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Sodium in PDB 7f0n: Structure of Deamidated Ubiquitin

Protein crystallography data

The structure of Structure of Deamidated Ubiquitin, PDB code: 7f0n was solved by K.Chauhan, N.Varshney, R.Das, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 35.24 / 1.60
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 48.01, 39.06, 35.29, 90, 93.12, 90
R / Rfree (%) 13.6 / 18.2

Other elements in 7f0n:

The structure of Structure of Deamidated Ubiquitin also contains other interesting chemical elements:

Potassium (K) 1 atom
Magnesium (Mg) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the Structure of Deamidated Ubiquitin (pdb code 7f0n). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 10 binding sites of Sodium where determined in the Structure of Deamidated Ubiquitin, PDB code: 7f0n:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Sodium binding site 1 out of 10 in 7f0n

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Sodium binding site 1 out of 10 in the Structure of Deamidated Ubiquitin


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of Deamidated Ubiquitin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na101

b:42.0
occ:1.00
 O A:HOH300 2.5 27.7 1.0
O A:HOH277 2.6 20.8 1.0
O A:HOH325 2.8 37.2 1.0
O A:HOH201 3.0 40.8 1.0
CD A:GLU64 3.4 18.1 1.0
OE2 A:GLU64 3.4 27.7 1.0
OE1 A:GLU64 3.6 24.8 1.0
CG A:GLU64 3.7 19.4 1.0
CD A:LYS63 4.1 21.6 1.0
O A:HOH322 4.2 42.0 1.0
NA A:NA107 4.4 36.7 1.0
CB A:LYS63 4.4 13.9 1.0
CG A:LYS63 4.5 15.6 1.0
CE A:LYS63 4.8 29.3 1.0
NZ A:LYS63 4.9 33.5 1.0
CB A:GLN2 5.0 15.9 1.0

Sodium binding site 2 out of 10 in 7f0n

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Sodium binding site 2 out of 10 in the Structure of Deamidated Ubiquitin


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structure of Deamidated Ubiquitin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na102

b:30.9
occ:1.00
 OD2 A:ASP58 2.6 13.4 1.0
O A:HOH344 2.7 34.7 1.0
O A:HOH273 2.8 20.0 1.0
CG A:ASP58 3.4 13.3 1.0
OD1 A:ASP58 3.4 13.4 1.0
O A:HOH218 4.0 38.6 1.0
CG2 A:THR55 4.2 11.9 1.0
OG1 A:THR55 4.2 13.3 1.0
O A:HOH241 4.3 18.0 1.0
O A:HOH319 4.4 42.9 1.0
N A:THR55 4.5 10.2 1.0
CA A:ARG54 4.6 11.3 1.0
O A:GLY53 4.7 16.4 1.0
CB A:THR55 4.8 11.7 1.0
CB A:ASP58 4.8 10.6 1.0
C A:ARG54 4.9 10.6 1.0

Sodium binding site 3 out of 10 in 7f0n

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Sodium binding site 3 out of 10 in the Structure of Deamidated Ubiquitin


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Structure of Deamidated Ubiquitin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na103

b:35.4
occ:1.00
 N A:GLY53 2.9 12.8 1.0
N A:ASP52 3.5 12.2 1.0
CA A:GLY53 3.6 11.8 1.0
CB A:GLU51 3.8 14.8 1.0
C A:GLU51 3.9 12.9 1.0
C A:ASP52 4.0 12.0 1.0
OE2 A:GLU51 4.1 45.5 1.0
CA A:ASP52 4.1 12.2 1.0
CB A:ASP52 4.2 15.7 1.0
CA A:GLU51 4.3 13.4 1.0
O A:GLU51 4.4 12.1 1.0
O A:HOH299 4.5 21.2 1.0
C A:GLY53 4.5 13.3 1.0
O A:HOH330 4.5 36.8 1.0
CD A:GLU51 4.6 36.3 1.0
N A:ARG54 4.6 11.8 1.0
CG A:GLU51 4.6 21.9 1.0

Sodium binding site 4 out of 10 in 7f0n

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Sodium binding site 4 out of 10 in the Structure of Deamidated Ubiquitin


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Structure of Deamidated Ubiquitin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na104

b:25.9
occ:0.50
 O A:HOH358 2.8 21.8 1.0
OG A:SER57 2.8 11.8 0.6
CB A:SER57 3.7 10.1 0.6
CB A:SER57 3.8 9.8 0.4
OG A:SER57 3.9 10.5 0.4
CB A:PRO19 3.9 11.2 1.0
N A:SER20 3.9 11.2 1.0
O A:HOH287 4.0 16.3 1.0
CA A:SER20 4.1 12.1 1.0
C A:PRO19 4.2 10.7 1.0
CB A:SER20 4.3 14.1 1.0
O A:PRO19 4.4 12.5 1.0
O A:HOH241 4.6 18.0 1.0
CA A:PRO19 4.7 10.8 1.0

Sodium binding site 5 out of 10 in 7f0n

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Sodium binding site 5 out of 10 in the Structure of Deamidated Ubiquitin


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Structure of Deamidated Ubiquitin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na105

b:35.0
occ:1.00
 O A:HOH338 2.8 33.8 1.0
CB A:GLU24 3.5 14.0 1.0
O A:ASP52 3.6 13.7 1.0
CB A:ASP52 3.6 15.7 1.0
C A:ASP52 3.6 12.0 1.0
O A:HOH372 3.6 32.5 1.0
O A:HOH208 3.7 39.5 1.0
N A:GLY53 3.8 12.8 1.0
CA A:GLY53 3.8 11.8 1.0
OE1 A:GLU24 3.9 34.9 0.7
CG A:GLU24 3.9 20.8 1.0
CD A:GLU24 4.2 24.9 0.4
CA A:ASP52 4.4 12.2 1.0
O A:HOH226 4.6 20.6 1.0
CG A:ASP52 4.6 16.1 1.0
CA A:GLU24 4.8 10.4 1.0
OD2 A:ASP52 4.8 21.6 1.0

Sodium binding site 6 out of 10 in 7f0n

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Sodium binding site 6 out of 10 in the Structure of Deamidated Ubiquitin


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Structure of Deamidated Ubiquitin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na106

b:41.3
occ:1.00
 CB A:ASP32 2.2 10.8 1.0
O A:HOH340 2.6 36.6 1.0
CA A:ASP32 2.9 10.2 1.0
CG A:ASP32 3.0 17.5 1.0
O A:ASP32 3.2 13.8 1.0
C A:ASP32 3.2 11.3 1.0
OD2 A:ASP32 3.6 23.4 1.0
OD1 A:ASP32 3.7 19.6 1.0
N A:LYS33 4.0 9.5 1.0
O A:HOH205 4.0 19.1 1.0
O A:HOH335 4.0 36.8 1.0
N A:ASP32 4.3 9.1 1.0
O A:HOH267 4.4 21.7 1.0
CA A:LYS33 4.9 9.1 1.0

Sodium binding site 7 out of 10 in 7f0n

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Sodium binding site 7 out of 10 in the Structure of Deamidated Ubiquitin


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of Structure of Deamidated Ubiquitin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na107

b:36.7
occ:1.00
 OE1 A:GLN2 1.9 16.9 1.0
O A:HOH300 2.3 27.7 1.0
OE2 A:GLU64 2.6 27.7 1.0
CB A:GLN2 2.8 15.9 1.0
CD A:GLN2 2.8 18.5 1.0
CZ A:PHE4 3.0 16.0 1.0
CG A:GLN2 3.1 20.7 1.0
CD A:GLU64 3.4 18.1 1.0
OE1 A:GLU64 3.5 24.8 1.0
CE1 A:PHE4 3.5 15.7 1.0
CE2 A:PHE4 3.9 16.8 1.0
NE2 A:GLN2 4.1 20.6 1.0
CA A:GLN2 4.2 13.3 1.0
NA A:NA101 4.4 42.0 1.0
C A:GLN2 4.5 9.8 1.0
O A:GLN2 4.7 9.8 1.0
CD1 A:PHE4 4.8 11.1 1.0
CG A:GLU64 4.8 19.4 1.0
O A:HOH277 4.9 20.8 1.0
CG2 A:THR14 4.9 16.2 1.0
O A:HOH201 4.9 40.8 1.0

Sodium binding site 8 out of 10 in 7f0n

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Sodium binding site 8 out of 10 in the Structure of Deamidated Ubiquitin


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of Structure of Deamidated Ubiquitin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na108

b:34.8
occ:1.00
 OE1 A:GLU64 2.8 24.8 1.0
O A:HOH201 3.0 40.8 1.0
CD A:GLU64 3.6 18.1 1.0
CG A:GLU64 3.8 19.4 1.0
CB A:GLU64 4.1 13.6 1.0
O A:HOH325 4.5 37.2 1.0
OE2 A:GLU64 4.7 27.7 1.0
O A:HOH302 4.9 40.4 1.0

Sodium binding site 9 out of 10 in 7f0n

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Sodium binding site 9 out of 10 in the Structure of Deamidated Ubiquitin


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 9 of Structure of Deamidated Ubiquitin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na109

b:52.3
occ:1.00
 O A:HOH254 2.3 27.5 1.0
O A:HOH333 3.3 33.9 1.0
CE A:LYS48 3.8 28.4 1.0
O A:HOH296 4.6 26.7 1.0
NZ A:LYS48 4.7 33.1 1.0
CG A:LYS48 4.8 18.6 1.0
O A:ALA46 4.8 13.8 1.0
CD A:LYS48 5.0 20.9 1.0

Sodium binding site 10 out of 10 in 7f0n

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Sodium binding site 10 out of 10 in the Structure of Deamidated Ubiquitin


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 10 of Structure of Deamidated Ubiquitin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na110

b:30.0
occ:1.00
 OD1 A:ASP32 2.6 19.6 1.0
O A:HOH207 2.6 40.1 1.0
O A:HOH257 2.7 27.1 1.0
O A:ALA28 3.0 7.3 1.0
OE1 A:GLN31 3.2 13.2 1.0
O A:HOH243 3.5 38.2 1.0
CG A:ASP32 3.5 17.5 1.0
C A:ALA28 3.8 7.5 1.0
CB A:GLN31 3.9 8.9 1.0
CA A:ALA28 3.9 6.6 1.0
CD A:GLN31 3.9 9.5 1.0
CB A:ALA28 4.0 8.9 1.0
O A:HOH353 4.1 32.2 1.0
CG A:GLN31 4.1 8.4 1.0
N A:ASP32 4.2 9.1 1.0
OD2 A:ASP32 4.2 23.4 1.0
O A:HOH232 4.3 31.1 1.0
C A:GLN31 4.6 8.2 1.0
CB A:ASP32 4.6 10.8 1.0
CA A:ASP32 4.6 10.2 1.0
CA A:GLN31 4.7 8.0 1.0
O A:HOH283 4.8 40.4 1.0
O A:HOH339 4.8 29.8 1.0
N A:LYS29 5.0 7.0 1.0

Reference:

R.Rashmi, P.Mohanty, R.Aravind, K.Chauhan, N.Varshney, R.Das. Structure of Deamidated Ubiquitin To Be Published.
Page generated: Mon Aug 18 09:46:44 2025

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