Sodium in PDB 9c7a: Crystal Structure of R149W Neurodevelopmental Disease-Associated U2AF2 Variant

The structure of Crystal Structure of R149W Neurodevelopmental Disease-Associated U2AF2 Variant, PDB code: 9c7a was solved by D.Maji, J.L.Jenkins, C.L.Kielkopf, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	38.78 / 1.40
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	43.25, 63.131, 77.559, 90, 90, 90
R / Rfree (%)	13 / 15.9

The structure of Crystal Structure of R149W Neurodevelopmental Disease-Associated U2AF2 Variant also contains other interesting chemical elements:

Bromine

(Br)

1 atom

The binding sites of Sodium atom in the Crystal Structure of R149W Neurodevelopmental Disease-Associated U2AF2 Variant (pdb code 9c7a). 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 R149W Neurodevelopmental Disease-Associated U2AF2 Variant, PDB code: 9c7a:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of R149W Neurodevelopmental Disease-Associated U2AF2 Variant


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 R149W Neurodevelopmental Disease-Associated U2AF2 Variant within 5.0Å range: probe atom residue distance (Å) B Occ A:Na402 b:33.9 occ:1.00 OD1 A:ASN155 2.7 18.3 1.0 OD1 A:ASN196 2.8 36.9 1.0 O A:HOH611 2.8 29.6 1.0 HD2 A:LYS292 3.1 32.3 1.0 O4 B:U6 3.1 22.4 1.0 HA A:ASN155 3.1 17.5 1.0 O A:HOH659 3.2 57.0 1.0 HA2 A:GLY297 3.2 27.7 1.0 HD3 A:LYS292 3.3 32.3 1.0 H3 B:U6 3.4 26.2 1.0 O A:HOH505 3.5 48.9 1.0 HD22 A:ASN196 3.6 43.1 1.0 CD A:LYS292 3.6 26.9 1.0 CG A:ASN196 3.6 35.4 1.0 HZ3 A:LYS292 3.8 34.3 1.0 CG A:ASN155 3.8 15.0 1.0 HA3 A:GLY297 3.8 27.7 1.0 HZ2 A:LYS292 3.9 34.3 1.0 ND2 A:ASN196 3.9 36.0 1.0 C4 B:U6 4.0 20.2 1.0 CA A:GLY297 4.0 23.1 1.0 CA A:ASN155 4.0 14.6 1.0 N3 B:U6 4.0 21.9 1.0 O A:HOH662 4.1 51.0 1.0 OE1 A:GLN222 4.1 29.6 0.5 HB2 A:LYS292 4.2 24.1 1.0 NZ A:LYS292 4.2 28.6 1.0 HE1 A:PHE158 4.2 40.5 0.5 HB3 A:LYS292 4.3 24.1 1.0 CB A:ASN155 4.4 13.8 1.0 O A:GLY297 4.5 26.1 1.0 HB2 A:ASN155 4.5 16.5 1.0 C A:ASN155 4.5 14.5 1.0 CE A:LYS292 4.6 26.3 1.0 CB A:LYS292 4.6 20.1 1.0 CG A:LYS292 4.7 24.2 1.0 HD21 A:ASN196 4.7 43.1 1.0 C A:GLY297 4.7 22.4 1.0 O B:HOH103 4.8 18.4 1.0 H A:ASN155 4.8 17.2 1.0 CE1 A:PHE158 4.8 33.7 0.5 CB A:ASN196 4.9 29.9 1.0 O A:ASN155 4.9 15.3 1.0 O A:ILE156 4.9 19.2 1.0 OE1 A:GLN222 4.9 34.2 0.5 ND2 A:ASN155 4.9 15.0 1.0 HE22 A:GLN222 4.9 38.1 0.5 HB3 A:ASN196 5.0 35.9 1.0 N A:ASN155 5.0 14.3 1.0 HB2 A:ASN196 5.0 35.9 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of R149W Neurodevelopmental Disease-Associated U2AF2 Variant


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 R149W Neurodevelopmental Disease-Associated U2AF2 Variant within 5.0Å range: probe atom residue distance (Å) B Occ A:Na403 b:37.9 occ:1.00 O A:HOH533 2.2 48.9 1.0 O A:SER294 2.3 26.6 1.0 O B:HOH130 2.5 50.6 1.0 O2 B:U6 2.5 22.3 1.0 O A:LYS195 2.9 35.8 1.0 HB3 A:ASN196 3.1 35.9 1.0 HA A:LYS195 3.3 41.9 1.0 C A:SER294 3.5 24.3 1.0 C A:LYS195 3.6 33.2 1.0 HB2 A:ASN196 3.6 35.9 1.0 C2 B:U6 3.6 20.4 1.0 HB2 A:SER294 3.6 34.7 1.0 O A:HOH662 3.6 51.0 1.0 O A:HOH504 3.7 24.0 1.0 CB A:ASN196 3.8 29.9 1.0 H3 B:U6 3.9 26.2 1.0 HA A:ALA295 3.9 30.5 1.0 HA A:SER294 4.0 30.0 1.0 CA A:LYS195 4.0 34.9 1.0 H1' B:U6 4.1 17.9 1.0 CA A:SER294 4.2 25.0 1.0 N3 B:U6 4.2 21.9 1.0 O A:HOH611 4.2 29.6 1.0 CB A:SER294 4.4 28.9 1.0 HB3 A:LYS195 4.4 44.2 1.0 N A:ASN196 4.5 27.0 1.0 N A:ALA295 4.5 24.1 1.0 O A:ASP194 4.5 39.1 1.0 CA A:ALA295 4.6 25.4 1.0 CG A:ASN196 4.7 35.4 1.0 N1 B:U6 4.7 16.1 1.0 CA A:ASN196 4.7 26.5 1.0 OD1 A:ASN196 4.8 36.9 1.0 CB A:LYS195 4.8 36.9 1.0 C1' B:U6 4.9 14.9 1.0

D.Maji, J.L.Jenkins, P.L.Boutz, C.L.Kielkopf. Recurrent Neurodevelopmentally-Associated Variants of the Pre-Mrna Splicing Factor U2AF2 Alter Rna Binding Affinities and Interactions To Be Published.