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Sodium in PDB 9nsm: Crystal Structure of the Bat Rotavirus Apo P[10] VP8* Receptor Binding Domain at 1.85 Angstrom Resolution

Protein crystallography data

The structure of Crystal Structure of the Bat Rotavirus Apo P[10] VP8* Receptor Binding Domain at 1.85 Angstrom Resolution, PDB code: 9nsm was solved by M.A.Kennedy, S.Ni, F.Li, D.Wang, S.Soni, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.84 / 1.85
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 158.345, 92.996, 42.534, 90, 93.48, 90
R / Rfree (%) 19.5 / 21.3

Sodium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Sodium atom in the Crystal Structure of the Bat Rotavirus Apo P[10] VP8* Receptor Binding Domain at 1.85 Angstrom Resolution (pdb code 9nsm). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 12 binding sites of Sodium where determined in the Crystal Structure of the Bat Rotavirus Apo P[10] VP8* Receptor Binding Domain at 1.85 Angstrom Resolution, PDB code: 9nsm:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Sodium binding site 1 out of 12 in 9nsm

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Sodium binding site 1 out of 12 in the Crystal Structure of the Bat Rotavirus Apo P[10] VP8* Receptor Binding Domain at 1.85 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of the Bat Rotavirus Apo P[10] VP8* Receptor Binding Domain at 1.85 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na201

b:29.5
occ:1.00
 O A:PRO14 2.7 23.4 1.0
O A:TYR17 2.7 20.5 1.0
N A:LYS106 2.9 20.3 1.0
O A:HOH363 3.0 33.7 1.0
CB A:LYS106 3.6 21.1 1.0
CA A:MET105 3.7 21.3 1.0
CA A:LYS106 3.7 21.4 1.0
C A:PRO14 3.8 24.4 1.0
C A:MET105 3.8 20.8 1.0
C A:TYR17 3.8 23.4 1.0
O A:LYS106 3.8 22.5 1.0
N A:TYR17 3.9 20.3 1.0
CG A:LYS106 4.0 20.0 1.0
CG A:MET105 4.0 20.7 1.0
CD A:LYS106 4.1 23.5 1.0
CA A:VAL15 4.1 23.7 1.0
C A:LYS106 4.2 22.6 1.0
CA A:TYR17 4.3 22.9 1.0
N A:ASN16 4.3 20.4 1.0
CB A:PRO13 4.3 24.3 1.0
CB A:MET105 4.3 19.2 1.0
C A:VAL15 4.3 25.0 1.0
N A:VAL15 4.4 22.1 1.0
CB A:TYR17 4.4 22.9 1.0
O A:ILE104 4.7 20.2 1.0
C A:PRO13 4.7 25.5 1.0
O A:PRO13 4.8 25.8 1.0
N A:PRO14 4.8 27.3 1.0
N A:MET105 4.9 20.0 1.0
CA A:PRO14 4.9 25.9 1.0
N A:TRP18 4.9 19.9 1.0
O A:MET105 5.0 20.2 1.0

Sodium binding site 2 out of 12 in 9nsm

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Sodium binding site 2 out of 12 in the Crystal Structure of the Bat Rotavirus Apo P[10] VP8* Receptor Binding Domain at 1.85 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of the Bat Rotavirus Apo P[10] VP8* Receptor Binding Domain at 1.85 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na202

b:27.1
occ:1.00
 O A:SER93 2.2 26.5 1.0
O A:TYR114 2.3 28.6 1.0
OH A:TYR102 2.6 25.7 1.0
OG A:SER93 2.6 28.1 1.0
OD2 A:ASP79 2.7 23.0 1.0
OG1 A:THR113 3.1 24.2 1.0
CB A:SER93 3.2 28.0 1.0
C A:SER93 3.3 25.3 1.0
C A:TYR114 3.4 23.9 1.0
CG A:ASP79 3.5 26.4 1.0
CZ A:TYR102 3.8 25.4 1.0
OD1 A:ASP79 3.9 22.2 1.0
CA A:SER93 3.9 24.2 1.0
CB A:THR113 4.0 22.6 1.0
N A:TYR114 4.1 24.1 1.0
CA A:ASP115 4.2 24.5 1.0
N A:ASP115 4.2 25.6 1.0
CE1 A:TYR102 4.2 25.3 1.0
CB A:ASP115 4.3 28.5 1.0
CA A:TYR114 4.4 24.8 1.0
N A:PRO94 4.4 24.1 1.0
C A:THR113 4.5 23.7 1.0
OH A:TYR126 4.5 24.8 1.0
C A:PRO94 4.6 24.6 1.0
CB A:ASP79 4.6 23.2 1.0
OD1 A:ASN124 4.6 36.3 1.0
O A:PRO94 4.7 24.6 1.0
CA A:PRO94 4.7 23.8 1.0
O A:HIS92 4.7 22.9 1.0
N A:LEU95 4.8 21.4 1.0
CE2 A:TYR102 4.9 21.1 1.0
CA A:THR113 4.9 24.3 1.0
OD2 A:ASP115 5.0 30.6 1.0
O A:THR113 5.0 27.1 1.0
N A:SER93 5.0 24.7 1.0

Sodium binding site 3 out of 12 in 9nsm

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Sodium binding site 3 out of 12 in the Crystal Structure of the Bat Rotavirus Apo P[10] VP8* Receptor Binding Domain at 1.85 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of the Bat Rotavirus Apo P[10] VP8* Receptor Binding Domain at 1.85 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na203

b:21.7
occ:1.00
 O1 B:GOL206 3.0 27.9 1.0
O B:HOH337 3.1 28.4 1.0
OG A:SER127 3.1 25.6 1.0
O B:HOH344 3.3 29.9 1.0
NE2 A:GLN110 3.4 25.1 1.0
CB A:SER127 3.5 23.8 1.0
C1 B:GOL206 3.6 28.1 1.0
CZ2 B:TRP112 3.8 22.4 1.0
CA A:SER127 4.0 23.9 1.0
CH2 B:TRP112 4.1 23.7 1.0
O A:HOH320 4.1 27.0 1.0
CG A:GLN110 4.2 21.2 1.0
O A:GLY109 4.2 21.6 1.0
CD A:GLN110 4.3 24.5 1.0
NE2 B:HIS107 4.5 26.5 1.0
C A:GLY109 4.8 23.8 1.0
O A:HOH351 4.8 38.6 1.0
CD2 B:HIS107 4.8 26.4 1.0
O B:HOH322 4.9 36.0 1.0
CE2 B:TRP112 4.9 25.2 1.0
OE1 B:GLN110 4.9 21.1 1.0
C2 B:GOL206 4.9 29.7 1.0

Sodium binding site 4 out of 12 in 9nsm

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Sodium binding site 4 out of 12 in the Crystal Structure of the Bat Rotavirus Apo P[10] VP8* Receptor Binding Domain at 1.85 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Crystal Structure of the Bat Rotavirus Apo P[10] VP8* Receptor Binding Domain at 1.85 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na204

b:30.5
occ:1.00
 O A:LEU101 2.6 23.0 1.0
O A:ILE157 2.6 26.3 1.0
OG A:SER97 2.7 23.7 1.0
N A:LEU101 3.1 25.3 1.0
C A:LEU101 3.4 25.8 1.0
CB A:SER97 3.6 25.2 1.0
CA A:LEU101 3.6 24.0 1.0
C A:ILE157 3.6 26.2 1.0
CB A:LEU101 3.8 23.4 1.0
CG2 A:THR118 3.8 25.1 1.0
CB A:PRO99 3.8 28.3 1.0
N A:LYS100 3.9 28.4 1.0
CG2 A:ILE157 3.9 27.6 1.0
CD A:PRO99 3.9 24.8 1.0
CA A:ILE157 4.0 24.4 1.0
CD2 A:LEU95 4.0 22.0 1.0
CG A:PRO99 4.1 28.1 1.0
C A:LYS100 4.2 26.1 1.0
C A:PRO99 4.3 25.1 1.0
N A:PRO99 4.4 26.6 1.0
CA A:PRO99 4.4 24.4 1.0
CA A:LYS100 4.4 27.0 1.0
CE2 A:PHE77 4.5 21.3 1.0
CB A:ILE157 4.6 23.8 1.0
CA A:SER97 4.6 23.7 1.0
N A:TYR102 4.7 23.8 1.0
CD1 A:ILE157 4.8 26.6 1.0
CG A:LEU101 4.8 24.9 1.0
N A:ASN158 4.8 27.8 1.0
CG A:LEU95 4.9 25.6 1.0
O A:TYR156 5.0 27.7 1.0

Sodium binding site 5 out of 12 in 9nsm

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Sodium binding site 5 out of 12 in the Crystal Structure of the Bat Rotavirus Apo P[10] VP8* Receptor Binding Domain at 1.85 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Crystal Structure of the Bat Rotavirus Apo P[10] VP8* Receptor Binding Domain at 1.85 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na205

b:30.0
occ:1.00
 O A:HOH370 2.4 36.0 1.0
ND2 A:ASN158 3.4 26.0 1.0
CA A:GLU155 3.6 29.2 1.0
CG2 A:THR154 3.6 23.9 1.0
O A:THR154 3.7 25.4 1.0
N A:GLU155 3.8 26.7 1.0
C A:THR154 3.9 26.6 1.0
CB A:ASN158 4.0 27.7 1.0
CG A:ASN158 4.2 26.4 1.0
O A:HOH306 4.2 28.7 1.0
CB A:GLU155 4.3 30.7 1.0
OD1 A:ASN159 4.4 34.1 1.0
CB A:THR154 4.5 29.6 1.0
CG A:GLU155 4.6 37.0 1.0
C A:GLU155 4.7 27.2 1.0
O A:PRO119 4.8 22.3 1.0
CA A:THR154 4.8 24.4 1.0
O A:GLU155 4.8 29.9 1.0

Sodium binding site 6 out of 12 in 9nsm

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Sodium binding site 6 out of 12 in the Crystal Structure of the Bat Rotavirus Apo P[10] VP8* Receptor Binding Domain at 1.85 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Crystal Structure of the Bat Rotavirus Apo P[10] VP8* Receptor Binding Domain at 1.85 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na201

b:31.7
occ:1.00
 O B:HOH374 2.6 32.2 1.0
OD2 B:ASP115 2.7 30.9 1.0
O B:PRO94 2.9 22.7 1.0
OD1 B:ASP115 3.1 28.6 1.0
CG B:ASP115 3.2 30.5 1.0
CD B:PRO94 3.2 25.9 1.0
N B:PRO94 3.4 24.1 1.0
N A:SER93 3.5 24.7 1.0
CG B:PRO94 3.6 26.9 1.0
CD A:PRO94 3.6 25.3 1.0
N B:GLY116 3.6 25.6 1.0
C B:SER93 3.7 24.7 1.0
C B:PRO94 3.8 25.2 1.0
CA B:SER93 3.9 24.7 1.0
CA B:GLY116 4.0 23.8 1.0
CA A:SER93 4.0 24.2 1.0
CA B:PRO94 4.1 24.4 1.0
O A:HOH311 4.3 26.9 1.0
CB B:ASP115 4.4 24.2 1.0
C B:ASP115 4.4 25.5 1.0
CB B:PRO94 4.4 28.4 1.0
C A:HIS92 4.5 24.8 1.0
O B:SER93 4.5 25.0 1.0
CA B:ASP115 4.5 24.4 1.0
CG A:PRO94 4.6 28.2 1.0
N A:PRO94 4.6 24.1 1.0
OG B:SER93 4.7 33.3 1.0
O B:HOH302 4.7 37.2 1.0
CA A:HIS92 4.7 25.0 1.0
O B:GLY116 4.8 25.9 1.0
N B:SER93 4.8 23.7 1.0
C B:GLY116 4.9 27.6 1.0
C A:SER93 4.9 25.3 1.0
OD2 A:ASP115 5.0 30.6 1.0
CB B:SER93 5.0 27.7 1.0

Sodium binding site 7 out of 12 in 9nsm

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Sodium binding site 7 out of 12 in the Crystal Structure of the Bat Rotavirus Apo P[10] VP8* Receptor Binding Domain at 1.85 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of Crystal Structure of the Bat Rotavirus Apo P[10] VP8* Receptor Binding Domain at 1.85 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na202

b:26.4
occ:1.00
 O B:HOH301 2.3 35.1 1.0
O B:SER93 2.4 25.0 1.0
O B:TYR114 2.5 24.6 1.0
OH B:TYR102 2.5 29.0 1.0
OD2 B:ASP79 2.8 25.0 1.0
OG B:SER93 2.9 33.3 1.0
OG1 B:THR113 3.0 25.4 1.0
CB B:SER93 3.3 27.7 1.0
C B:SER93 3.5 24.7 1.0
CG B:ASP79 3.5 28.0 1.0
C B:TYR114 3.5 26.8 1.0
OD1 B:ASP79 3.8 24.3 1.0
CZ B:TYR102 3.8 26.4 1.0
CB B:THR113 3.9 25.8 1.0
CA B:SER93 4.0 24.7 1.0
N B:TYR114 4.1 24.9 1.0
CE1 B:TYR102 4.2 25.4 1.0
CA B:ASP115 4.3 24.4 1.0
N B:ASP115 4.3 23.8 1.0
CA B:TYR114 4.4 24.3 1.0
CB B:ASP115 4.5 24.2 1.0
OH B:TYR126 4.5 25.9 1.0
C B:THR113 4.6 27.5 1.0
N B:PRO94 4.6 24.1 1.0
CB B:ASP79 4.6 20.7 1.0
O B:HIS92 4.7 23.0 1.0
C B:PRO94 4.7 25.2 1.0
OD1 B:ASN124 4.8 35.3 1.0
O B:PRO94 4.8 22.7 1.0
CA B:PRO94 4.9 24.4 1.0
CA B:THR113 4.9 24.2 1.0
CE2 B:TYR102 4.9 23.3 1.0
OD2 B:ASP115 4.9 30.9 1.0
CG2 B:THR113 5.0 23.6 1.0

Sodium binding site 8 out of 12 in 9nsm

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Sodium binding site 8 out of 12 in the Crystal Structure of the Bat Rotavirus Apo P[10] VP8* Receptor Binding Domain at 1.85 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of Crystal Structure of the Bat Rotavirus Apo P[10] VP8* Receptor Binding Domain at 1.85 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na203

b:30.1
occ:1.00
 OG B:SER97 2.6 25.4 1.0
O B:LEU101 2.6 24.3 1.0
O B:ILE157 2.8 23.3 1.0
N B:LEU101 2.9 24.6 1.0
C B:LEU101 3.4 23.8 1.0
CA B:LEU101 3.5 22.7 1.0
CB B:SER97 3.5 28.2 1.0
N B:LYS100 3.7 25.4 1.0
CB B:LEU101 3.7 24.4 1.0
C B:ILE157 3.8 28.1 1.0
CB B:PRO99 3.8 29.9 1.0
CG2 B:THR118 3.9 23.7 1.0
CD B:PRO99 3.9 31.3 1.0
C B:LYS100 4.0 25.3 1.0
CG B:PRO99 4.0 31.9 1.0
CG2 B:ILE157 4.0 23.5 1.0
CA B:ILE157 4.0 27.3 1.0
C B:PRO99 4.2 26.0 1.0
CD2 B:LEU95 4.2 25.7 1.0
CA B:LYS100 4.2 24.7 1.0
N B:PRO99 4.3 29.8 1.0
CA B:PRO99 4.4 27.5 1.0
CE2 B:PHE77 4.5 26.1 1.0
CG B:LEU101 4.6 23.3 1.0
CA B:SER97 4.6 24.7 1.0
CB B:ILE157 4.6 26.8 1.0
N B:TYR102 4.7 24.5 1.0
CD1 B:ILE157 4.8 26.2 1.0
O B:TYR156 4.9 31.0 1.0
O B:PRO99 4.9 24.5 1.0

Sodium binding site 9 out of 12 in 9nsm

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Sodium binding site 9 out of 12 in the Crystal Structure of the Bat Rotavirus Apo P[10] VP8* Receptor Binding Domain at 1.85 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 9 of Crystal Structure of the Bat Rotavirus Apo P[10] VP8* Receptor Binding Domain at 1.85 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na204

b:31.3
occ:1.00
 O B:TYR17 2.6 25.3 1.0
O B:PRO14 2.6 28.9 1.0
O B:HOH362 2.8 35.9 1.0
N B:LYS106 3.0 20.8 1.0
C B:TYR17 3.7 27.2 1.0
CB B:LYS106 3.7 22.3 1.0
C B:PRO14 3.7 30.8 1.0
CA B:MET105 3.7 24.1 1.0
N B:TYR17 3.7 25.1 1.0
C B:MET105 3.8 24.5 1.0
CA B:LYS106 3.8 22.8 1.0
O B:LYS106 3.9 24.8 1.0
CG B:MET105 4.0 24.9 1.0
CG B:LYS106 4.1 23.3 1.0
CD B:LYS106 4.1 27.9 1.0
CA B:VAL15 4.1 31.0 1.0
CA B:TYR17 4.1 29.9 1.0
N B:ASN16 4.2 27.6 1.0
CB B:PRO13 4.2 29.2 1.0
C B:VAL15 4.3 31.4 1.0
CB B:TYR17 4.3 29.5 1.0
CB B:MET105 4.4 23.4 1.0
C B:LYS106 4.4 27.3 1.0
N B:VAL15 4.4 28.9 1.0
O B:ILE104 4.6 24.0 1.0
C B:PRO13 4.7 31.8 1.0
O B:PRO13 4.7 29.2 1.0
N B:PRO14 4.7 31.4 1.0
N B:TRP18 4.8 27.6 1.0
C B:ASN16 4.9 29.1 1.0
CA B:PRO14 4.9 30.6 1.0
N B:MET105 4.9 23.1 1.0
O B:VAL15 5.0 31.4 1.0

Sodium binding site 10 out of 12 in 9nsm

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Sodium binding site 10 out of 12 in the Crystal Structure of the Bat Rotavirus Apo P[10] VP8* Receptor Binding Domain at 1.85 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 10 of Crystal Structure of the Bat Rotavirus Apo P[10] VP8* Receptor Binding Domain at 1.85 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na205

b:43.7
occ:1.00
 O C:HOH358 3.0 35.5 1.0
NE2 C:GLN7 3.9 35.4 1.0
OD1 B:ASN35 4.2 37.1 1.0
CB B:PHE59 4.5 27.4 1.0
CD1 B:PHE59 4.6 26.7 1.0
O B:HOH339 4.7 37.4 1.0
O B:PHE59 4.8 26.0 1.0
CG2 B:THR33 4.8 28.4 1.0
CD C:GLN7 4.8 33.2 1.0
O B:HOH311 4.9 31.7 1.0

Reference:

M.A.Kennedy, S.Ni, F.Li, D.Wang, S.Soni. Crystal Structure of the Bat Rotavirus Apo P[10] VP8* Receptor Binding Domain at 1.85 Angstrom Resolution To Be Published.
Page generated: Mon Aug 18 17:30:34 2025

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