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

Protein crystallography data

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

Zinc Binding Sites:

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 6haz

Go back to Zinc Binding Sites List in 6haz
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 6haz

Go back to Zinc Binding Sites List in 6haz
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

Reference:

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
Page generated: Wed Dec 16 11:56:20 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy