Sodium in PDB 5tee: Crystal Structure of GEMIN5 WD40 Repeats in Apo Form

The structure of Crystal Structure of GEMIN5 WD40 Repeats in Apo Form, PDB code: 5tee was solved by X.Chao, W.Tempel, C.Bian, T.Cerovina, H.He, J.R.Walker, A.Seitova, C.Bountra, C.H.Arrowsmith, A.M.Edwards, J.Min, Structural Genomicsconsortium (Sgc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.47 / 1.65
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	60.811, 124.407, 61.034, 90.00, 119.49, 90.00
R / Rfree (%)	16.4 / 19.5

The binding sites of Sodium atom in the Crystal Structure of GEMIN5 WD40 Repeats in Apo Form (pdb code 5tee). 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 GEMIN5 WD40 Repeats in Apo Form, PDB code: 5tee:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of GEMIN5 WD40 Repeats in Apo Form


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 GEMIN5 WD40 Repeats in Apo Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Na839 b:32.3 occ:1.00 O A:HOH1265 2.2 37.8 1.0 O A:HOH1284 2.3 30.6 1.0 O A:ALA106 2.4 19.6 1.0 O A:HOH1290 2.4 38.5 1.0 O A:HOH1031 2.5 23.1 1.0 O A:HIS108 2.5 19.3 1.0 C A:ALA106 3.5 18.5 1.0 C A:HIS108 3.6 16.8 1.0 CB A:ALA106 4.1 19.3 1.0 C A:LEU107 4.2 18.9 1.0 UNK A:UNX816 4.2 31.2 1.0 N A:HIS108 4.3 15.7 1.0 CA A:ALA106 4.3 17.7 1.0 O A:LEU107 4.4 17.2 1.0 N A:GLN109 4.4 16.9 1.0 CA A:GLN109 4.4 19.9 1.0 N A:LEU107 4.4 18.3 1.0 O A:HOH1244 4.5 25.3 0.5 CA A:HIS108 4.6 14.6 1.0 CA A:LEU107 4.6 18.8 1.0 CG A:GLN109 4.6 30.5 1.0 O A:GLY89 4.8 17.5 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of GEMIN5 WD40 Repeats in Apo Form


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 GEMIN5 WD40 Repeats in Apo Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Na840 b:38.5 occ:1.00 O A:HOH1066 2.3 16.5 0.5 O A:ARG679 2.4 16.9 1.0 O A:HIS681 2.5 19.1 1.0 C A:ARG679 3.5 16.2 1.0 C A:HIS681 3.7 19.0 1.0 UNK A:UNX806 3.9 30.4 1.0 CA A:ARG679 4.2 15.4 1.0 CB A:ARG679 4.3 17.0 1.0 N A:HIS681 4.3 14.3 1.0 NE2 A:GLN682 4.4 39.1 1.0 C A:GLY680 4.4 14.9 1.0 N A:GLN682 4.5 19.4 0.7 CA A:GLN682 4.5 24.2 0.7 N A:GLY680 4.5 14.2 1.0 N A:GLN682 4.6 20.1 0.3 O A:GLY662 4.6 15.6 1.0 CD A:GLN682 4.6 37.5 1.0 CA A:HIS681 4.6 15.1 1.0 CA A:GLN682 4.7 23.1 0.3 CA A:GLY680 4.8 15.1 1.0 OE1 A:GLN682 4.8 50.5 1.0 O A:GLY680 4.9 15.6 1.0 O A:HOH1068 5.0 13.7 1.0

C.Xu, H.Ishikawa, K.Izumikawa, L.Li, H.He, Y.Nobe, Y.Yamauchi, H.M.Shahjee, X.H.Wu, Y.T.Yu, T.Isobe, N.Takahashi, J.Min. Structural Insights Into GEMIN5-Guided Selection of Pre-Snrnas For Snrnp Assembly. Genes Dev. V. 30 2376 2016.
ISSN: ISSN 1549-5477
PubMed: 27881600
DOI: 10.1101/GAD.288340.116