Sodium in PDB 7s3a: Crystal Structure of Intact U2AF65 Rrm-Region Bound to Adml-C5 Oligonucleotide

The structure of Crystal Structure of Intact U2AF65 Rrm-Region Bound to Adml-C5 Oligonucleotide, PDB code: 7s3a was solved by J.L.Jenkins, S.Henderson, C.L.Kielkopf, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	37.76 / 1.48
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	43.245, 63.022, 77.491, 90, 90, 90
R / Rfree (%)	13.1 / 15.7

The structure of Crystal Structure of Intact U2AF65 Rrm-Region Bound to Adml-C5 Oligonucleotide also contains other interesting chemical elements:

Bromine

(Br)

1 atom

The binding sites of Sodium atom in the Crystal Structure of Intact U2AF65 Rrm-Region Bound to Adml-C5 Oligonucleotide (pdb code 7s3a). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Crystal Structure of Intact U2AF65 Rrm-Region Bound to Adml-C5 Oligonucleotide, PDB code: 7s3a:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Crystal Structure of Intact U2AF65 Rrm-Region Bound to Adml-C5 Oligonucleotide


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 Intact U2AF65 Rrm-Region Bound to Adml-C5 Oligonucleotide within 5.0Å range: probe atom residue distance (Å) B Occ A:Na401 b:41.2 occ:1.00 O A:HOH537 2.2 42.8 1.0 O B:HOH231 2.2 37.4 1.0 O A:SER294 2.3 26.0 1.0 O2 B:U6 2.4 21.5 1.0 HB3 A:ASN196 2.8 33.5 1.0 O A:LYS195 2.9 30.9 1.0 O A:HOH608 3.0 50.1 1.0 HB2 A:ASN196 3.3 33.5 1.0 C A:SER294 3.4 23.0 1.0 HA A:LYS195 3.4 32.6 1.0 CB A:ASN196 3.5 27.9 1.0 HB3 A:SER294 3.5 27.4 0.6 C A:LYS195 3.5 27.4 1.0 HB2 A:SER294 3.5 31.0 0.4 C2 B:U6 3.5 19.5 1.0 H3 B:U6 3.7 24.7 1.0 HA A:SER294 3.8 26.5 0.6 HA A:SER294 3.8 27.8 0.4 O B:HOH206 4.0 24.1 1.0 CA A:LYS195 4.0 27.1 1.0 HA A:ALA295 4.0 26.6 1.0 CA A:SER294 4.0 22.1 0.6 CA A:SER294 4.0 23.2 0.4 N3 B:U6 4.1 20.6 1.0 CB A:SER294 4.2 22.8 0.6 H1' B:U6 4.2 19.7 1.0 CB A:SER294 4.3 25.8 0.4 N A:ASN196 4.3 25.3 1.0 CG A:ASN196 4.4 31.9 1.0 O A:ASP194 4.4 34.2 1.0 N A:ALA295 4.4 21.7 1.0 OD1 A:ASN196 4.5 34.1 1.0 CA A:ASN196 4.5 24.6 1.0 HG A:SER294 4.5 27.6 0.6 CA A:ALA295 4.6 22.2 1.0 N1 B:U6 4.7 17.5 1.0 OG A:SER294 4.9 23.0 0.6 HB3 A:SER294 4.9 31.0 0.4 CB A:LYS195 4.9 26.9 1.0 HB2 A:SER294 4.9 27.4 0.6 C1' B:U6 5.0 16.4 1.0

Sodium binding site 2 out of 3 in the Crystal Structure of Intact U2AF65 Rrm-Region Bound to Adml-C5 Oligonucleotide


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 Intact U2AF65 Rrm-Region Bound to Adml-C5 Oligonucleotide within 5.0Å range: probe atom residue distance (Å) B Occ A:Na402 b:31.9 occ:1.00 OD1 A:ASN155 2.8 15.3 1.0 OD1 A:ASN196 2.8 34.1 1.0 HA A:ASN155 3.0 16.1 1.0 O A:HOH617 3.0 39.8 1.0 O4 B:U6 3.0 22.0 1.0 HE22 A:GLN222 3.1 37.3 1.0 HA2 A:GLY297 3.3 27.8 1.0 HD21 A:ASN196 3.4 37.4 1.0 HG3 A:LYS292 3.5 31.1 1.0 H3 B:U6 3.5 24.7 1.0 O A:HOH608 3.5 50.1 1.0 CG A:ASN196 3.7 31.9 1.0 HZ2 A:LYS292 3.7 32.9 1.0 HZ3 A:LYS292 3.8 32.9 1.0 NE2 A:GLN222 3.9 31.1 1.0 CG A:ASN155 3.9 13.3 1.0 ND2 A:ASN196 3.9 31.2 1.0 CA A:ASN155 3.9 13.4 1.0 HA3 A:GLY297 3.9 27.8 1.0 O A:HOH510 3.9 36.0 1.0 C4 B:U6 3.9 20.2 1.0 CA A:GLY297 4.0 23.2 1.0 N3 B:U6 4.1 20.6 1.0 NZ A:LYS292 4.2 27.4 1.0 HE21 A:GLN222 4.2 37.3 1.0 HB2 A:LYS292 4.2 22.7 1.0 HB3 A:LYS292 4.3 22.7 1.0 CG A:LYS292 4.3 25.9 1.0 CB A:ASN155 4.3 13.6 1.0 C A:ASN155 4.3 13.0 1.0 HD2 A:LYS292 4.4 33.4 1.0 O A:GLY297 4.4 26.6 1.0 HB2 A:ASN155 4.5 16.3 1.0 CB A:LYS292 4.5 18.9 1.0 O A:ILE156 4.6 17.4 1.0 HD22 A:ASN196 4.6 37.4 1.0 C A:GLY297 4.7 23.2 1.0 O B:HOH213 4.7 19.7 1.0 O A:ASN155 4.7 14.1 1.0 H A:ASN155 4.7 15.4 1.0 CD A:GLN222 4.8 28.6 1.0 CD A:LYS292 4.8 27.9 1.0 O A:HOH503 4.8 40.1 1.0 O A:HOH689 4.8 47.9 1.0 OE1 A:GLN222 4.8 33.8 1.0 HZ1 A:LYS292 4.9 32.9 1.0 N A:ASN155 4.9 12.8 1.0 N A:ILE156 4.9 14.3 1.0 H A:ILE156 4.9 17.1 1.0 CB A:ASN196 5.0 27.9 1.0

Sodium binding site 3 out of 3 in the Crystal Structure of Intact U2AF65 Rrm-Region Bound to Adml-C5 Oligonucleotide


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 Intact U2AF65 Rrm-Region Bound to Adml-C5 Oligonucleotide within 5.0Å range: probe atom residue distance (Å) B Occ B:Na101 b:25.9 occ:1.00 BR B:BRU7 2.1 24.4 1.0 C5 B:BRU7 3.0 17.3 1.0 O B:HOH209 3.1 23.1 1.0 H5'' B:U6 3.1 19.1 1.0 H3' B:U6 3.2 19.8 1.0 H6 B:BRU7 3.3 20.3 1.0 NE2 A:HIS230 3.4 18.9 1.0 C6 B:BRU7 3.5 16.9 1.0 HE1 A:HIS230 3.5 21.2 1.0 O5' B:U6 3.5 15.4 1.0 C5' B:U6 3.8 15.9 1.0 OP1 B:U6 3.8 16.8 1.0 CE1 A:HIS230 3.8 17.7 1.0 OP2 B:BRU7 3.9 20.2 1.0 P B:U6 4.0 16.0 1.0 C4 B:BRU7 4.0 15.7 1.0 C3' B:U6 4.1 16.5 1.0 O B:HOH222 4.2 20.7 1.0 OP2 B:U6 4.2 16.6 1.0 O4 B:BRU7 4.3 15.8 1.0 H2' B:BRU7 4.4 20.1 1.0 C4' B:U6 4.5 16.8 1.0 H5' B:U6 4.5 19.1 1.0 O5' B:BRU7 4.6 17.9 1.0 N1 B:BRU7 4.6 15.5 1.0 CD2 A:HIS230 4.7 18.1 1.0 H2' B:U6 4.8 20.1 1.0 P B:BRU7 4.8 18.4 1.0 O B:HOH224 4.8 22.0 1.0 H4' B:U6 4.9 20.2 1.0

E.Glasser, D.Maji, G.Biancon, A.M.K.Puthenpeedikakkal, C.E.Cavender, T.Tebaldi, J.L.Jenkins, D.H.Mathews, S.Halene, C.L.Kielkopf. Pre-Mrna Splicing Factor U2AF2 Recognizes Distinct Conformations of Nucleotide Variants at the Center of the Pre-Mrna Splice Site Signal. Nucleic Acids Res. V. 50 5299 2022.
ISSN: ESSN 1362-4962
PubMed: 35524551
DOI: 10.1093/NAR/GKAC287