Zinc in PDB 8qjt: Brm (SMARCA2) Bromodomain in Complex with Ligand 10

The structure of Brm (SMARCA2) Bromodomain in Complex with Ligand 10, PDB code: 8qjt was solved by P.S.Kerry, A.J.Hole, J.I.Perez-Dorado, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	55.21 / 2.57
Space group	P 31
Cell size a, b, c (Å), α, β, γ (°)	63.75, 63.75, 88.51, 90, 90, 120
R / Rfree (%)	20.3 / 26.3

The structure of Brm (SMARCA2) Bromodomain in Complex with Ligand 10 also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Zinc atom in the Brm (SMARCA2) Bromodomain in Complex with Ligand 10 (pdb code 8qjt). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Brm (SMARCA2) Bromodomain in Complex with Ligand 10, PDB code: 8qjt:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Brm (SMARCA2) Bromodomain in Complex with Ligand 10


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Brm (SMARCA2) Bromodomain in Complex with Ligand 10 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1501 b:54.5 occ:1.00 OE1 A:GLU1417 1.9 60.5 1.0 N5 A:VLC1503 2.0 49.9 1.0 OE2 B:GLU1491 2.2 89.7 1.0 CD A:GLU1417 2.8 62.9 1.0 CD B:GLU1491 2.9 89.3 1.0 C18 A:VLC1503 2.9 49.3 1.0 OE1 B:GLU1491 2.9 90.3 1.0 C19 A:VLC1503 3.0 50.6 1.0 OE2 A:GLU1417 3.1 69.4 1.0 O1 A:VLC1503 3.2 51.7 1.0 O B:HOH1611 4.1 52.6 1.0 CG A:GLU1417 4.1 55.8 1.0 C20 A:VLC1503 4.1 52.1 1.0 C17 A:VLC1503 4.2 49.0 1.0 C23 A:VLC1503 4.3 50.1 1.0 CG B:GLU1491 4.3 85.4 1.0 CB A:PRO1413 4.4 49.1 1.0 CA A:PRO1413 4.5 48.8 1.0 C21 A:VLC1503 4.5 52.3 1.0 CB A:GLU1417 4.6 52.9 1.0 O A:HOH1608 4.7 51.8 1.0 C16 A:VLC1503 4.8 49.0 1.0 O2 A:VLC1503 4.9 52.7 1.0

Zinc binding site 2 out of 4 in the Brm (SMARCA2) Bromodomain in Complex with Ligand 10


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Brm (SMARCA2) Bromodomain in Complex with Ligand 10 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1502 b:67.6 occ:1.00 NE2 A:HIS1441 2.1 52.4 1.0 CE1 A:HIS1441 3.0 51.7 1.0 CD2 A:HIS1441 3.2 51.3 1.0 O A:ARG1439 4.2 48.0 1.0 ND1 A:HIS1441 4.2 51.0 1.0 CG A:HIS1441 4.3 49.7 1.0

Zinc binding site 3 out of 4 in the Brm (SMARCA2) Bromodomain in Complex with Ligand 10


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Brm (SMARCA2) Bromodomain in Complex with Ligand 10 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1501 b:58.2 occ:1.00 NE2 B:HIS1441 2.1 62.7 1.0 O B:HOH1630 2.8 51.1 1.0 CE1 B:HIS1441 3.0 61.6 1.0 CD2 B:HIS1441 3.2 61.4 1.0 O B:ARG1439 4.1 54.9 1.0 ND1 B:HIS1441 4.2 60.7 1.0 CG B:HIS1441 4.3 59.5 1.0

Zinc binding site 4 out of 4 in the Brm (SMARCA2) Bromodomain in Complex with Ligand 10


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Brm (SMARCA2) Bromodomain in Complex with Ligand 10 within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn1501 b:56.7 occ:1.00 O C:HOH1617 2.1 34.8 1.0 NE2 C:HIS1441 2.2 56.7 1.0 O C:HOH1647 2.6 31.3 1.0 CD2 C:HIS1441 3.2 55.5 1.0 CE1 C:HIS1441 3.2 56.2 1.0 O C:ARG1439 4.2 53.0 1.0 CG C:HIS1441 4.3 53.9 1.0 ND1 C:HIS1441 4.3 56.0 1.0

M.Berlin, J.Cantley, M.Bookbinder, E.Bortolon, F.Broccatelli, G.Cadelina, E.W.Chan, H.Chen, X.Chen, Y.Cheng, T.K.Cheung, K.Davenport, D.Dinicola, D.Gordon, B.D.Hamman, A.Harbin, R.Haskell, M.He, A.J.Hole, T.Januario, P.S.Kerry, S.G.Koenig, L.Li, M.Merchant, I.Perez-Dorado, J.Pizzano, C.Quinn, C.M.Rose, E.Rousseau, L.Soto, L.R.Staben, H.Sun, Q.Tian, J.Wang, W.Wang, C.S.Ye, X.Ye, P.Zhang, Y.Zhou, R.Yauch, P.S.Dragovich. Protacs Targeting Brm (SMARCA2) Afford Selective in Vivo Degradation Over BRG1 (SMARCA4) and Are Active in BRG1 Mutant Xenograft Tumor Models. J.Med.Chem. 2024.
ISSN: ISSN 0022-2623
PubMed: 38180485
DOI: 10.1021/ACS.JMEDCHEM.3C01781