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

The structure of Crystal Structure of Zad-Domain of Serendipity-D Protein From D.Melanogaster, PDB code: 7poh was solved by K.M.Boyko, G.S.Kachalova, 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)	70.12 / 2.85
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	99.161, 99.161, 117.667, 90, 90, 90
R / Rfree (%)	21.8 / 24

The binding sites of Zinc atom in the Crystal Structure of Zad-Domain of Serendipity-D Protein From D.Melanogaster (pdb code 7poh). 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 Serendipity-D Protein From D.Melanogaster, PDB code: 7poh:
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 Serendipity-D 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 Serendipity-D Protein From D.Melanogaster within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn101 b:68.9 occ:1.00 SG A:CYS61 2.3 68.8 1.0 SG A:CYS4 2.3 64.4 1.0 SG A:CYS7 2.3 74.2 1.0 SG A:CYS64 2.3 69.5 1.0 CB A:CYS4 2.9 72.8 1.0 CB A:CYS64 3.4 73.9 1.0 CB A:CYS61 3.4 68.2 1.0 N A:CYS7 3.8 71.5 1.0 CB A:CYS7 3.9 72.4 1.0 N A:CYS61 4.0 67.5 1.0 C A:PHE6 4.1 66.6 1.0 NH2 A:ARG63 4.2 79.1 1.0 CA A:CYS61 4.3 68.2 1.0 CA A:CYS7 4.3 69.5 1.0 CA A:CYS4 4.4 71.4 1.0 CB A:PHE6 4.5 66.7 1.0 N A:CYS64 4.5 74.6 1.0 O A:PHE6 4.5 63.8 1.0 CA A:CYS64 4.5 72.4 1.0 N A:GLY8 4.6 78.7 1.0 CA A:PHE6 4.7 62.6 1.0 C A:CYS7 4.8 72.7 1.0 N A:PHE6 4.9 62.9 1.0 CZ A:ARG63 4.9 72.0 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of Zad-Domain of Serendipity-D 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 Serendipity-D Protein From D.Melanogaster within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn102 b:132.0 occ:1.00 O A:PRO56 2.8 123.4 1.0 NH2 A:ARG59 3.6 109.1 1.0 NH1 A:ARG59 3.9 109.0 1.0 C A:PRO56 4.0 123.4 1.0 CZ A:ARG59 4.2 104.4 1.0 CG2 A:THR25 4.4 97.6 1.0 CA A:PRO56 4.5 129.2 1.0 CB A:PRO56 4.6 130.6 1.0 CB A:THR25 5.0 91.5 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of Zad-Domain of Serendipity-D 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 Serendipity-D Protein From D.Melanogaster within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn101 b:130.3 occ:1.00 NH2 B:ARG59 3.1 102.5 1.0 O B:PRO56 3.2 123.9 1.0 C B:PRO56 4.3 123.4 1.0 CA B:GLY57 4.3 102.0 1.0 CZ B:ARG59 4.4 99.5 1.0 CG2 B:THR25 4.4 111.2 1.0 N B:GLY57 4.7 105.8 1.0 CB B:THR25 4.8 108.1 1.0 NH1 B:ARG59 4.9 104.8 1.0 C B:GLY57 5.0 93.2 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of Zad-Domain of Serendipity-D 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 Serendipity-D Protein From D.Melanogaster within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn102 b:65.6 occ:1.00 SG B:CYS61 2.2 63.1 1.0 SG B:CYS7 2.3 62.5 1.0 SG B:CYS4 2.3 65.6 1.0 SG B:CYS64 2.3 79.4 1.0 CB B:CYS64 3.1 76.5 1.0 CB B:CYS7 3.1 67.4 1.0 CB B:CYS4 3.2 70.1 1.0 CB B:CYS61 3.3 68.6 1.0 N B:CYS7 3.6 71.2 1.0 NH2 B:ARG63 3.8 74.5 1.0 N B:CYS61 3.9 69.2 1.0 CA B:CYS7 4.0 68.3 1.0 CA B:CYS61 4.2 68.2 1.0 N B:CYS64 4.2 69.8 1.0 CA B:CYS64 4.2 73.8 1.0 NE B:ARG63 4.5 72.1 1.0 C B:PHE6 4.6 73.2 1.0 O B:CYS61 4.6 70.9 1.0 CZ B:ARG63 4.6 75.7 1.0 CA B:CYS4 4.7 69.6 1.0 CB B:PHE6 4.7 71.3 1.0 C B:CYS61 4.8 70.5 1.0 C B:CYS7 4.8 70.0 1.0 N B:GLY8 4.8 66.3 1.0 N B:PHE6 4.9 67.4 1.0 CB B:ALA9 5.0 60.7 1.0 CA B:PHE6 5.0 69.6 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.