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Sodium in PDB 4oq9: Satellite Tobacco Mosaic Virus Refined to 1.4 A Resolution Using Non- Crystallographic Symmetry Restraints

Protein crystallography data

The structure of Satellite Tobacco Mosaic Virus Refined to 1.4 A Resolution Using Non- Crystallographic Symmetry Restraints, PDB code: 4oq9 was solved by S.B.Larson, J.S.Day, A.Mcpherson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.35 / 1.45
Space group I 2 2 2 1
Cell size a, b, c (Å), α, β, γ (°) 172.690, 190.300, 201.690, 90.00, 90.00, 90.00
R / Rfree (%) 21.7 / 25

Other elements in 4oq9:

The structure of Satellite Tobacco Mosaic Virus Refined to 1.4 A Resolution Using Non- Crystallographic Symmetry Restraints also contains other interesting chemical elements:

Magnesium (Mg) 3 atoms

Sodium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 17;

Binding sites:

The binding sites of Sodium atom in the Satellite Tobacco Mosaic Virus Refined to 1.4 A Resolution Using Non- Crystallographic Symmetry Restraints (pdb code 4oq9). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 17 binding sites of Sodium where determined in the Satellite Tobacco Mosaic Virus Refined to 1.4 A Resolution Using Non- Crystallographic Symmetry Restraints, PDB code: 4oq9:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Sodium binding site 1 out of 17 in 4oq9

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Sodium binding site 1 out of 17 in the Satellite Tobacco Mosaic Virus Refined to 1.4 A Resolution Using Non- Crystallographic Symmetry Restraints


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Satellite Tobacco Mosaic Virus Refined to 1.4 A Resolution Using Non- Crystallographic Symmetry Restraints within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na203

b:46.6
occ:0.55
 NA O:NA202 2.2 47.3 0.5
OD1 A:ASP68 2.3 38.8 1.0
O O:HOH434 2.5 50.1 1.0
O O:HOH337 2.7 29.6 1.0
OD1 O:ASP68 3.2 39.0 1.0
O A:HOH520 3.2 29.7 1.0
CG A:ASP68 3.2 35.1 1.0
OD2 A:ASP68 3.5 50.4 1.0
CG O:ASP68 3.7 35.0 1.0
OD2 O:ASP68 3.8 50.5 1.0
O A:HOH725 3.9 25.7 0.3
C A:ARG66 3.9 25.5 1.0
O A:ARG66 4.0 25.0 1.0
CA A:ARG66 4.0 24.6 1.0
CB O:SER69 4.1 27.1 1.0
N O:SER69 4.2 26.2 1.0
N A:ASP68 4.3 26.6 1.0
OG O:SER69 4.3 26.4 1.0
N A:THR67 4.5 25.1 1.0
CB A:ASP68 4.6 28.8 1.0
O O:ARG66 4.6 25.2 1.0
CA O:SER69 4.7 26.4 1.0
CB A:ARG66 4.7 24.8 1.0
N O:ASP68 4.8 26.8 1.0
CA A:ALA63 4.8 29.0 1.0
N A:SER69 4.8 26.1 1.0
CA A:ASP68 4.9 28.0 1.0
C O:ASP68 4.9 27.9 1.0
C O:ARG66 4.9 24.0 1.0

Sodium binding site 2 out of 17 in 4oq9

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Sodium binding site 2 out of 17 in the Satellite Tobacco Mosaic Virus Refined to 1.4 A Resolution Using Non- Crystallographic Symmetry Restraints


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Satellite Tobacco Mosaic Virus Refined to 1.4 A Resolution Using Non- Crystallographic Symmetry Restraints within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na202

b:97.7
occ:0.50
 OD2 B:ASP68 2.7 50.5 1.0
O B:HOH516 3.0 45.4 0.5
O B:HOH426 3.3 50.6 1.0
CG B:ASP68 3.9 35.2 1.0
O B:HOH495 4.2 49.9 0.5
OD1 B:ASP68 4.4 39.1 1.0
O B:HOH515 4.5 65.3 1.0
NA B:NA203 4.7 0.0 1.0
O B:HOH460 4.7 38.8 0.5

Sodium binding site 3 out of 17 in 4oq9

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Sodium binding site 3 out of 17 in the Satellite Tobacco Mosaic Virus Refined to 1.4 A Resolution Using Non- Crystallographic Symmetry Restraints


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Satellite Tobacco Mosaic Virus Refined to 1.4 A Resolution Using Non- Crystallographic Symmetry Restraints within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na203

b:0.0
occ:1.00
 OD1 B:ASP68 2.0 39.1 1.0
O B:HOH426 2.6 50.6 1.0
CG B:ASP68 3.1 35.2 1.0
O B:HOH326 3.4 26.8 1.0
CA B:ARG66 3.5 24.6 1.0
OD2 B:ASP68 3.6 50.5 1.0
C B:ARG66 3.6 25.4 1.0
O B:ARG66 3.9 25.5 1.0
N B:THR67 4.0 25.1 1.0
N B:ASP68 4.1 26.4 1.0
CA B:ALA63 4.2 29.0 1.0
CB B:ASP68 4.4 28.6 1.0
CB B:ARG66 4.4 24.8 1.0
O B:HOH460 4.5 38.8 0.5
N B:ARG66 4.5 24.4 1.0
O B:ALA63 4.6 27.6 1.0
CB B:ALA63 4.7 30.2 1.0
NA B:NA202 4.7 97.7 0.5
CA B:ASP68 4.8 27.7 1.0
C B:ALA63 4.9 28.0 1.0
O B:SER62 4.9 26.7 1.0
CA B:THR67 4.9 24.6 1.0
C B:THR67 5.0 26.1 1.0
N B:SER69 5.0 26.9 1.0

Sodium binding site 4 out of 17 in 4oq9

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Sodium binding site 4 out of 17 in the Satellite Tobacco Mosaic Virus Refined to 1.4 A Resolution Using Non- Crystallographic Symmetry Restraints


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Satellite Tobacco Mosaic Virus Refined to 1.4 A Resolution Using Non- Crystallographic Symmetry Restraints within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na202

b:47.1
occ:0.40
 OD1 C:ASP68 2.5 39.2 1.0
O C:HOH498 2.8 58.6 1.0
O C:HOH323 3.3 23.9 1.0
CG C:ASP68 3.5 35.1 1.0
OD2 C:ASP68 3.8 50.6 1.0
CA C:ARG66 3.9 24.4 1.0
C C:ARG66 4.0 25.5 1.0
O C:ARG66 4.0 24.9 1.0
N C:ASP68 4.5 26.9 1.0
N C:THR67 4.5 25.0 1.0
CB C:ARG66 4.6 25.0 1.0
CB C:ASP68 4.8 28.8 1.0
CA C:ALA63 4.9 28.7 1.0
N C:SER69 5.0 26.6 1.0

Sodium binding site 5 out of 17 in 4oq9

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Sodium binding site 5 out of 17 in the Satellite Tobacco Mosaic Virus Refined to 1.4 A Resolution Using Non- Crystallographic Symmetry Restraints


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Satellite Tobacco Mosaic Virus Refined to 1.4 A Resolution Using Non- Crystallographic Symmetry Restraints within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na202

b:0.5
occ:1.00
 OD1 D:ASP68 2.4 39.1 1.0
CG D:ASP68 3.4 35.0 1.0
OD2 D:ASP68 3.6 50.7 1.0
O D:HOH326 3.9 28.1 1.0
CA D:ARG66 3.9 24.0 1.0
C D:ARG66 4.2 25.6 1.0
CA D:ALA63 4.3 28.7 1.0
O D:ARG66 4.3 25.0 1.0
CB D:ALA63 4.6 30.2 1.0
N D:THR67 4.7 24.7 1.0
N D:ASP68 4.7 26.7 1.0
O D:ALA63 4.7 27.4 1.0
CB D:ARG66 4.7 24.6 1.0
CB D:ASP68 4.7 29.1 1.0
N D:ARG66 4.9 24.3 1.0

Sodium binding site 6 out of 17 in 4oq9

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Sodium binding site 6 out of 17 in the Satellite Tobacco Mosaic Virus Refined to 1.4 A Resolution Using Non- Crystallographic Symmetry Restraints


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Satellite Tobacco Mosaic Virus Refined to 1.4 A Resolution Using Non- Crystallographic Symmetry Restraints within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Na204

b:64.6
occ:1.00
 OD1 E:ASP68 2.3 39.1 1.0
O F:HOH423 2.7 34.2 0.5
O F:HOH325 2.9 27.7 1.0
NA F:NA203 3.1 68.0 1.0
CG E:ASP68 3.3 35.0 1.0
CB F:SER69 3.5 27.2 1.0
OD2 E:ASP68 3.6 50.5 1.0
OD1 F:ASP68 3.6 39.0 1.0
OD2 F:ASP68 3.7 50.6 1.0
CG F:ASP68 3.9 35.0 1.0
NA E:NA205 3.9 0.6 1.0
CA E:ARG66 3.9 24.3 1.0
N F:SER69 4.0 26.3 1.0
O E:HOH334 4.1 25.6 1.0
OG F:SER69 4.1 26.3 1.0
CA E:ALA63 4.1 28.9 1.0
C E:ARG66 4.2 25.4 1.0
CA F:SER69 4.3 26.2 1.0
CB E:ALA63 4.4 30.1 1.0
O E:ARG66 4.5 25.1 1.0
O E:ALA63 4.5 27.6 1.0
O F:HOH305 4.6 51.9 1.0
N E:ASP68 4.7 26.6 1.0
N E:THR67 4.7 24.9 1.0
CB E:ARG66 4.7 24.9 1.0
CB E:ASP68 4.7 28.9 1.0
C F:ASP68 4.7 27.6 1.0
N E:ARG66 4.8 23.8 1.0
C E:ALA63 4.9 27.9 1.0
O E:HOH432 4.9 49.9 1.0

Sodium binding site 7 out of 17 in 4oq9

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Sodium binding site 7 out of 17 in the Satellite Tobacco Mosaic Virus Refined to 1.4 A Resolution Using Non- Crystallographic Symmetry Restraints


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of Satellite Tobacco Mosaic Virus Refined to 1.4 A Resolution Using Non- Crystallographic Symmetry Restraints within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Na205

b:0.6
occ:1.00
 OD2 F:ASP68 2.2 50.6 1.0
OD2 E:ASP68 2.4 50.5 1.0
O E:HOH496 2.9 41.2 0.5
O E:HOH432 3.1 49.9 1.0
O F:HOH512 3.2 47.5 0.5
CG F:ASP68 3.4 35.0 1.0
O F:HOH423 3.5 34.2 0.5
CG E:ASP68 3.5 35.0 1.0
OD1 F:ASP68 3.8 39.0 1.0
OD1 E:ASP68 3.9 39.1 1.0
NA E:NA204 3.9 64.6 1.0
O F:HOH488 3.9 65.4 1.0
NA F:NA203 4.0 68.0 1.0
O E:HOH518 4.1 53.3 1.0
O E:HOH491 4.2 75.4 1.0
CB F:ASP68 4.6 29.1 1.0
CB E:ASP68 4.7 28.9 1.0

Sodium binding site 8 out of 17 in 4oq9

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Sodium binding site 8 out of 17 in the Satellite Tobacco Mosaic Virus Refined to 1.4 A Resolution Using Non- Crystallographic Symmetry Restraints


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of Satellite Tobacco Mosaic Virus Refined to 1.4 A Resolution Using Non- Crystallographic Symmetry Restraints within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Na203

b:68.0
occ:1.00
 OD1 F:ASP68 2.5 39.0 1.0
O E:HOH334 2.8 25.6 1.0
O E:HOH432 2.8 49.9 1.0
NA E:NA204 3.1 64.6 1.0
CG F:ASP68 3.5 35.0 1.0
OD1 E:ASP68 3.5 39.1 1.0
CB E:SER69 3.5 27.2 1.0
OD2 F:ASP68 3.7 50.6 1.0
CA F:ARG66 3.8 24.5 1.0
OD2 E:ASP68 3.8 50.5 1.0
O F:HOH325 3.8 27.7 1.0
CG E:ASP68 3.9 35.0 1.0
N E:SER69 3.9 26.8 1.0
OG E:SER69 3.9 26.4 1.0
C F:ARG66 4.0 25.4 1.0
NA E:NA205 4.0 0.6 1.0
O F:ARG66 4.2 25.5 1.0
CA E:SER69 4.2 26.3 1.0
CA F:ALA63 4.4 28.9 1.0
CB F:ARG66 4.6 25.1 1.0
N F:THR67 4.6 25.0 1.0
N F:ASP68 4.7 26.3 1.0
O F:ALA63 4.7 27.5 1.0
C E:ASP68 4.7 27.6 1.0
CB F:ALA63 4.7 30.3 1.0
CB F:ASP68 4.8 29.1 1.0
N E:ASP68 4.8 26.6 1.0
N F:ARG66 4.8 23.9 1.0
O E:ARG66 4.9 25.1 1.0

Sodium binding site 9 out of 17 in 4oq9

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Sodium binding site 9 out of 17 in the Satellite Tobacco Mosaic Virus Refined to 1.4 A Resolution Using Non- Crystallographic Symmetry Restraints


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 9 of Satellite Tobacco Mosaic Virus Refined to 1.4 A Resolution Using Non- Crystallographic Symmetry Restraints within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Na203

b:66.2
occ:1.00
 OD1 G:ASP68 2.0 39.1 1.0
O G:HOH433 3.0 48.9 1.0
CG G:ASP68 3.1 35.1 1.0
O G:HOH331 3.5 28.6 1.0
OD2 G:ASP68 3.5 50.6 1.0
CA G:ARG66 3.7 24.6 1.0
C G:ARG66 3.7 25.4 1.0
O G:ARG66 4.0 25.0 1.0
N G:ASP68 4.2 26.5 1.0
N G:THR67 4.2 25.2 1.0
CA G:ALA63 4.3 28.8 1.0
CB G:ASP68 4.4 29.1 1.0
CB G:ARG66 4.5 24.9 1.0
N G:ARG66 4.7 24.4 1.0
CB G:ALA63 4.7 30.1 1.0
O G:ALA63 4.8 27.8 1.0
O G:HOH469 4.8 53.6 1.0
CA G:ASP68 4.8 27.8 1.0
N G:SER69 5.0 26.7 1.0

Sodium binding site 10 out of 17 in 4oq9

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Sodium binding site 10 out of 17 in the Satellite Tobacco Mosaic Virus Refined to 1.4 A Resolution Using Non- Crystallographic Symmetry Restraints


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 10 of Satellite Tobacco Mosaic Virus Refined to 1.4 A Resolution Using Non- Crystallographic Symmetry Restraints within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Na203

b:61.5
occ:1.00
 OD1 H:ASP68 2.4 39.3 1.0
CG H:ASP68 3.4 35.2 1.0
OD2 H:ASP68 3.7 50.5 1.0
O H:HOH325 3.8 23.7 1.0
CA H:ARG66 3.8 24.6 1.0
C H:ARG66 4.0 25.2 1.0
O H:ARG66 4.3 24.9 1.0
CA H:ALA63 4.3 29.0 1.0
N H:THR67 4.5 25.0 1.0
N H:ASP68 4.6 26.7 1.0
CB H:ALA63 4.6 30.2 1.0
CB H:ARG66 4.6 25.0 1.0
O H:ALA63 4.7 27.8 1.0
CB H:ASP68 4.7 28.8 1.0
N H:ARG66 4.8 23.9 1.0
O H:HOH461 4.9 44.6 1.0

Reference:

S.B.Larson, J.S.Day, A.Mcpherson. Satellite Tobacco Mosaic Virus Refined to 1.4 Angstrom Resolution. Acta Crystallogr.,Sect.D V. 70 2316 2014.
ISSN: ISSN 0907-4449
PubMed: 25195746
DOI: 10.1107/S1399004714013789
Page generated: Tue Dec 15 06:57:12 2020

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