Zinc in PDB 8gdx: Crystal Structure of JADE1 Pzp Domain

The structure of Crystal Structure of JADE1 Pzp Domain, PDB code: 8gdx was solved by B.J.Klein, J.Liu, T.G.Kutateladze, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	28.79 / 2.74
Space group	P 21 3
Cell size a, b, c (Å), α, β, γ (°)	81.439, 81.439, 81.439, 90, 90, 90
R / Rfree (%)	22 / 26.9

The binding sites of Zinc atom in the Crystal Structure of JADE1 Pzp Domain (pdb code 8gdx). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 5 binding sites of Zinc where determined in the Crystal Structure of JADE1 Pzp Domain, PDB code: 8gdx:
Jump to Zinc binding site number: 1; 2; 3; 4; 5;

Zinc binding site 1 out of 5 in the Crystal Structure of JADE1 Pzp Domain


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 JADE1 Pzp Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:33.2 occ:1.00 ND1 A:HIS231 2.0 48.0 1.0 SG A:CYS209 2.3 36.5 1.0 SG A:CYS206 2.3 32.1 1.0 SG A:CYS234 2.3 28.6 1.0 CE1 A:HIS231 3.0 47.4 1.0 CG A:HIS231 3.1 44.2 1.0 CB A:CYS206 3.1 38.1 1.0 CB A:CYS209 3.4 36.0 1.0 CB A:CYS234 3.4 30.2 1.0 CB A:HIS231 3.4 37.1 1.0 N A:CYS209 3.7 40.2 1.0 N A:HIS231 4.0 34.5 1.0 NE2 A:HIS231 4.1 47.2 1.0 CA A:CYS209 4.1 38.6 1.0 CD2 A:HIS231 4.2 46.5 1.0 CA A:HIS231 4.3 35.7 1.0 CB A:VAL208 4.5 39.2 1.0 CA A:CYS206 4.6 36.2 1.0 CA A:CYS234 4.8 32.3 1.0 C A:VAL208 4.8 41.0 1.0 C A:CYS209 4.9 40.4 1.0 N A:VAL208 4.9 36.4 1.0 C A:CYS206 5.0 37.6 1.0 CA A:VAL208 5.0 37.6 1.0

Zinc binding site 2 out of 5 in the Crystal Structure of JADE1 Pzp Domain


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 JADE1 Pzp Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn402 b:35.6 occ:1.00 ND1 A:HIS279 2.0 46.8 1.0 SG A:CYS261 2.3 29.6 1.0 SG A:CYS282 2.3 28.9 1.0 SG A:CYS258 2.3 38.3 1.0 CG A:HIS279 2.9 44.9 1.0 CE1 A:HIS279 3.1 45.5 1.0 CB A:HIS279 3.1 39.4 1.0 CB A:CYS258 3.2 39.8 1.0 CB A:CYS261 3.3 32.5 1.0 CB A:CYS282 3.5 36.0 1.0 N A:CYS261 3.8 34.4 1.0 CG2 A:THR340 4.0 38.9 1.0 N A:HIS279 4.0 39.7 1.0 CA A:CYS261 4.1 34.2 1.0 CD2 A:HIS279 4.1 47.3 1.0 NE2 A:HIS279 4.2 46.9 1.0 CA A:HIS279 4.2 37.8 1.0 OG1 A:THR340 4.4 39.9 1.0 C A:LEU260 4.5 33.9 1.0 O A:CYS261 4.5 39.6 1.0 C A:CYS261 4.6 36.9 1.0 CA A:CYS258 4.7 39.6 1.0 CB A:LEU260 4.7 28.1 1.0 CA A:CYS282 4.8 34.9 1.0 CB A:THR340 4.8 37.7 1.0 N A:LEU260 4.9 34.2 1.0 CA A:LEU260 4.9 32.6 1.0

Zinc binding site 3 out of 5 in the Crystal Structure of JADE1 Pzp Domain


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 JADE1 Pzp Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn403 b:34.7 occ:1.00 ND1 A:HIS338 2.0 49.3 1.0 SG A:CYS341 2.3 30.4 1.0 SG A:CYS318 2.3 40.1 1.0 SG A:CYS315 2.3 33.2 1.0 CE1 A:HIS338 2.9 49.0 1.0 CB A:CYS315 3.1 36.3 1.0 CG A:HIS338 3.1 44.6 1.0 CB A:CYS341 3.2 29.1 1.0 CB A:CYS318 3.3 43.3 1.0 CB A:HIS338 3.6 38.5 1.0 N A:CYS318 3.8 38.1 1.0 NE2 A:HIS338 4.1 49.3 1.0 CA A:CYS318 4.1 41.5 1.0 N A:HIS338 4.1 36.1 1.0 CD2 A:HIS338 4.2 47.6 1.0 CA A:HIS338 4.5 35.5 1.0 CA A:CYS315 4.5 39.8 1.0 CA A:CYS341 4.6 31.3 1.0 CB A:LEU317 4.6 37.3 1.0 CG A:PRO262 4.7 36.5 1.0 CD A:PRO262 4.7 36.5 1.0 C A:LEU317 4.7 41.7 1.0 C A:CYS318 4.9 42.5 1.0 N A:ASN319 4.9 45.1 1.0 C A:CYS315 5.0 39.5 1.0 O A:CYS315 5.0 43.1 1.0

Zinc binding site 4 out of 5 in the Crystal Structure of JADE1 Pzp Domain


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 JADE1 Pzp Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn404 b:37.9 occ:1.00 ND1 A:HIS368 2.0 61.7 1.0 SG A:CYS333 2.3 41.7 1.0 SG A:CYS365 2.3 42.9 1.0 SG A:CYS328 2.3 36.7 1.0 CE1 A:HIS368 2.6 59.6 1.0 CG A:HIS368 3.0 56.8 1.0 CB A:CYS333 3.1 43.9 1.0 CB A:CYS328 3.1 36.4 1.0 CB A:CYS365 3.4 42.5 1.0 NE2 A:HIS368 3.6 59.1 1.0 CB A:HIS368 3.7 50.8 1.0 CD2 A:HIS368 3.9 58.6 1.0 N A:CYS365 4.0 47.1 1.0 CA A:CYS365 4.3 45.5 1.0 CB A:VAL330 4.5 47.6 1.0 CG2 A:VAL330 4.5 42.8 1.0 N A:HIS368 4.5 44.9 1.0 CA A:CYS333 4.5 47.9 1.0 CA A:CYS328 4.6 36.7 1.0 CA A:HIS368 4.8 47.4 1.0 C A:CYS365 5.0 45.1 1.0 CB A:THR335 5.0 35.6 1.0

Zinc binding site 5 out of 5 in the Crystal Structure of JADE1 Pzp Domain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of JADE1 Pzp Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn405 b:47.2 occ:1.00 SG A:CYS247 2.3 38.9 1.0 SG A:CYS223 2.3 40.0 1.0 SG A:CYS250 2.3 49.0 1.0 SG A:CYS226 2.3 49.3 1.0 CB A:CYS226 3.2 51.9 1.0 CB A:CYS250 3.2 45.8 1.0 CB A:CYS223 3.3 40.9 1.0 N A:CYS226 3.6 56.9 1.0 CB A:CYS247 3.7 34.5 1.0 CA A:CYS226 3.9 58.6 1.0 N A:CYS247 4.1 38.4 1.0 CG2 A:ILE228 4.3 46.4 1.0 CA A:CYS250 4.4 43.8 1.0 N A:CYS250 4.5 40.3 1.0 CA A:CYS247 4.5 34.2 1.0 C A:CYS226 4.7 61.3 1.0 CA A:CYS223 4.7 40.7 1.0 CB A:LYS225 4.7 52.9 1.0 C A:LYS225 4.8 55.9 1.0 N A:ASN227 4.9 62.3 1.0 OG1 A:THR249 4.9 34.8 1.0 N A:LYS225 5.0 47.4 1.0

N.Gaurav, A.Kanai, C.Lachance, K.L.Cox, J.Liu, A.T.Grzybowski, N.Saksouk, B.J.Klein, Y.Komata, S.Asada, A.J.Ruthenburg, M.G.Poirier, J.Cote, A.Yokoyama, T.G.Kutateladze. Guiding the HBO1 Complex Function Through the Jade Subunit Nat.Struct.Mol.Biol. 2024.
ISSN: ESSN 1545-9985
DOI: 10.1038/S41594-024-01245-2