atomic Structure of the Murine Norovirus Protruding Domain and SCD300LF Receptor Complex, PDB code: 5or7 was solved by T.Kilic, G.S.Hansman, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 42.83 / 2.05
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 75.110, 77.460, 140.950, 90.00, 90.00, 90.00
R / Rfree (%) 18 / 21.7

Sodium Binding Sites:

The binding sites of Sodium atom in the Atomic Structure of the Murine Norovirus Protruding Domain and SCD300LF Receptor Complex (pdb code 5or7). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 6 binding sites of Sodium where determined in the Atomic Structure of the Murine Norovirus Protruding Domain and SCD300LF Receptor Complex, PDB code: 5or7:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6;

Sodium binding site 1 out of 6 in 5or7

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Sodium binding site 1 out of 6 in the Atomic Structure of the Murine Norovirus Protruding Domain and SCD300LF Receptor Complex


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Atomic Structure of the Murine Norovirus Protruding Domain and SCD300LF Receptor Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na600

b:27.5
occ:1.00
OH A:TYR408 2.6 18.4 1.0
O A:TYR328 2.7 19.3 1.0
OG1 A:THR278 2.9 19.3 1.0
O A:PRO329 3.2 21.1 1.0
CE1 A:TYR408 3.4 20.8 1.0
CZ A:TYR408 3.5 22.6 1.0
CB A:ASP330 3.5 18.3 1.0
C A:TYR328 3.6 16.6 1.0
C A:PRO329 3.6 21.7 1.0
CG2 A:THR278 3.7 18.5 1.0
CA A:ASP330 3.7 20.3 1.0
CB A:THR278 3.8 19.6 1.0
CB A:GLN265 3.8 19.1 1.0
N A:ASP330 3.8 21.7 1.0
CB A:TYR328 4.2 18.3 1.0
ND2 A:ASN266 4.3 21.4 1.0
CA A:TYR328 4.3 15.8 1.0
CD1 A:TYR328 4.3 18.0 1.0
N A:PRO329 4.4 18.4 1.0
OD1 A:ASN266 4.5 23.4 1.0
CG A:GLN265 4.5 26.9 1.0
CA A:PRO329 4.5 20.2 1.0
N A:TYR328 4.6 16.8 1.0
CG A:ASN266 4.6 22.4 1.0
CB A:ALA324 4.7 17.2 1.0
CE2 A:TYR408 4.8 20.3 1.0
CG A:ASP330 4.8 22.6 1.0
CD1 A:TYR408 4.8 17.6 1.0
CG A:TYR328 4.8 19.3 1.0

Sodium binding site 2 out of 6 in 5or7

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Sodium binding site 2 out of 6 in the Atomic Structure of the Murine Norovirus Protruding Domain and SCD300LF Receptor Complex


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Atomic Structure of the Murine Norovirus Protruding Domain and SCD300LF Receptor Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na601

b:47.7
occ:1.00
O A:HOH737 2.7 41.9 1.0
O A:PRO361 2.7 29.2 1.0
O A:ILE405 2.7 19.9 1.0
O A:PRO406 3.2 21.4 1.0
C A:PRO406 3.4 23.9 1.0
C A:PRO361 3.5 27.8 1.0
CA A:PRO361 3.6 27.7 1.0
C A:ILE405 3.8 21.8 1.0
N A:GLU407 3.9 20.8 1.0
CB A:PRO361 4.0 28.3 1.0
CA A:PRO406 4.0 23.0 1.0
O A:HOH846 4.0 48.2 1.0
O A:HOH775 4.2 31.0 1.0
CA A:GLU407 4.2 21.4 1.0
N A:PRO406 4.3 22.9 1.0
CG1 A:ILE405 4.4 31.0 1.0
N A:THR362 4.7 26.2 1.0
OG A:SER332 4.8 19.0 1.0
CB A:GLU407 4.9 19.9 1.0
CA A:ILE405 4.9 25.4 1.0

Sodium binding site 3 out of 6 in 5or7

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Sodium binding site 3 out of 6 in the Atomic Structure of the Murine Norovirus Protruding Domain and SCD300LF Receptor Complex


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Atomic Structure of the Murine Norovirus Protruding Domain and SCD300LF Receptor Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na600

b:29.5
occ:1.00
OH B:TYR408 2.7 21.2 1.0
O B:TYR328 2.7 21.0 1.0
OG1 B:THR278 2.8 21.5 1.0
O B:PRO329 3.3 19.5 1.0
CZ B:TYR408 3.5 22.6 1.0
CE1 B:TYR408 3.5 22.3 1.0
CB B:ASP330 3.6 20.8 1.0
C B:TYR328 3.6 21.3 1.0
C B:PRO329 3.7 20.9 1.0
CG2 B:THR278 3.7 19.7 1.0
CB B:GLN265 3.7 19.5 1.0
CB B:THR278 3.7 18.2 1.0
CA B:ASP330 3.8 20.5 1.0
N B:ASP330 3.9 19.8 1.0
CB B:TYR328 4.2 19.4 1.0
ND2 B:ASN266 4.2 17.9 1.0
CA B:TYR328 4.3 21.5 1.0
CG B:GLN265 4.4 20.3 1.0
CD1 B:TYR328 4.4 21.9 1.0
N B:PRO329 4.5 20.5 1.0
OD1 B:ASN266 4.5 24.5 1.0
CG B:ASN266 4.6 25.5 1.0
N B:TYR328 4.6 20.9 1.0
CA B:PRO329 4.6 20.2 1.0
CB B:ALA324 4.7 20.5 1.0
CE2 B:TYR408 4.8 22.4 1.0
CG B:ASP330 4.8 21.1 1.0
CD1 B:TYR408 4.8 23.9 1.0
CG B:TYR328 4.8 21.8 1.0
CA B:GLN265 4.9 22.8 1.0
C B:GLN265 5.0 24.9 1.0

Sodium binding site 4 out of 6 in 5or7

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Sodium binding site 4 out of 6 in the Atomic Structure of the Murine Norovirus Protruding Domain and SCD300LF Receptor Complex


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Atomic Structure of the Murine Norovirus Protruding Domain and SCD300LF Receptor Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na601

b:44.2
occ:1.00
O B:THR306 2.7 31.5 1.0
OG1 B:THR308 2.8 36.1 1.0
O B:HOH862 3.1 52.0 1.0
O B:GLU292 3.2 34.2 1.0
N B:THR308 3.4 27.4 1.0
CB B:ALA294 3.6 39.7 1.0
C B:THR306 3.6 31.9 1.0
CB B:THR308 3.7 31.7 1.0
CG2 B:THR306 3.7 38.7 1.0
N B:ALA294 3.7 38.0 1.0
C B:PHE307 4.1 27.2 1.0
CB B:THR306 4.1 39.9 1.0
CA B:THR308 4.1 25.9 1.0
C B:GLU292 4.2 34.8 1.0
N B:PHE307 4.2 30.1 1.0
CA B:PHE307 4.3 26.9 1.0
CA B:ALA294 4.3 39.1 1.0
C B:ALA293 4.3 37.5 1.0
O B:HOH855 4.4 53.3 1.0
CA B:THR306 4.5 36.4 1.0
CA B:ALA293 4.5 34.5 1.0
N B:ALA293 4.7 33.5 1.0
O B:PHE307 5.0 26.2 1.0

Sodium binding site 5 out of 6 in 5or7

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Sodium binding site 5 out of 6 in the Atomic Structure of the Murine Norovirus Protruding Domain and SCD300LF Receptor Complex


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Atomic Structure of the Murine Norovirus Protruding Domain and SCD300LF Receptor Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na401

b:26.2
occ:1.00
O C:LYS94 2.3 30.0 1.0
O C:GLY96 2.3 28.4 1.0
O A:ASN364 2.4 24.2 1.0
OD1 C:ASP98 2.5 24.1 1.0
O A:HOH815 2.5 33.0 1.0
OD2 A:ASP366 2.9 34.3 1.0
CG C:ASP98 3.3 24.9 1.0
C A:ASN364 3.4 23.5 1.0
C C:GLY96 3.5 29.1 1.0
C C:LYS94 3.5 31.9 1.0
N C:GLY96 3.6 29.9 1.0
OD2 C:ASP98 3.7 26.1 1.0
CA A:VAL365 3.9 29.7 1.0
N A:VAL365 4.0 22.1 1.0
O C:HOH504 4.0 31.7 1.0
CG A:ASP366 4.0 32.2 1.0
N C:LYS94 4.1 26.1 1.0
CA C:GLY96 4.1 30.0 1.0
C A:VAL365 4.1 29.1 1.0
N C:ASP98 4.2 25.3 1.0
C C:GLY95 4.2 31.3 1.0
O A:HOH858 4.3 42.1 1.0
CB C:ASP98 4.4 25.8 1.0
N C:GLY95 4.4 34.2 1.0
CA C:GLY95 4.4 34.3 1.0
CA C:LYS94 4.4 29.7 1.0
CA A:ASN364 4.4 24.5 1.0
N A:ASP366 4.5 24.9 1.0
O A:VAL365 4.5 25.5 1.0
C C:LEU97 4.5 29.5 1.0
CA C:ASP98 4.5 26.7 1.0
N C:LEU97 4.5 25.4 1.0
OD1 A:ASP366 4.8 34.0 1.0
CB A:ASN364 4.8 25.7 1.0
CA C:LEU97 4.8 24.0 1.0
O C:GLY95 4.9 32.0 1.0
CB A:ASP366 4.9 26.5 1.0

Sodium binding site 6 out of 6 in 5or7

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Sodium binding site 6 out of 6 in the Atomic Structure of the Murine Norovirus Protruding Domain and SCD300LF Receptor Complex


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Atomic Structure of the Murine Norovirus Protruding Domain and SCD300LF Receptor Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na402

b:39.8
occ:1.00
OG1 C:THR50 2.6 25.5 1.0
OD2 C:ASP66 2.8 23.4 1.0
O C:SER53 2.8 28.1 1.0
CA C:ALA52 3.2 31.1 1.0
C C:ALA52 3.3 31.3 1.0
CB C:ASP66 3.3 24.7 1.0
CB C:THR50 3.3 24.8 1.0
N C:SER53 3.3 32.1 1.0
CG C:ASP66 3.5 25.7 1.0
N C:ALA52 3.5 27.3 1.0
NE2 C:GLN68 3.6 29.5 1.0
C C:SER53 3.7 29.8 1.0
O C:TYR31 3.8 25.4 1.0
CG2 C:THR50 3.9 23.4 1.0
O C:ALA52 3.9 31.4 1.0
CG C:LYS33 4.0 21.4 1.0
CA C:SER53 4.1 32.4 1.0
NZ C:LYS33 4.1 22.2 1.0
O C:HOH527 4.1 27.5 1.0
N C:LYS33 4.4 21.6 1.0
CB C:ALA52 4.5 31.2 1.0
OD1 C:ASP66 4.7 27.1 1.0
CA C:LYS32 4.7 23.2 1.0
CA C:THR50 4.7 25.8 1.0
CB C:LYS33 4.7 23.7 1.0
C C:ASP51 4.7 34.5 1.0
CA C:ASP66 4.8 23.5 1.0
C C:TYR31 4.8 25.2 1.0
CD C:GLN68 4.8 34.1 1.0
N C:ASP51 4.8 28.4 1.0
C C:THR50 4.9 28.5 1.0
N C:GLU54 4.9 29.2 1.0
CD C:LYS33 5.0 18.9 1.0
C C:LYS32 5.0 23.3 1.0

Reference:

T.Kilic, A.Koromyslova, V.Malak, G.S.Hansman. Atomic Structure of the Murine Norovirus Protruding Domain and Soluble CD300LF Receptor Complex. J. Virol. V. 92 2018.
ISSN: ESSN 1098-5514
PubMed: 29563286
DOI: 10.1128/JVI.00413-18
Page generated: Tue Dec 15 11:25:39 2020

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