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Sodium in PDB 4of8: Crystal Structure of Rst D1-D2

Protein crystallography data

The structure of Crystal Structure of Rst D1-D2, PDB code: 4of8 was solved by E.Ozkan, K.C.Garcia, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 44.57 / 1.90
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 59.941, 77.935, 121.097, 90.00, 95.44, 90.00
R / Rfree (%) 17.3 / 20.8

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Rst D1-D2 (pdb code 4of8). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Crystal Structure of Rst D1-D2, PDB code: 4of8:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 4of8

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Sodium binding site 1 out of 4 in the Crystal Structure of Rst D1-D2


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 Rst D1-D2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na301

b:20.6
occ:1.00
 O A:PHE76 2.1 15.8 1.0
O A:ASP72 2.3 21.1 1.0
O A:TYR79 2.4 19.5 1.0
O A:HOH401 2.4 19.6 1.0
O A:LEU73 2.5 17.7 1.0
O A:HOH402 2.5 41.2 1.0
C A:LEU73 3.1 18.8 1.0
C A:PHE76 3.2 18.0 1.0
C A:ASP72 3.5 20.9 1.0
C A:TYR79 3.5 16.3 1.0
CB A:LEU73 3.6 18.9 1.0
O A:HOH451 3.6 28.2 1.0
CA A:LEU73 3.8 15.2 1.0
N A:SER74 4.0 24.9 1.0
N A:TYR79 4.0 13.3 1.0
N A:LEU73 4.1 17.8 1.0
N A:GLU77 4.1 16.4 1.0
CA A:PHE76 4.1 16.5 1.0
CA A:GLU77 4.1 25.0 1.0
N A:PHE76 4.2 17.0 1.0
CA A:TYR79 4.2 14.5 1.0
C A:GLU77 4.3 19.8 1.0
CB A:PHE76 4.4 17.9 1.0
O B:HOH520 4.4 46.5 1.0
O A:HOH426 4.4 25.8 1.0
CA A:SER74 4.4 24.2 1.0
O A:HOH547 4.5 44.1 1.0
O A:GLU77 4.5 25.6 1.0
N A:ALA80 4.6 14.6 1.0
CB A:TYR79 4.6 15.3 1.0
N A:ARG78 4.7 17.9 1.0
CA A:ASP72 4.7 19.0 1.0
CA A:ALA80 4.8 14.6 1.0
CG A:LEU73 4.9 18.6 1.0
C A:SER74 5.0 26.4 1.0

Sodium binding site 2 out of 4 in 4of8

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Sodium binding site 2 out of 4 in the Crystal Structure of Rst D1-D2


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 Rst D1-D2 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na301

b:19.9
occ:1.00
 O B:PHE76 2.3 18.2 1.0
O B:TYR79 2.3 19.7 1.0
O B:ASP72 2.4 27.9 1.0
O B:HOH402 2.4 40.7 1.0
O B:LEU73 2.4 20.2 1.0
O B:HOH401 2.5 25.6 1.0
C B:LEU73 3.2 26.1 1.0
C B:PHE76 3.3 20.9 1.0
C B:TYR79 3.5 20.1 1.0
C B:ASP72 3.5 19.6 1.0
CB B:LEU73 3.6 17.8 1.0
O B:HOH570 3.7 34.4 1.0
CA B:LEU73 3.8 19.0 1.0
N B:TYR79 3.9 20.8 1.0
CA B:GLU77 4.0 26.5 1.0
N B:GLU77 4.1 18.5 1.0
N B:LEU73 4.1 19.5 1.0
N B:SER74 4.1 32.2 1.0
CA B:TYR79 4.1 19.6 1.0
C B:GLU77 4.2 24.1 1.0
CA B:PHE76 4.2 22.5 1.0
N B:PHE76 4.2 22.2 1.0
O B:GLU77 4.4 24.5 1.0
CB B:PHE76 4.4 21.9 1.0
CB B:TYR79 4.5 19.2 1.0
CA B:SER74 4.5 35.0 1.0
N B:ALA80 4.5 19.1 1.0
N B:ARG78 4.6 17.5 1.0
O B:HOH447 4.6 31.5 1.0
CA B:ASP72 4.8 26.3 1.0
CA B:ALA80 4.8 17.1 1.0
O B:HOH476 4.9 33.3 1.0
CG B:LEU73 4.9 17.8 1.0
O2 B:GOL302 4.9 57.6 1.0
C B:SER74 4.9 27.2 1.0

Sodium binding site 3 out of 4 in 4of8

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Sodium binding site 3 out of 4 in the Crystal Structure of Rst D1-D2


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 Rst D1-D2 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na301

b:23.4
occ:1.00
 O C:PHE76 2.2 19.1 1.0
O C:TYR79 2.3 20.2 1.0
O C:HOH402 2.4 23.9 1.0
O C:ASP72 2.4 25.7 1.0
O C:LEU73 2.5 20.3 1.0
O C:HOH401 2.5 39.8 1.0
C C:PHE76 3.2 20.7 1.0
C C:LEU73 3.2 23.2 1.0
C C:TYR79 3.5 20.9 1.0
C C:ASP72 3.6 22.1 1.0
CB C:LEU73 3.6 20.8 1.0
O C:HOH449 3.7 29.1 1.0
CA C:LEU73 3.8 21.2 1.0
N C:TYR79 4.0 18.2 1.0
N C:GLU77 4.0 18.3 1.0
CA C:GLU77 4.0 25.8 1.0
N C:SER74 4.1 30.1 1.0
CA C:PHE76 4.1 19.2 1.0
N C:LEU73 4.2 20.6 1.0
C C:GLU77 4.2 24.4 1.0
CA C:TYR79 4.2 21.1 1.0
O C:HOH625 4.2 35.0 1.0
N C:PHE76 4.2 21.0 1.0
CB C:PHE76 4.3 18.6 1.0
CA C:SER74 4.4 34.0 1.0
O C:GLU77 4.4 26.9 1.0
O C:HOH460 4.6 32.3 1.0
CB C:TYR79 4.6 22.5 1.0
N C:ALA80 4.6 20.4 1.0
N C:ARG78 4.6 21.9 1.0
O C:HOH520 4.7 40.5 1.0
CA C:ASP72 4.8 25.2 1.0
CA C:ALA80 4.8 18.9 1.0
C C:SER74 4.9 31.5 1.0
CG C:LEU73 4.9 17.5 1.0

Sodium binding site 4 out of 4 in 4of8

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Sodium binding site 4 out of 4 in the Crystal Structure of Rst D1-D2


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 Rst D1-D2 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na301

b:19.5
occ:1.00
 O D:PHE76 2.2 19.0 1.0
O D:TYR79 2.3 19.3 1.0
O D:LEU73 2.4 23.2 1.0
O D:ASP72 2.4 24.4 1.0
O D:HOH401 2.5 21.4 1.0
O D:HOH402 2.5 36.1 1.0
C D:LEU73 3.1 25.5 1.0
C D:PHE76 3.3 19.1 1.0
C D:TYR79 3.5 21.0 1.0
CB D:LEU73 3.5 18.8 1.0
C D:ASP72 3.5 19.1 1.0
CA D:LEU73 3.7 20.2 1.0
N D:TYR79 3.9 18.0 1.0
N D:LEU73 4.1 17.1 1.0
N D:SER74 4.1 27.4 1.0
O D:HOH599 4.1 35.0 1.0
CA D:TYR79 4.1 15.0 1.0
N D:GLU77 4.1 18.7 1.0
CA D:PHE76 4.1 19.5 1.0
CA D:GLU77 4.2 23.9 1.0
C D:GLU77 4.2 20.3 1.0
N D:PHE76 4.2 22.8 1.0
CB D:PHE76 4.3 21.4 1.0
O D:GLU77 4.4 25.8 1.0
CA D:SER74 4.4 37.0 1.0
CB D:TYR79 4.4 14.2 1.0
O D:HOH428 4.5 29.2 1.0
N D:ALA80 4.5 20.8 1.0
O D:HOH469 4.6 36.0 1.0
N D:ARG78 4.6 17.9 1.0
CA D:ALA80 4.8 20.7 1.0
CG D:LEU73 4.8 20.0 1.0
CA D:ASP72 4.8 23.4 1.0
C D:SER74 4.9 19.0 1.0
CB D:ALA80 5.0 19.7 1.0

Reference:

E.Ozkan, P.H.Chia, R.R.Wang, N.Goriatcheva, D.Borek, Z.Otwinowski, T.Walz, K.Shen, K.C.Garcia. Extracellular Architecture of the Syg-1/Syg-2 Adhesion Complex Instructs Synaptogenesis. Cell(Cambridge,Mass.) V. 156 482 2014.
ISSN: ISSN 0092-8674
PubMed: 24485456
DOI: 10.1016/J.CELL.2014.01.004
Page generated: Mon Oct 7 17:26:56 2024

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