Zinc in PDB 5z28: ATVAL2 Phd-Like Domain

The structure of ATVAL2 Phd-Like Domain, PDB code: 5z28 was solved by B.X.Wu, M.M.Zhang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	26.88 / 2.25
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	71.558, 76.022, 76.046, 90.00, 90.00, 90.00
R / Rfree (%)	18.4 / 23.7

The binding sites of Zinc atom in the ATVAL2 Phd-Like Domain (pdb code 5z28). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the ATVAL2 Phd-Like Domain, PDB code: 5z28:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in the ATVAL2 Phd-Like Domain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of ATVAL2 Phd-Like Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn201 b:31.2 occ:1.00 SG A:CYS36 2.3 28.4 1.0 SG A:CYS12 2.4 30.3 1.0 SG A:CYS7 2.4 29.4 1.0 SG A:CYS39 2.4 30.9 1.0 CB A:CYS12 3.2 30.5 1.0 CB A:CYS7 3.3 28.4 1.0 CB A:CYS36 3.4 30.1 1.0 CB A:CYS39 3.5 29.4 1.0 N A:CYS36 4.1 26.4 1.0 N A:CYS39 4.3 31.0 1.0 CA A:CYS36 4.3 31.0 1.0 CB A:ASN9 4.4 27.5 1.0 CA A:CYS39 4.5 31.8 1.0 ND2 A:ASN9 4.6 26.4 1.0 CA A:CYS12 4.6 33.0 1.0 CB A:ALA14 4.7 27.1 1.0 CA A:CYS7 4.7 29.5 1.0 N A:ALA14 4.9 28.1 1.0 N A:GLY13 5.0 31.8 1.0 CG A:ASN9 5.0 28.9 1.0 C A:CYS36 5.0 31.0 1.0

Zinc binding site 2 out of 6 in the ATVAL2 Phd-Like Domain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of ATVAL2 Phd-Like Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn202 b:23.4 occ:1.00 ND1 A:HIS53 2.0 25.2 1.0 ND1 A:HIS70 2.0 22.4 1.0 SG A:CYS73 2.3 25.8 1.0 SG A:CYS49 2.3 28.3 1.0 CE1 A:HIS70 2.9 24.5 1.0 CE1 A:HIS53 2.9 25.1 1.0 CG A:HIS53 3.1 23.6 1.0 CG A:HIS70 3.1 23.0 1.0 CB A:CYS73 3.2 26.0 1.0 CB A:CYS49 3.3 28.9 1.0 CB A:HIS53 3.5 25.9 1.0 CB A:HIS70 3.6 22.4 1.0 NE2 A:HIS70 4.1 25.3 1.0 NE2 A:HIS53 4.1 26.2 1.0 CA A:CYS49 4.2 28.3 1.0 CD2 A:HIS53 4.2 21.4 1.0 CD2 A:HIS70 4.2 24.6 1.0 CB A:ALA75 4.5 21.0 1.0 OG A:SER76 4.6 29.0 1.0 CA A:CYS73 4.7 27.7 1.0 O A:HIS70 4.8 25.9 1.0 CA A:HIS70 4.9 27.5 1.0

Zinc binding site 3 out of 6 in the ATVAL2 Phd-Like Domain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of ATVAL2 Phd-Like Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn203 b:30.8 occ:1.00 SG A:CYS65 2.3 28.4 1.0 SG A:CYS62 2.3 27.8 1.0 SG A:CYS93 2.3 30.3 1.0 SG A:CYS90 2.4 25.4 1.0 CB A:CYS62 3.3 25.6 1.0 CB A:CYS65 3.3 27.1 1.0 CB A:CYS93 3.4 30.4 1.0 CB A:CYS90 3.5 25.3 1.0 N A:CYS65 3.8 30.6 1.0 N A:CYS90 3.9 24.7 1.0 CA A:CYS65 4.1 31.2 1.0 CA A:CYS90 4.3 30.3 1.0 C A:SER64 4.3 34.3 1.0 N A:CYS93 4.4 34.3 1.0 CA A:CYS93 4.5 36.9 1.0 CB A:SER64 4.6 29.4 1.0 C A:CYS65 4.6 32.4 1.0 CB A:LYS67 4.7 31.0 1.0 CA A:CYS62 4.8 25.7 1.0 N A:SER64 4.8 29.2 1.0 CA A:SER64 4.8 30.7 1.0 C A:CYS90 4.8 35.2 1.0 O A:SER64 4.9 35.2 1.0 O A:CYS65 4.9 31.4 1.0 O A:CYS90 4.9 28.8 1.0

Zinc binding site 4 out of 6 in the ATVAL2 Phd-Like Domain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of ATVAL2 Phd-Like Domain within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn201 b:27.5 occ:1.00 SG B:CYS65 2.3 28.2 1.0 SG B:CYS62 2.3 26.8 1.0 SG B:CYS90 2.4 22.7 1.0 SG B:CYS93 2.4 30.8 1.0 CB B:CYS62 3.2 25.8 1.0 CB B:CYS65 3.3 30.4 1.0 CB B:CYS93 3.4 30.7 1.0 CB B:CYS90 3.5 24.2 1.0 N B:CYS65 3.9 32.0 1.0 N B:CYS90 4.0 23.2 1.0 CA B:CYS65 4.1 28.9 1.0 OG B:SER64 4.2 29.1 1.0 N B:CYS93 4.3 33.1 1.0 CA B:CYS90 4.3 25.0 1.0 C B:SER64 4.4 33.1 1.0 CA B:CYS93 4.5 35.1 1.0 CB B:LYS67 4.6 27.8 1.0 C B:CYS65 4.7 32.4 1.0 CA B:CYS62 4.7 26.9 1.0 OG1 B:THR89 4.8 30.3 1.0 O B:SER64 4.8 34.2 1.0 N B:SER64 4.9 33.2 1.0 C B:CYS90 4.9 27.1 1.0 O B:CYS65 4.9 36.2 1.0

Zinc binding site 5 out of 6 in the ATVAL2 Phd-Like Domain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of ATVAL2 Phd-Like Domain within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn202 b:21.8 occ:1.00 ND1 B:HIS53 2.0 27.6 1.0 ND1 B:HIS70 2.1 19.1 1.0 SG B:CYS73 2.3 20.7 1.0 SG B:CYS49 2.4 24.6 1.0 CE1 B:HIS53 2.8 28.1 1.0 CE1 B:HIS70 3.0 23.1 1.0 CG B:HIS53 3.1 26.7 1.0 CG B:HIS70 3.2 22.2 1.0 CB B:CYS73 3.3 21.3 1.0 CB B:CYS49 3.3 23.2 1.0 CB B:HIS70 3.6 19.0 1.0 CB B:HIS53 3.6 23.1 1.0 NE2 B:HIS53 4.0 28.8 1.0 OG B:SER76 4.2 30.3 1.0 CA B:CYS49 4.2 24.8 1.0 CD2 B:HIS53 4.2 27.8 1.0 NE2 B:HIS70 4.2 25.1 1.0 CD2 B:HIS70 4.3 21.1 1.0 CB B:ALA75 4.5 24.1 1.0 CA B:CYS73 4.7 23.3 1.0 CB B:SER76 4.7 24.4 1.0 O B:HIS70 4.8 21.9 1.0 N B:SER76 4.9 25.1 1.0 CA B:HIS70 5.0 22.7 1.0 OE1 B:GLU56 5.0 31.3 1.0

Zinc binding site 6 out of 6 in the ATVAL2 Phd-Like Domain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of ATVAL2 Phd-Like Domain within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn203 b:32.9 occ:1.00 SG B:CYS12 2.3 34.6 1.0 SG B:CYS7 2.3 32.0 1.0 SG B:CYS36 2.4 31.0 1.0 SG B:CYS39 2.4 32.6 1.0 CB B:CYS12 3.1 38.1 1.0 CB B:CYS39 3.2 28.0 1.0 CB B:CYS7 3.3 34.1 1.0 CB B:CYS36 3.5 30.7 1.0 N B:CYS36 4.0 29.9 1.0 N B:CYS39 4.2 27.2 1.0 CA B:CYS36 4.3 28.6 1.0 CA B:CYS39 4.4 27.1 1.0 CA B:CYS12 4.6 40.5 1.0 CB B:ASN9 4.6 36.6 1.0 CA B:CYS7 4.7 36.9 1.0 ND2 B:ASN9 4.8 35.2 1.0 CB B:ALA14 4.8 35.6 1.0 N B:GLY13 4.9 34.6 1.0 C B:CYS36 4.9 30.0 1.0 N B:ALA14 5.0 31.4 1.0

B.X.Wu, M.M.Zhang. Crystal Structure of ATVAL12 Phd-Like Domain To Be Published.