Zinc in PDB 7by1: Crystal Structure of GCN5 Pcaf N-Terminal Domain

The structure of Crystal Structure of GCN5 Pcaf N-Terminal Domain, PDB code: 7by1 was solved by R.Hibi, S.Toma-Fukai, T.Shimizu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.70 / 1.80
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	43.069, 148.857, 58.998, 90.00, 101.03, 90.00
R / Rfree (%)	19.6 / 23.1

The binding sites of Zinc atom in the Crystal Structure of GCN5 Pcaf N-Terminal Domain (pdb code 7by1). 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 GCN5 Pcaf N-Terminal Domain, PDB code: 7by1:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of GCN5 Pcaf N-Terminal 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 GCN5 Pcaf N-Terminal Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:28.9 occ:1.00 SG A:CYS113 2.2 35.0 1.0 ND1 A:HIS147 2.2 31.5 1.0 SG A:CYS107 2.3 27.1 1.0 SG A:CYS145 2.4 23.2 1.0 CB A:CYS107 3.0 28.7 1.0 CG A:HIS147 3.2 30.3 1.0 CE1 A:HIS147 3.2 33.0 1.0 CB A:CYS145 3.2 26.7 1.0 CB A:CYS113 3.3 40.7 1.0 CB A:HIS147 3.4 26.4 1.0 ZN A:ZN402 4.2 23.7 1.0 CB A:ALA109 4.3 30.7 1.0 CB A:CYS115 4.3 26.2 1.0 NE2 A:HIS147 4.3 31.9 1.0 CD2 A:HIS147 4.3 30.3 1.0 O A:CYS145 4.4 28.6 1.0 NE2 A:HIS152 4.4 22.7 1.0 CE1 A:HIS152 4.5 22.4 1.0 CA A:CYS107 4.5 26.5 1.0 CA A:CYS145 4.5 26.6 1.0 CA A:HIS147 4.6 26.3 1.0 C A:CYS145 4.6 27.9 1.0 N A:HIS147 4.7 28.9 1.0 CA A:CYS113 4.7 39.9 1.0 N A:ALA109 4.9 31.0 1.0 C A:CYS107 5.0 27.9 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of GCN5 Pcaf N-Terminal 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 GCN5 Pcaf N-Terminal Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn402 b:23.7 occ:1.00 NE2 A:HIS152 2.2 22.7 1.0 SG A:CYS115 2.2 26.3 1.0 SG A:CYS142 2.3 23.4 1.0 SG A:CYS145 2.5 23.2 1.0 CE1 A:HIS152 3.1 22.4 1.0 CB A:CYS142 3.2 22.4 1.0 CB A:CYS115 3.2 26.2 1.0 CD2 A:HIS152 3.2 20.9 1.0 CB A:CYS145 3.4 26.7 1.0 O A:GLY117 3.7 24.9 1.0 N A:CYS145 4.0 28.6 1.0 ZN A:ZN401 4.2 28.9 1.0 C A:GLY117 4.2 25.1 1.0 ND1 A:HIS152 4.3 22.1 1.0 CA A:CYS145 4.3 26.6 1.0 CA A:TRP118 4.3 22.7 1.0 CG A:HIS152 4.3 21.5 1.0 CB A:CYS107 4.4 28.7 1.0 N A:TRP118 4.5 23.4 1.0 CB A:SER144 4.6 34.2 1.0 CA A:CYS115 4.6 29.5 1.0 CA A:CYS142 4.6 23.6 1.0 SG A:CYS107 4.8 27.1 1.0 N A:GLY117 5.0 23.6 1.0 C A:CYS145 5.0 27.9 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of GCN5 Pcaf N-Terminal 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 GCN5 Pcaf N-Terminal Domain within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn401 b:26.5 occ:1.00 NE2 B:HIS152 2.2 27.4 1.0 SG B:CYS115 2.2 28.9 1.0 SG B:CYS142 2.3 26.1 1.0 SG B:CYS145 2.5 23.1 1.0 CE1 B:HIS152 3.1 27.8 1.0 CB B:CYS142 3.2 24.8 1.0 CD2 B:HIS152 3.2 30.3 1.0 CB B:CYS115 3.2 27.5 1.0 CB B:CYS145 3.3 30.5 1.0 O B:GLY117 3.7 26.2 1.0 N B:CYS145 4.0 29.4 1.0 ZN B:ZN402 4.2 32.5 1.0 C B:GLY117 4.2 27.9 1.0 CA B:CYS145 4.3 30.5 1.0 ND1 B:HIS152 4.3 25.2 1.0 CB B:CYS107 4.3 33.1 1.0 CG B:HIS152 4.3 28.6 1.0 CA B:TRP118 4.3 26.5 1.0 N B:TRP118 4.5 26.6 1.0 CB B:SER144 4.6 37.0 1.0 CA B:CYS115 4.6 29.4 1.0 CA B:CYS142 4.7 25.4 1.0 SG B:CYS107 4.8 30.7 1.0 O B:HOH512 4.9 39.6 1.0 N B:GLY117 5.0 29.9 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of GCN5 Pcaf N-Terminal 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 GCN5 Pcaf N-Terminal Domain within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn402 b:32.5 occ:1.00 SG B:CYS113 2.2 37.5 1.0 ND1 B:HIS147 2.3 40.5 1.0 SG B:CYS107 2.3 30.7 1.0 SG B:CYS145 2.4 23.1 1.0 CB B:CYS107 3.0 33.1 1.0 CG B:HIS147 3.2 37.1 1.0 CB B:CYS145 3.2 30.5 1.0 CE1 B:HIS147 3.3 44.4 1.0 CB B:CYS113 3.3 44.2 1.0 CB B:HIS147 3.4 32.9 1.0 ZN B:ZN401 4.2 26.5 1.0 CB B:ALA109 4.3 34.9 1.0 CB B:CYS115 4.3 27.5 1.0 NE2 B:HIS147 4.4 36.6 1.0 CD2 B:HIS147 4.4 37.4 1.0 O B:CYS145 4.4 36.7 1.0 NE2 B:HIS152 4.4 27.4 1.0 CA B:CYS107 4.5 30.5 1.0 CA B:CYS145 4.5 30.5 1.0 CE1 B:HIS152 4.5 27.8 1.0 CA B:HIS147 4.6 32.2 1.0 C B:CYS145 4.7 29.7 1.0 N B:HIS147 4.7 30.3 1.0 CA B:CYS113 4.7 44.2 1.0 C B:CYS107 4.9 32.2 1.0 N B:ALA109 4.9 35.6 1.0

S.Toma-Fukai, R.Hibi, T.Naganuma, M.Sakai, S.Saijo, N.Shimizu, M.Matsumoto, T.Shimizu. Crystal Structure of GCN5 Pcaf N-Terminal Domain Reveals Atypical Ubiquitin Ligase Structure. J.Biol.Chem. V. 295 14630 2020.
ISSN: ESSN 1083-351X
PubMed: 32820047
DOI: 10.1074/JBC.RA120.013431