Zinc in PDB 5yuh: ATVAL1 Phd-Like Domain in the P6122 Space Group

The structure of ATVAL1 Phd-Like Domain in the P6122 Space Group, PDB code: 5yuh was solved by M.M.Zhang, B.X.Wu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	26.37 / 1.80
Space group	P 61 2 2
Cell size a, b, c (Å), α, β, γ (°)	52.743, 52.743, 125.030, 90.00, 90.00, 120.00
R / Rfree (%)	24.6 / 27.8

The binding sites of Zinc atom in the ATVAL1 Phd-Like Domain in the P6122 Space Group (pdb code 5yuh). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the ATVAL1 Phd-Like Domain in the P6122 Space Group, PDB code: 5yuh:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the ATVAL1 Phd-Like Domain in the P6122 Space Group


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of ATVAL1 Phd-Like Domain in the P6122 Space Group within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn201 b:16.2 occ:1.00 ND1 A:HIS73 1.9 14.7 1.0 ND1 A:HIS56 2.1 18.4 1.0 SG A:CYS52 2.3 16.0 1.0 SG A:CYS76 2.3 13.8 1.0 CE1 A:HIS73 2.7 18.0 1.0 CE1 A:HIS56 3.0 20.4 1.0 CG A:HIS73 3.1 14.8 1.0 CG A:HIS56 3.1 21.4 1.0 CB A:CYS76 3.2 15.2 1.0 CB A:CYS52 3.3 20.7 1.0 CB A:HIS56 3.5 20.0 1.0 CB A:HIS73 3.6 14.4 1.0 NE2 A:HIS73 3.9 17.0 1.0 CA A:CYS52 4.1 20.6 1.0 NE2 A:HIS56 4.1 23.6 1.0 CD2 A:HIS73 4.1 17.5 1.0 CD2 A:HIS56 4.2 22.2 1.0 CB A:ALA78 4.5 16.6 1.0 OG A:SER79 4.6 19.6 1.0 CA A:CYS76 4.7 14.7 1.0 O A:HIS73 4.8 14.6 1.0 OE1 A:GLN59 5.0 25.4 1.0 CA A:HIS73 5.0 14.3 1.0 N A:CYS52 5.0 18.6 1.0

Zinc binding site 2 out of 3 in the ATVAL1 Phd-Like Domain in the P6122 Space Group


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of ATVAL1 Phd-Like Domain in the P6122 Space Group within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn202 b:19.4 occ:1.00 SG A:CYS96 2.3 27.7 1.0 SG A:CYS68 2.3 18.7 1.0 SG A:CYS65 2.3 17.9 1.0 SG A:CYS93 2.6 30.1 1.0 CB A:CYS65 3.2 18.0 1.0 CB A:CYS93 3.2 26.2 1.0 CB A:CYS68 3.3 20.0 1.0 CB A:CYS96 3.3 26.9 1.0 N A:CYS68 3.8 22.5 1.0 N A:CYS93 3.8 20.4 1.0 CA A:CYS68 4.1 19.2 1.0 CA A:CYS93 4.1 21.8 1.0 CA A:CYS96 4.6 30.3 1.0 N A:CYS96 4.6 32.5 1.0 CB A:LYS70 4.6 17.2 1.0 CA A:CYS65 4.6 16.3 1.0 C A:CYS68 4.7 21.0 1.0 C A:LEU67 4.8 22.7 1.0 N A:SER69 4.9 18.9 1.0 CB A:LEU67 5.0 24.0 1.0 N A:LYS70 5.0 17.7 1.0 C A:GLY92 5.0 20.3 1.0

Zinc binding site 3 out of 3 in the ATVAL1 Phd-Like Domain in the P6122 Space Group


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of ATVAL1 Phd-Like Domain in the P6122 Space Group within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn203 b:27.6 occ:1.00 SG A:CYS39 2.3 28.9 1.0 SG A:CYS16 2.3 28.8 1.0 SG A:CYS11 2.4 27.5 1.0 SG A:CYS42 2.5 28.6 1.0 CB A:CYS16 3.0 28.9 1.0 CB A:CYS11 3.3 31.6 1.0 CB A:CYS42 3.3 25.5 1.0 CB A:CYS39 3.4 29.6 1.0 N A:CYS39 3.9 28.2 1.0 N A:CYS42 4.2 29.2 1.0 CG2 A:THR18 4.2 33.7 1.0 CA A:CYS39 4.2 29.3 1.0 CA A:CYS42 4.4 24.1 1.0 CB A:ASN13 4.4 30.9 1.0 NH2 A:ARG41 4.5 42.2 1.0 CA A:CYS16 4.5 36.0 1.0 N A:GLY17 4.6 36.3 1.0 ND2 A:ASN13 4.7 23.8 1.0 CA A:CYS11 4.7 32.6 1.0 C A:CYS39 4.9 28.4 1.0 C A:CYS16 5.0 37.4 1.0

M.M.Zhang, B.X.Wu. ATVAL1 Phd-Like Domain in the P6122 Space Group To Be Published.