Zinc in PDB 7pok: Crystal Structure of Zad-Domain of Pita Protein From D.Melanogaster

The structure of Crystal Structure of Zad-Domain of Pita Protein From D.Melanogaster, PDB code: 7pok was solved by K.M.Boyko, A.N.Bonchuk, A.Y.Nikolaeva, P.G.Georgiev, V.O.Popov, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	62.81 / 1.80
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	87.265, 90.489, 105.77, 90, 90, 90
R / Rfree (%)	19 / 22.2

The binding sites of Zinc atom in the Crystal Structure of Zad-Domain of Pita Protein From D.Melanogaster (pdb code 7pok). 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 Zad-Domain of Pita Protein From D.Melanogaster, PDB code: 7pok:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of Zad-Domain of Pita Protein From D.Melanogaster


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 Zad-Domain of Pita Protein From D.Melanogaster within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn201 b:30.8 occ:1.00 SG A:CYS66 2.2 32.2 1.0 SG A:CYS18 2.3 28.9 1.0 SG A:CYS69 2.3 28.8 1.0 SG A:CYS21 2.4 30.4 1.0 CB A:CYS69 3.1 31.0 1.0 CB A:CYS18 3.2 30.8 1.0 CB A:CYS21 3.2 28.5 1.0 CB A:CYS66 3.4 32.1 1.0 N A:CYS21 3.7 27.3 1.0 N A:CYS66 3.9 30.8 1.0 CA A:CYS21 4.0 28.9 1.0 N A:CYS69 4.2 29.1 1.0 CG2 A:THR23 4.2 37.5 1.0 CA A:CYS66 4.2 31.6 1.0 CD D:LYS105 4.2 48.8 1.0 CA A:CYS69 4.2 30.3 1.0 NZ D:LYS105 4.5 53.2 1.0 CE D:LYS105 4.5 50.9 1.0 C A:PHE20 4.6 26.6 1.0 CA A:CYS18 4.7 29.0 1.0 CB A:PHE20 4.7 24.9 1.0 C A:CYS21 4.7 29.7 1.0 O A:CYS66 4.8 31.2 1.0 C A:CYS66 4.8 31.7 1.0 CG D:LYS105 4.9 46.1 1.0 N A:LEU22 4.9 30.1 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of Zad-Domain of Pita Protein From D.Melanogaster


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 Zad-Domain of Pita Protein From D.Melanogaster within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn201 b:47.4 occ:1.00 SG B:CYS21 2.3 51.6 1.0 SG B:CYS69 2.3 45.3 1.0 SG B:CYS18 2.3 46.1 1.0 SG B:CYS66 2.3 52.4 1.0 CB B:CYS69 3.1 46.8 1.0 CB B:CYS18 3.2 52.2 1.0 CB B:CYS21 3.3 51.5 1.0 CB B:CYS66 3.4 52.2 1.0 N B:CYS21 3.7 44.1 1.0 N B:CYS66 4.0 48.5 1.0 CA B:CYS21 4.1 46.6 1.0 CG2 B:THR23 4.1 55.9 1.0 N B:CYS69 4.2 48.2 1.0 CA B:CYS69 4.2 46.2 1.0 CA B:CYS66 4.2 51.5 1.0 NZ C:LYS105 4.4 84.0 1.0 CA B:CYS18 4.7 51.9 1.0 C B:PHE20 4.7 42.3 1.0 C B:CYS21 4.7 48.8 1.0 CE C:LYS105 4.7 83.9 1.0 O B:CYS66 4.8 48.4 1.0 CD C:LYS105 4.8 83.2 1.0 C B:CYS66 4.9 52.2 1.0 CB B:PHE20 4.9 41.0 1.0 N B:LEU22 4.9 49.8 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of Zad-Domain of Pita Protein From D.Melanogaster


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 Zad-Domain of Pita Protein From D.Melanogaster within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn201 b:40.8 occ:1.00 SG C:CYS18 2.2 39.2 1.0 SG C:CYS69 2.3 42.0 1.0 SG C:CYS21 2.3 43.5 1.0 SG C:CYS66 2.4 43.1 1.0 CB C:CYS69 3.1 44.1 1.0 CB C:CYS21 3.2 43.1 1.0 CB C:CYS18 3.2 43.4 1.0 CB C:CYS66 3.4 50.2 1.0 N C:CYS21 3.7 40.2 1.0 N C:CYS66 3.9 43.9 1.0 CA C:CYS21 4.0 40.1 1.0 N C:CYS69 4.1 45.0 1.0 CG2 C:THR23 4.2 51.9 1.0 CA C:CYS69 4.2 44.0 1.0 CA C:CYS66 4.2 47.2 1.0 CD B:LYS105 4.2 64.7 1.0 CE B:LYS105 4.4 63.6 1.0 NZ B:LYS105 4.5 63.5 1.0 C C:PHE20 4.7 35.5 1.0 CA C:CYS18 4.7 41.0 1.0 C C:CYS21 4.7 39.5 1.0 O C:CYS66 4.8 44.0 1.0 CG B:LYS105 4.8 59.6 1.0 C C:CYS66 4.8 47.4 1.0 CB C:PHE20 4.8 34.0 1.0 N C:LEU22 5.0 40.3 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of Zad-Domain of Pita Protein From D.Melanogaster


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 Zad-Domain of Pita Protein From D.Melanogaster within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn201 b:37.9 occ:1.00 SG D:CYS18 2.2 36.6 1.0 SG D:CYS21 2.3 41.3 1.0 SG D:CYS66 2.4 43.6 1.0 SG D:CYS69 2.4 33.7 1.0 CB D:CYS69 3.1 34.6 1.0 CB D:CYS18 3.2 41.5 1.0 CB D:CYS21 3.4 38.9 1.0 CB D:CYS66 3.4 43.2 1.0 N D:CYS21 3.7 33.6 1.0 N D:CYS66 4.0 34.5 1.0 CA D:CYS21 4.0 34.6 1.0 CG2 D:THR23 4.2 50.2 1.0 CA D:CYS66 4.2 38.1 1.0 N D:CYS69 4.3 40.7 1.0 CA D:CYS69 4.3 35.9 1.0 CE A:LYS105 4.3 55.4 0.5 C D:PHE20 4.6 31.3 1.0 CA D:CYS18 4.7 38.6 1.0 CE A:LYS105 4.7 48.5 0.5 NZ A:LYS105 4.7 49.6 0.5 C D:CYS21 4.8 36.6 1.0 CB D:PHE20 4.8 32.8 1.0 O D:CYS66 4.8 37.6 1.0 C D:CYS66 4.8 42.9 1.0 NZ A:LYS105 4.9 49.5 0.5 N D:LEU22 4.9 36.0 1.0

A.N.Bonchuk, K.M.Boyko, A.Y.Nikolaeva, A.D.Burtseva, V.O.Popov, P.G.Georgiev. Structural Insights Into Highly Similar Spatial Organization of Zinc-Finger Associated (Zad) Domains with A Very Low Sequence Similarity To Be Published.