Sodium in PDB 5ev1: Structure I of Intact U2AF65 Recognizing A 3' Splice Site Signal

The structure of Structure I of Intact U2AF65 Recognizing A 3' Splice Site Signal, PDB code: 5ev1 was solved by A.A.Agrawal, 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)	32.46 / 2.04
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	62.052, 114.241, 59.418, 90.00, 90.00, 90.00
R / Rfree (%)	17.3 / 22.8

The structure of Structure I of Intact U2AF65 Recognizing A 3' Splice Site Signal also contains other interesting chemical elements:

Bromine

(Br)

1 atom

The binding sites of Sodium atom in the Structure I of Intact U2AF65 Recognizing A 3' Splice Site Signal (pdb code 5ev1). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Structure I of Intact U2AF65 Recognizing A 3' Splice Site Signal, PDB code: 5ev1:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Structure I of Intact U2AF65 Recognizing A 3' Splice Site Signal


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure I of Intact U2AF65 Recognizing A 3' Splice Site Signal within 5.0Å range: probe atom residue distance (Å) B Occ A:Na401 b:69.3 occ:0.50 OD2 A:ASP206 2.5 59.3 1.0 HB2 A:MET238 3.2 90.0 1.0 CG A:ASP206 3.4 63.8 1.0 OD1 A:ASP206 3.6 67.2 1.0 HA A:MET238 4.1 93.6 1.0 CB A:MET238 4.1 75.0 1.0 HG12 A:VAL205 4.3 41.3 1.0 HB3 A:MET238 4.6 90.0 1.0 HG11 A:VAL205 4.6 41.3 1.0 CA A:MET238 4.7 78.0 1.0 HG3 A:MET238 4.7 83.9 1.0 CB A:ASP206 4.7 34.7 1.0 O A:GLY237 4.7 77.5 1.0 HA A:ASP206 4.8 36.5 1.0 HB2 A:ASP206 4.8 41.7 1.0 CG1 A:VAL205 4.9 34.4 1.0 CG A:MET238 5.0 69.9 1.0

Sodium binding site 2 out of 2 in the Structure I of Intact U2AF65 Recognizing A 3' Splice Site Signal


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structure I of Intact U2AF65 Recognizing A 3' Splice Site Signal within 5.0Å range: probe atom residue distance (Å) B Occ B:Na101 b:87.1 occ:0.50 H5'' B:U2 2.0 99.4 1.0 OP1 B:U3 2.6 75.2 1.0 H3' B:U2 2.8 0.9 1.0 C5' B:U2 3.0 82.9 1.0 H5' B:U2 3.5 99.4 1.0 C3' B:U2 3.6 84.1 1.0 O5' B:U2 3.6 85.0 1.0 C4' B:U2 3.7 85.5 1.0 HO5' B:U2 3.9 0.1 1.0 P B:U3 4.0 70.1 1.0 H4' B:U2 4.0 0.6 1.0 O3' B:U2 4.3 69.1 1.0 H2' B:U2 4.6 0.2 1.0 HE2 A:TYR302 4.7 53.9 1.0 C2' B:U2 4.8 84.4 1.0 O5' B:U3 4.8 68.2 1.0

A.A.Agrawal, E.Salsi, R.Chatrikhi, S.Henderson, J.L.Jenkins, M.R.Green, D.N.Ermolenko, C.L.Kielkopf. An Extended U2AF(65)-Rna-Binding Domain Recognizes the 3' Splice Site Signal. Nat Commun V. 7 10950 2016.
ISSN: ESSN 2041-1723
PubMed: 26952537
DOI: 10.1038/NCOMMS10950