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Sodium in PDB 4ofi: Crystal Structure of Duf (Kirre) D1

Protein crystallography data

The structure of Crystal Structure of Duf (Kirre) D1, PDB code: 4ofi 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) 37.50 / 2.30
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 74.330, 84.358, 82.633, 90.00, 115.27, 90.00
R / Rfree (%) 19.2 / 24.3

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Duf (Kirre) D1 (pdb code 4ofi). 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 Duf (Kirre) D1, PDB code: 4ofi:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 4ofi

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Sodium binding site 1 out of 4 in the Crystal Structure of Duf (Kirre) D1


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 Duf (Kirre) D1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na801

b:22.1
occ:1.00
 O A:PHE130 2.3 22.3 1.0
O A:TYR133 2.4 22.9 1.0
O A:ASN126 2.4 26.6 1.0
O A:LEU127 2.6 23.2 1.0
O A:HOH942 3.1 45.4 1.0
C A:PHE130 3.2 23.6 1.0
C A:LEU127 3.3 28.2 1.0
C A:TYR133 3.5 22.9 1.0
C A:ASN126 3.6 31.1 1.0
CB A:LEU127 3.7 18.8 1.0
N A:TYR133 3.9 23.7 1.0
CA A:LEU127 3.9 24.4 1.0
CA A:GLU131 3.9 26.4 1.0
N A:GLU131 3.9 24.7 1.0
C A:GLU131 4.1 22.6 1.0
CA A:PHE130 4.1 24.3 1.0
CA A:TYR133 4.2 22.3 1.0
N A:LEU127 4.2 31.1 1.0
N A:SER128 4.2 34.8 1.0
N A:PHE130 4.3 25.6 1.0
O A:GLU131 4.3 20.4 1.0
CB A:PHE130 4.4 21.2 1.0
CB A:TYR133 4.5 20.9 1.0
N A:ARG132 4.5 19.3 1.0
CA A:SER128 4.6 38.9 1.0
N A:SER134 4.6 21.8 1.0
CA A:ASN126 4.8 36.4 1.0
CA A:SER134 4.8 22.5 1.0
C A:ARG132 4.9 23.9 1.0

Sodium binding site 2 out of 4 in 4ofi

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Sodium binding site 2 out of 4 in the Crystal Structure of Duf (Kirre) D1


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 Duf (Kirre) D1 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na801

b:31.8
occ:1.00
 O C:PHE130 2.2 28.7 1.0
O C:TYR133 2.4 25.9 1.0
O C:ASN126 2.5 25.3 1.0
O C:HOH949 2.5 49.2 1.0
O C:LEU127 2.7 22.5 1.0
C C:PHE130 3.2 24.9 1.0
C C:LEU127 3.4 26.5 1.0
O C:HOH950 3.4 53.0 1.0
C C:TYR133 3.6 24.4 1.0
C C:ASN126 3.6 30.7 1.0
CB C:LEU127 3.7 23.4 1.0
N C:TYR133 3.9 26.1 1.0
CA C:LEU127 4.0 26.3 1.0
N C:GLU131 4.0 24.8 1.0
CA C:PHE130 4.1 23.2 1.0
CA C:GLU131 4.1 27.1 1.0
C C:GLU131 4.1 25.2 1.0
N C:PHE130 4.2 22.1 1.0
CA C:TYR133 4.2 23.6 1.0
N C:SER128 4.2 34.0 1.0
N C:LEU127 4.3 30.1 1.0
CB C:PHE130 4.3 18.9 1.0
O C:GLU131 4.4 22.1 1.0
N C:ARG132 4.5 25.8 1.0
CA C:SER128 4.5 40.1 1.0
CB C:TYR133 4.5 21.9 1.0
N C:SER134 4.6 24.9 1.0
CA C:ASN126 4.8 34.4 1.0
CA C:SER134 4.9 27.1 1.0
CG C:LEU127 4.9 22.1 1.0
C C:ARG132 4.9 23.8 1.0
C C:SER128 5.0 43.7 1.0

Sodium binding site 3 out of 4 in 4ofi

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Sodium binding site 3 out of 4 in the Crystal Structure of Duf (Kirre) D1


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 Duf (Kirre) D1 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Na801

b:34.8
occ:1.00
 O E:PHE130 2.2 36.1 1.0
O E:TYR133 2.3 30.1 1.0
O E:ASN126 2.3 32.0 1.0
O E:HOH934 2.5 34.4 1.0
O E:LEU127 2.7 38.6 1.0
C E:LEU127 3.3 39.1 1.0
C E:PHE130 3.3 38.1 1.0
O E:HOH917 3.4 42.7 1.0
C E:ASN126 3.5 37.6 1.0
C E:TYR133 3.5 29.4 1.0
CB E:LEU127 3.6 35.8 1.0
CA E:LEU127 3.8 38.0 1.0
N E:TYR133 4.0 28.8 1.0
N E:LEU127 4.1 37.5 1.0
N E:SER128 4.1 43.3 1.0
CA E:TYR133 4.2 28.2 1.0
C E:GLU131 4.2 37.8 1.0
N E:GLU131 4.2 40.1 1.0
O E:GLU131 4.2 36.3 1.0
CA E:PHE130 4.2 35.3 1.0
CA E:GLU131 4.3 42.6 1.0
N E:PHE130 4.4 38.9 1.0
CB E:PHE130 4.4 33.3 1.0
CB E:TYR133 4.5 27.9 1.0
CA E:SER128 4.5 48.0 1.0
N E:SER134 4.5 29.4 1.0
CA E:ASN126 4.6 46.2 1.0
N E:ARG132 4.7 29.5 1.0
CA E:SER134 4.8 29.0 1.0
CG E:LEU127 4.9 36.8 1.0
C E:SER128 5.0 49.2 1.0

Sodium binding site 4 out of 4 in 4ofi

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Sodium binding site 4 out of 4 in the Crystal Structure of Duf (Kirre) D1


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 Duf (Kirre) D1 within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Na801

b:41.1
occ:1.00
 O G:TYR133 2.3 33.7 1.0
O G:ASN126 2.4 54.8 1.0
O G:PHE130 2.4 35.8 1.0
O G:HOH924 2.5 43.0 1.0
O G:LEU127 2.6 41.0 1.0
C G:LEU127 3.2 45.0 1.0
C G:TYR133 3.4 34.1 1.0
C G:ASN126 3.4 56.9 1.0
C G:PHE130 3.4 37.3 1.0
CB G:LEU127 3.6 39.2 1.0
CA G:LEU127 3.8 45.2 1.0
N G:TYR133 3.9 30.1 1.0
N G:LEU127 4.0 51.6 1.0
N G:SER128 4.1 50.6 1.0
C G:GLU131 4.1 37.6 1.0
CA G:TYR133 4.1 30.9 1.0
CA G:GLU131 4.1 41.3 1.0
O G:GLU131 4.1 37.3 1.0
N G:GLU131 4.2 38.5 1.0
CA G:PHE130 4.4 39.6 1.0
CB G:TYR133 4.4 32.3 1.0
N G:SER134 4.5 35.5 1.0
CA G:SER128 4.5 55.2 1.0
N G:PHE130 4.5 42.5 1.0
CA G:ASN126 4.6 67.5 1.0
CB G:PHE130 4.6 38.6 1.0
N G:ARG132 4.7 33.7 1.0
CA G:SER134 4.7 38.2 1.0
CG G:LEU127 4.9 38.1 1.0
C G:ARG132 5.0 32.9 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 17:27:22 2024

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