Sodium in PDB 4q04: Crystal Structure of URE3-Bp From Entomaeba Histolytica Without Calcium

The structure of Crystal Structure of URE3-Bp From Entomaeba Histolytica Without Calcium, PDB code: 4q04 was solved by Seattle Structural Genomics Center For Infectious Disease (Ssgcid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 1.90
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	69.420, 69.420, 187.360, 90.00, 90.00, 90.00
R / Rfree (%)	18.2 / 23.9

The structure of Crystal Structure of URE3-Bp From Entomaeba Histolytica Without Calcium also contains other interesting chemical elements:

Magnesium

(Mg)

1 atom

The binding sites of Sodium atom in the Crystal Structure of URE3-Bp From Entomaeba Histolytica Without Calcium (pdb code 4q04). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structure of URE3-Bp From Entomaeba Histolytica Without Calcium, PDB code: 4q04:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of URE3-Bp From Entomaeba Histolytica Without Calcium


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 URE3-Bp From Entomaeba Histolytica Without Calcium within 5.0Å range: probe atom residue distance (Å) B Occ A:Na301 b:22.9 occ:1.00 O A:HOH496 2.0 36.7 1.0 OD1 A:ASP127 2.2 16.2 1.0 OD1 A:ASN129 2.3 24.5 1.0 O A:HOH497 2.3 23.8 1.0 O A:THR133 2.4 18.6 1.0 OG A:SER131 2.5 19.6 1.0 CG A:ASP127 3.4 16.5 1.0 CG A:ASN129 3.4 25.6 1.0 CB A:SER131 3.5 21.9 1.0 C A:THR133 3.6 18.9 1.0 N A:SER131 3.9 21.5 1.0 ND2 A:ASN129 3.9 27.2 1.0 CA A:ASP127 4.0 17.4 1.0 OG1 A:THR133 4.1 19.0 1.0 CB A:ASP127 4.2 16.4 1.0 N A:THR133 4.2 18.8 1.0 O A:HOH436 4.2 37.3 1.0 OD2 A:ASP127 4.2 16.6 1.0 C A:ASP127 4.2 18.3 1.0 CA A:SER131 4.3 21.9 1.0 N A:ASN129 4.3 22.6 1.0 OE1 A:GLU138 4.4 25.0 1.0 N A:ARG128 4.5 19.7 1.0 CA A:THR133 4.5 18.6 1.0 N A:LEU134 4.6 18.9 1.0 CA A:LEU134 4.6 20.2 1.0 CB A:ASN129 4.7 25.6 1.0 N A:ARG130 4.7 22.4 1.0 N A:GLY132 4.7 20.8 1.0 CD2 A:LEU134 4.7 18.5 1.0 O A:ASP127 4.8 18.6 1.0 C A:SER131 4.8 20.9 1.0 C A:ASN129 4.8 23.5 1.0 CA A:ASN129 4.8 23.9 1.0 CB A:THR133 5.0 18.7 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of URE3-Bp From Entomaeba Histolytica Without Calcium


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 URE3-Bp From Entomaeba Histolytica Without Calcium within 5.0Å range: probe atom residue distance (Å) B Occ B:Na301 b:14.7 occ:1.00 O B:HOH405 2.2 16.1 1.0 O B:THR133 2.3 16.9 1.0 O B:HOH432 2.4 16.6 1.0 OD1 B:ASN129 2.4 18.8 1.0 OD1 B:ASP127 2.4 19.4 1.0 OG B:SER131 2.5 18.3 1.0 CG B:ASN129 3.3 19.6 1.0 C B:THR133 3.5 16.7 1.0 ND2 B:ASN129 3.6 19.6 1.0 CG B:ASP127 3.6 18.9 1.0 CB B:SER131 3.7 19.3 1.0 O B:HOH419 3.7 12.8 1.0 CA B:ASP127 4.0 18.7 1.0 O B:HOH402 4.0 19.6 1.0 N B:SER131 4.1 19.1 1.0 OE1 B:GLU138 4.1 23.4 1.0 N B:THR133 4.2 16.5 1.0 CB B:ASP127 4.3 18.6 1.0 CA B:SER131 4.3 19.5 1.0 N B:LEU134 4.4 16.2 1.0 N B:GLY132 4.4 18.2 1.0 C B:ASP127 4.4 20.2 1.0 CA B:LEU134 4.4 16.4 1.0 OD2 B:ASP127 4.5 18.9 1.0 CA B:THR133 4.5 16.0 1.0 C B:SER131 4.7 19.0 1.0 N B:ASN129 4.7 20.7 1.0 CB B:ASN129 4.7 20.3 1.0 N B:ARG130 4.7 21.1 1.0 CD2 B:LEU134 4.7 16.3 1.0 N B:ARG128 4.8 21.5 1.0 OE2 B:GLU138 4.9 26.1 1.0 CD B:GLU138 4.9 23.5 1.0 O B:ASN126 4.9 17.4 1.0 O B:ASP127 4.9 19.1 1.0

T.E.Edwards, J.Abendroth, Seattle Structural Genomics Center For Infectious Disease. Crystal Structure of URE3-Bp From Entomaeba Histolytica To Be Published.