Zinc in PDB 6haz: Crystal Structure of the Bromodomain of Human SMARCA2 in Complex with Smarca-Bd Ligand

The structure of Crystal Structure of the Bromodomain of Human SMARCA2 in Complex with Smarca-Bd Ligand, PDB code: 6haz was solved by G.Bader, S.Steurer, A.Weiss-Puxbaum, A.Zoephel, M.Roy, A.Ciulli, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	26.00 / 1.31
Space group	P 41
Cell size a, b, c (Å), α, β, γ (°)	42.549, 42.549, 164.230, 90.00, 90.00, 90.00
R / Rfree (%)	17.8 / 19.3

The binding sites of Zinc atom in the Crystal Structure of the Bromodomain of Human SMARCA2 in Complex with Smarca-Bd Ligand (pdb code 6haz). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of the Bromodomain of Human SMARCA2 in Complex with Smarca-Bd Ligand, PDB code: 6haz:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of the Bromodomain of Human SMARCA2 in Complex with Smarca-Bd Ligand


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of the Bromodomain of Human SMARCA2 in Complex with Smarca-Bd Ligand within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1502 b:17.6 occ:1.00 OE2 A:GLU1417 1.9 22.8 1.0 ND1 B:HIS1458 2.0 16.4 1.0 O A:HOH1725 2.2 8.6 1.0 O A:HOH1704 2.2 10.3 1.0 CD A:GLU1417 2.7 21.5 1.0 OE1 A:GLU1417 2.8 19.4 1.0 CE1 B:HIS1458 3.0 17.0 1.0 CG B:HIS1458 3.1 14.2 1.0 HB2 B:HIS1458 3.1 12.7 0.0 HE1 B:HIS1458 3.2 17.9 0.0 HB3 B:HIS1458 3.4 12.4 0.0 CB B:HIS1458 3.4 12.3 1.0 HB3 A:PRO1413 3.7 18.9 0.0 HG3 A:PRO1413 4.0 23.2 0.0 O A:HOH1627 4.0 35.9 1.0 H33 A:FX51501 4.0 21.4 0.0 NE2 B:HIS1458 4.1 16.2 1.0 CG A:GLU1417 4.2 20.6 1.0 CD2 B:HIS1458 4.2 15.4 1.0 HA A:PRO1413 4.2 16.2 0.0 HB3 B:MET1454 4.3 15.3 0.0 HA B:LEU1455 4.3 13.3 0.0 HG2 A:GLU1417 4.4 19.7 0.0 O A:HOH1758 4.6 33.2 1.0 CB A:PRO1413 4.6 18.4 1.0 HG3 A:GLU1417 4.6 21.2 0.0 O B:HOH1636 4.7 27.3 1.0 O B:MET1454 4.7 14.7 1.0 CG A:PRO1413 4.8 23.2 1.0 O B:HOH1613 4.8 13.2 1.0 H38 A:FX51501 4.9 20.4 0.0 CA A:PRO1413 4.9 15.8 1.0 H35 A:FX51501 4.9 23.2 0.0 CA B:HIS1458 5.0 11.9 1.0 N18 A:FX51501 5.0 21.4 1.0 O A:HOH1753 5.0 63.4 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of the Bromodomain of Human SMARCA2 in Complex with Smarca-Bd Ligand


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of the Bromodomain of Human SMARCA2 in Complex with Smarca-Bd Ligand within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1502 b:17.5 occ:1.00 OE2 B:GLU1417 2.0 22.3 1.0 O B:HOH1725 2.2 8.6 1.0 O B:HOH1703 2.2 10.6 1.0 CD B:GLU1417 2.7 20.6 1.0 OE1 B:GLU1417 2.9 19.0 1.0 HB3 B:PRO1413 3.8 18.0 0.0 HG3 B:PRO1413 4.0 22.4 0.0 H33 B:FX51501 4.0 21.8 0.0 O B:HOH1637 4.0 33.3 1.0 CG B:GLU1417 4.2 21.0 1.0 HA B:PRO1413 4.2 15.8 0.0 HG2 B:GLU1417 4.4 20.2 0.0 O B:HOH1711 4.5 57.3 1.0 O B:HOH1752 4.6 33.6 1.0 CB B:PRO1413 4.6 17.5 1.0 HG3 B:GLU1417 4.7 21.7 0.0 CG B:PRO1413 4.8 22.3 1.0 H38 B:FX51501 4.9 19.8 0.0 H35 B:FX51501 4.9 21.8 0.0 CA B:PRO1413 4.9 15.3 1.0 N18 B:FX51501 5.0 21.6 1.0

W.Farnaby, M.Koegl, M.J.Roy, C.Whitworth, E.Diers, N.Trainor, D.Zollman, S.Steurer, J.Karolyi-Oezguer, C.Riedmueller, T.Gmaschitz, J.Wachter, C.Dank, M.Galant, B.Sharps, K.Rumpel, E.Traxler, T.Gerstberger, R.Schnitzer, O.Petermann, P.Greb, H.Weinstabl, G.Bader, A.Zoephel, A.Weiss-Puxbaum, K.Ehrenhofer-Wolfer, S.Wohrle, G.Boehmelt, J.Rinnenthal, H.Arnhof, N.Wiechens, M.Y.Wu, T.Owen-Hughes, P.Ettmayer, M.Pearson, D.B.Mcconnell, A.Ciulli. Baf Complex Vulnerabilities in Cancer Demonstrated Via Structure-Based Protac Design. Nat.Chem.Biol. V. 15 672 2019.
ISSN: ESSN 1552-4469
PubMed: 31178587
DOI: 10.1038/S41589-019-0294-6