Sodium in PDB 4lg8: Crystal Structure of PRPF19 WD40 Repeats

The structure of Crystal Structure of PRPF19 WD40 Repeats, PDB code: 4lg8 was solved by C.Xu, W.Tempel, H.He, E.Dobrovetsky, A.Seitova, C.Bountra, C.H.Arrowsmith, A.M.Edwards, J.Min, Structural Genomics Consortium (Sgc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 1.89
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	83.055, 83.055, 75.533, 90.00, 90.00, 120.00
R / Rfree (%)	15.6 / 19.7

The binding sites of Sodium atom in the Crystal Structure of PRPF19 WD40 Repeats (pdb code 4lg8). 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 PRPF19 WD40 Repeats, PDB code: 4lg8:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of PRPF19 WD40 Repeats


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 PRPF19 WD40 Repeats within 5.0Å range: probe atom residue distance (Å) B Occ A:Na601 b:33.7 occ:1.00 O A:HOH702 2.3 39.0 1.0 O A:ASP412 2.4 43.6 1.0 O A:HOH701 2.4 38.3 1.0 OG A:SER414 2.4 32.2 1.0 O A:HOH703 2.4 38.5 1.0 O A:ASN434 2.5 36.0 1.0 C A:ASN434 3.5 33.6 1.0 C A:ASP412 3.5 38.8 1.0 CB A:SER414 3.6 32.3 1.0 O A:HOH805 3.7 36.9 1.0 N A:SER414 3.8 30.0 1.0 CA A:ASN434 3.9 33.6 1.0 C A:ASP413 4.0 31.8 1.0 O A:PHE436 4.1 33.4 1.0 CA A:ASP413 4.2 35.1 1.0 CA A:SER414 4.3 31.4 1.0 N A:ASP413 4.3 36.8 1.0 CB A:ASN434 4.4 36.1 1.0 CA A:ASP412 4.5 38.5 1.0 O A:ASP413 4.5 28.5 1.0 N A:ASN435 4.7 34.1 1.0 O A:ASP433 5.0 35.0 1.0 CB A:ASP412 5.0 40.4 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of PRPF19 WD40 Repeats


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 PRPF19 WD40 Repeats within 5.0Å range: probe atom residue distance (Å) B Occ A:Na602 b:33.3 occ:1.00 UNK A:UNX615 2.1 39.5 1.0 O A:THR472 2.4 25.3 1.0 O A:HOH726 2.5 33.0 1.0 O A:HOH809 2.6 42.0 1.0 C A:THR472 3.6 25.3 1.0 OG1 A:THR472 3.8 23.6 1.0 CB A:THR472 4.2 22.8 1.0 CA A:GLU473 4.3 25.5 1.0 N A:GLU473 4.4 24.6 1.0 O A:GLU473 4.4 25.1 1.0 CA A:THR472 4.5 23.8 1.0 C A:GLU473 4.5 25.4 1.0 O A:HIS474 4.6 26.1 1.0

Y.Zhang, Y.Li, X.Liang, Z.Zhu, H.Sun, H.He, J.Min, S.Liao, Y.Liu. Crystal Structure of the WD40 Domain of Human PRPF19. Biochem. Biophys. Res. V. 493 1250 2017COMMUN..
ISSN: ESSN 1090-2104
PubMed: 28962858
DOI: 10.1016/J.BBRC.2017.09.145