Zinc in PDB 7z78: Crystal Structure of Compound 4 in Complex with the Bromodomain of Human SMARCA2 and Pvhl:Elonginc:Elonginb

The structure of Crystal Structure of Compound 4 in Complex with the Bromodomain of Human SMARCA2 and Pvhl:Elonginc:Elonginb, PDB code: 7z78 was solved by G.Bader, J.Boettcher, B.Wolkerstorfer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	26.40 / 1.32
Space group	P 31
Cell size a, b, c (Å), α, β, γ (°)	61.064, 61.064, 89.275, 90, 90, 120
R / Rfree (%)	18.7 / 21

The structure of Crystal Structure of Compound 4 in Complex with the Bromodomain of Human SMARCA2 and Pvhl:Elonginc:Elonginb also contains other interesting chemical elements:

Bromine

(Br)

3 atoms

The binding sites of Zinc atom in the Crystal Structure of Compound 4 in Complex with the Bromodomain of Human SMARCA2 and Pvhl:Elonginc:Elonginb (pdb code 7z78). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of Compound 4 in Complex with the Bromodomain of Human SMARCA2 and Pvhl:Elonginc:Elonginb, PDB code: 7z78:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of Compound 4 in Complex with the Bromodomain of Human SMARCA2 and Pvhl:Elonginc:Elonginb


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 Compound 4 in Complex with the Bromodomain of Human SMARCA2 and Pvhl:Elonginc:Elonginb within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1502 b:23.1 occ:1.00 O A:HOH1641 1.8 31.3 1.0 NE2 A:HIS1441 2.0 17.7 1.0 O A:HOH1717 2.2 27.3 1.0 O A:HOH1615 2.9 21.5 1.0 CE1 A:HIS1441 3.0 19.0 1.0 CD2 A:HIS1441 3.1 17.9 1.0 O A:ARG1439 4.0 16.1 1.0 ND1 A:HIS1441 4.1 19.6 1.0 CG A:HIS1441 4.2 17.9 1.0 O A:HOH1742 4.7 44.9 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of Compound 4 in Complex with the Bromodomain of Human SMARCA2 and Pvhl:Elonginc:Elonginb


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 Compound 4 in Complex with the Bromodomain of Human SMARCA2 and Pvhl:Elonginc:Elonginb within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1503 b:255.4 occ:1.00 O A:HOH1740 2.1 32.9 1.0 NE2 A:HIS1458 4.4 16.9 1.0 CE1 A:HIS1458 4.7 16.8 1.0 CD2 A:HIS1458 4.8 17.0 1.0 O A:HOH1753 5.0 37.1 1.0 O A:HOH1725 5.0 22.7 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of Compound 4 in Complex with the Bromodomain of Human SMARCA2 and Pvhl:Elonginc:Elonginb


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of Compound 4 in Complex with the Bromodomain of Human SMARCA2 and Pvhl:Elonginc:Elonginb within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1502 b:27.2 occ:1.00 O B:HOH1601 1.8 19.2 1.0 NE2 B:HIS1441 2.2 23.2 1.0 O B:HOH1618 2.6 31.5 1.0 CE1 B:HIS1441 3.1 22.8 1.0 CD2 B:HIS1441 3.3 23.4 1.0 O B:ARG1439 3.8 18.2 1.0 ND1 B:HIS1441 4.3 23.5 1.0 CG B:HIS1441 4.4 21.5 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of Compound 4 in Complex with the Bromodomain of Human SMARCA2 and Pvhl:Elonginc:Elonginb


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of Compound 4 in Complex with the Bromodomain of Human SMARCA2 and Pvhl:Elonginc:Elonginb within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn1502 b:21.6 occ:1.00 NE2 C:HIS1441 2.0 21.8 1.0 O C:HOH1621 2.4 24.4 1.0 O C:HOH1667 2.5 30.7 1.0 CE1 C:HIS1441 3.0 22.3 1.0 CD2 C:HIS1441 3.1 21.2 1.0 O C:ARG1439 3.9 21.9 1.0 ND1 C:HIS1441 4.1 23.0 1.0 CG C:HIS1441 4.2 20.0 1.0

C.Kofink, N.Trainor, B.Mair, S.Wohrle, M.Wurm, N.Mischerikow, M.J.Roy, G.Bader, P.Greb, G.Garavel, E.Diers, R.Mclennan, C.Whitworth, V.Vetma, K.Rumpel, M.Scharnweber, J.E.Fuchs, T.Gerstberger, Y.Cui, G.Gremel, P.Chetta, S.Hopf, N.Budano, J.Rinnenthal, G.Gmaschitz, M.Mayer, M.Koegl, A.Ciulli, H.Weinstabl, W.Farnaby. A Selective and Orally Bioavailable Vhl-Recruiting Protac Achieves SMARCA2 Degradation in Vivo. Nat Commun V. 13 5969 2022.
ISSN: ESSN 2041-1723
PubMed: 36216795
DOI: 10.1038/S41467-022-33430-6