Sodium in PDB 6bhd: Crystal Structure of SETDB1 with A Modified H3 Peptide

All present enzymatic activity of Crystal Structure of SETDB1 with A Modified H3 Peptide:
2.1.1.43;

The structure of Crystal Structure of SETDB1 with A Modified H3 Peptide, PDB code: 6bhd was solved by S.Qin, W.Tempel, C.Bountra, C.H.Arrowsmith, A.M.Edwards, J.Min, Structuralgenomics Consortium (Sgc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	41.57 / 1.25
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	37.258, 72.448, 52.505, 90.00, 104.84, 90.00
R / Rfree (%)	14.7 / 18.3

The binding sites of Sodium atom in the Crystal Structure of SETDB1 with A Modified H3 Peptide (pdb code 6bhd). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the Crystal Structure of SETDB1 with A Modified H3 Peptide, PDB code: 6bhd:

Sodium binding site 1 out of 1 in the Crystal Structure of SETDB1 with A Modified H3 Peptide


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 SETDB1 with A Modified H3 Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Na535 b:25.0 occ:1.00 O A:HOH734 2.3 34.1 1.0 O A:HOH668 2.4 19.6 1.0 O A:THR338 2.4 15.4 1.0 O A:HOH783 2.5 31.6 1.0 O A:HOH746 2.5 26.5 1.0 C A:THR338 3.7 12.9 1.0 O A:HOH627 4.0 24.0 1.0 O A:TYR340 4.3 12.0 1.0 O A:HOH674 4.5 30.0 1.0 O A:HOH787 4.5 36.2 1.0 CA A:THR338 4.5 13.5 0.5 CA A:THR338 4.5 12.3 0.5 CG2 A:THR338 4.6 11.3 0.5 N A:ALA339 4.6 11.5 1.0 CA A:ALA339 4.6 12.1 1.0 C A:ALA339 4.8 10.8 1.0 O A:ALA339 4.9 11.3 1.0

R.Z.Jurkowska, S.Qin, G.Kungulovski, W.Tempel, Y.Liu, P.Bashtrykov, J.Stiefelmaier, T.P.Jurkowski, S.Kudithipudi, S.Weirich, R.Tamas, H.Wu, L.Dombrovski, P.Loppnau, R.Reinhardt, J.Min, A.Jeltsch. H3K14AC Is Linked to Methylation of H3K9 By the Triple Tudor Domain of SETDB1. Nat Commun V. 8 2057 2017.
ISSN: ESSN 2041-1723
PubMed: 29234025
DOI: 10.1038/S41467-017-02259-9