Sodium in PDB 6gd1: Structure of Hur RRM3

The structure of Structure of Hur RRM3, PDB code: 6gd1 was solved by M.Pabis, M.Sattler, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	8.98 / 2.01
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	42.920, 67.660, 70.140, 90.00, 91.01, 90.00
R / Rfree (%)	17.6 / 24.4

The binding sites of Sodium atom in the Structure of Hur RRM3 (pdb code 6gd1). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Structure of Hur RRM3, PDB code: 6gd1:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the Structure of Hur RRM3


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of Hur RRM3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na201 b:59.7 occ:1.00 O A:ALA139 2.7 26.1 1.0 OE1 A:GLU167 2.7 46.3 1.0 N A:ASN164 3.2 40.8 1.0 N A:THR163 3.2 42.7 1.0 N A:ALA139 3.3 41.1 1.0 C A:ALA139 3.5 36.0 1.0 CE A:MET162 3.7 35.4 1.0 CD A:GLU167 3.7 52.4 1.0 CB A:MET162 3.7 32.3 1.0 ND2 A:ASN164 3.8 43.1 1.0 CA A:ALA139 3.8 44.8 1.0 C A:MET162 3.8 37.3 1.0 C A:GLY138 3.8 38.9 1.0 CB A:GLU167 3.8 45.1 1.0 CA A:THR163 3.9 44.3 1.0 CA A:MET162 4.0 38.1 1.0 C A:THR163 4.0 47.5 1.0 CB A:THR163 4.0 50.4 1.0 O A:ASN164 4.1 53.5 1.0 CB A:ALA139 4.1 46.5 1.0 CA A:GLY138 4.1 35.9 1.0 CA A:ASN164 4.2 40.3 1.0 CB A:ASN164 4.2 41.8 1.0 CG A:MET162 4.3 36.0 1.0 CG A:ASN164 4.3 47.2 1.0 CG A:GLU167 4.4 48.4 1.0 O A:GLY138 4.5 40.2 1.0 OG1 A:THR163 4.6 42.5 1.0 C A:ASN164 4.6 44.8 1.0 OE2 A:GLU167 4.6 57.7 1.0 O A:MET162 4.7 38.8 1.0 SD A:MET162 4.7 34.2 1.0 N A:VAL140 4.7 38.8 1.0

Sodium binding site 2 out of 4 in the Structure of Hur RRM3


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structure of Hur RRM3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na202 b:46.5 occ:1.00 OD2 A:ASP61 2.6 42.8 1.0 ND2 A:ASN59 2.9 31.2 1.0 N A:GLU30 3.1 32.6 1.0 CB A:GLU30 3.4 40.3 1.0 O A:HOH351 3.4 61.0 1.0 OD1 A:ASN59 3.5 32.9 1.0 CG A:ASP61 3.5 37.1 1.0 CG A:ASN59 3.6 30.9 1.0 CB A:ASP61 3.7 38.6 1.0 CA A:GLU30 3.8 34.1 1.0 O A:HOH314 3.9 36.9 1.0 CA A:ALA29 4.0 26.8 1.0 CB A:ALA29 4.0 28.4 1.0 C A:ALA29 4.0 31.5 1.0 NE2 A:GLN62 4.3 54.5 1.0 CG A:GLU30 4.6 50.3 1.0 OD1 A:ASP61 4.6 41.7 1.0 CA A:ASP61 4.9 35.2 1.0 OE1 A:GLU30 4.9 53.7 1.0 N A:ASP61 5.0 35.5 1.0 C A:GLU30 5.0 34.0 1.0

Sodium binding site 3 out of 4 in the Structure of Hur RRM3


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Structure of Hur RRM3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na203 b:47.8 occ:1.00 O A:HOH391 2.8 34.5 1.0 O A:HOH411 2.9 35.1 1.0 O A:HOH370 3.0 23.6 1.0 O A:THR141 3.5 41.5 1.0 O A:THR89 3.7 23.8 1.0 CZ2 A:TRP131 3.7 26.9 1.0 CB B:PRO136 4.0 26.0 1.0 CG B:PRO136 4.1 25.8 1.0 CH2 A:TRP131 4.2 28.9 1.0 OD1 A:ASN142 4.2 49.7 1.0 O A:HOH360 4.3 43.3 1.0 CB A:THR89 4.4 27.0 1.0 C A:THR141 4.4 37.5 1.0 O B:HOH421 4.4 38.7 1.0 CA A:ASN142 4.4 34.4 1.0 C A:THR89 4.6 25.6 1.0 O A:HOH336 4.7 28.5 1.0 CA B:PRO136 4.7 24.2 1.0 N A:THR89 4.7 24.7 1.0 N A:ASN142 4.8 34.6 1.0 CA A:THR89 4.8 24.4 1.0 CE2 A:TRP131 4.9 24.5 1.0 O A:HOH408 5.0 34.7 1.0

Sodium binding site 4 out of 4 in the Structure of Hur RRM3


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Structure of Hur RRM3 within 5.0Å range: probe atom residue distance (Å) B Occ B:Na201 b:30.8 occ:1.00 OE1 B:GLU167 2.6 34.8 1.0 O B:ALA139 2.7 26.9 1.0 N B:ASN164 3.1 24.0 1.0 N B:ALA139 3.3 24.3 1.0 N B:THR163 3.3 24.6 1.0 C B:ALA139 3.6 28.2 1.0 CB B:GLU167 3.6 25.2 1.0 CD B:GLU167 3.7 31.4 1.0 CA B:ALA139 3.7 26.6 1.0 CB B:ASN164 3.7 24.3 1.0 ND2 B:ASN164 3.7 26.8 1.0 CB B:MET162 3.7 21.3 1.0 CE B:MET162 3.7 24.2 1.0 CB B:ALA139 3.8 28.3 1.0 O B:ASN164 3.8 24.9 1.0 CA B:ASN164 3.8 26.3 1.0 C B:MET162 3.9 26.7 1.0 CA B:THR163 3.9 27.6 1.0 C B:THR163 4.0 27.8 1.0 C B:GLY138 4.0 26.8 1.0 CG B:ASN164 4.0 28.1 1.0 CA B:MET162 4.1 22.8 1.0 CB B:THR163 4.1 26.8 1.0 CG B:GLU167 4.2 29.5 1.0 C B:ASN164 4.3 26.5 1.0 CG B:MET162 4.5 21.9 1.0 CA B:GLY138 4.5 26.2 1.0 OG1 B:THR163 4.6 24.0 1.0 O B:GLY138 4.7 29.4 1.0 OE2 B:GLU167 4.7 36.3 1.0 O B:HOH337 4.7 46.1 1.0 SD B:MET162 4.8 23.9 1.0 O B:MET162 4.8 26.0 1.0 N B:VAL140 4.8 25.0 1.0 CA B:GLU167 4.9 26.2 1.0 N B:ALA168 4.9 24.2 1.0 OD1 B:ASN164 5.0 28.3 1.0

M.Pabis, G.M.Popowicz, R.Stehle, D.Fernandez-Ramos, S.Asami, L.Warner, S.M.Garcia-Maurino, A.Schlundt, M.L.Martinez-Chantar, I.Diaz-Moreno, M.Sattler. Hur Biological Function Involves RRM3-Mediated Dimerization and Rna Binding By All Three Rrms. Nucleic Acids Res. V. 47 1011 2019.
ISSN: ESSN 1362-4962
PubMed: 30418581
DOI: 10.1093/NAR/GKY1138