Zinc in PDB 2yyr: Structural Analysis of Phd Domain of Pygopus Complexed with Trimethylated Histone H3 Peptide

The structure of Structural Analysis of Phd Domain of Pygopus Complexed with Trimethylated Histone H3 Peptide, PDB code: 2yyr was solved by Y.Nakamura, B.Padmanabhan, S.Yokoyama, Riken Structuralgenomics/Proteomics Initiative (Rsgi), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.43 / 2.50
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	59.518, 59.518, 95.853, 90.00, 90.00, 90.00
R / Rfree (%)	21.3 / 23.4

The binding sites of Zinc atom in the Structural Analysis of Phd Domain of Pygopus Complexed with Trimethylated Histone H3 Peptide (pdb code 2yyr). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Structural Analysis of Phd Domain of Pygopus Complexed with Trimethylated Histone H3 Peptide, PDB code: 2yyr:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Structural Analysis of Phd Domain of Pygopus Complexed with Trimethylated Histone H3 Peptide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structural Analysis of Phd Domain of Pygopus Complexed with Trimethylated Histone H3 Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:28.9 occ:1.00 ND1 A:HIS366 2.1 25.4 1.0 SG A:CYS369 2.2 31.2 1.0 SG A:CYS341 2.3 31.8 1.0 SG A:CYS344 2.4 31.9 1.0 CG A:HIS366 3.0 27.9 1.0 CB A:CYS341 3.0 33.3 1.0 CE1 A:HIS366 3.2 26.9 1.0 CB A:HIS366 3.2 27.2 1.0 CB A:CYS344 3.3 31.8 1.0 CB A:CYS369 3.4 32.6 1.0 N A:CYS344 3.9 33.2 1.0 N A:HIS366 4.1 28.6 1.0 CA A:CYS344 4.1 33.4 1.0 CD2 A:HIS366 4.2 28.7 1.0 NE2 A:HIS366 4.2 26.6 1.0 CA A:HIS366 4.3 28.0 1.0 CA A:CYS341 4.5 33.6 1.0 CA A:CYS369 4.7 31.5 1.0 C A:CYS344 4.9 34.2 1.0 N A:THR345 5.0 34.6 1.0

Zinc binding site 2 out of 4 in the Structural Analysis of Phd Domain of Pygopus Complexed with Trimethylated Histone H3 Peptide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structural Analysis of Phd Domain of Pygopus Complexed with Trimethylated Histone H3 Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn402 b:41.8 occ:1.00 SG A:CYS361 2.2 49.3 1.0 SG A:CYS390 2.2 36.6 1.0 SG A:CYS393 2.3 54.1 1.0 SG A:CYS357 2.4 34.1 1.0 CB A:CYS357 3.2 36.6 1.0 CB A:CYS361 3.2 52.1 1.0 CB A:CYS393 3.3 55.9 1.0 CB A:CYS390 3.5 38.3 1.0 N A:CYS361 3.7 54.8 1.0 N A:CYS390 3.9 37.1 1.0 CA A:CYS361 4.0 52.4 1.0 O A:HOH38 4.1 50.1 1.0 CZ A:PHE365 4.2 29.9 1.0 N A:CYS393 4.2 55.6 1.0 CA A:CYS390 4.3 39.9 1.0 CE1 A:PHE365 4.3 28.5 1.0 CA A:CYS393 4.4 57.4 1.0 CA A:CYS357 4.7 39.9 1.0 C A:CYS361 4.8 51.5 1.0 C A:SER360 4.8 56.4 1.0 O A:CYS390 4.8 44.4 1.0 O A:CYS357 4.8 42.8 1.0 N A:GLN362 4.9 50.3 1.0 C A:CYS390 4.9 42.9 1.0 N A:SER360 4.9 57.9 1.0

Zinc binding site 3 out of 4 in the Structural Analysis of Phd Domain of Pygopus Complexed with Trimethylated Histone H3 Peptide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structural Analysis of Phd Domain of Pygopus Complexed with Trimethylated Histone H3 Peptide within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn403 b:28.4 occ:1.00 ND1 B:HIS366 2.2 25.2 1.0 SG B:CYS369 2.3 26.8 1.0 SG B:CYS341 2.4 26.3 1.0 SG B:CYS344 2.4 30.0 1.0 CB B:CYS341 2.9 26.7 1.0 CG B:HIS366 3.1 27.2 1.0 CB B:HIS366 3.3 25.1 1.0 CE1 B:HIS366 3.3 26.3 1.0 CB B:CYS344 3.4 28.8 1.0 CB B:CYS369 3.4 26.7 1.0 N B:CYS344 3.9 28.8 1.0 N B:HIS366 4.1 25.9 1.0 CA B:CYS344 4.2 28.7 1.0 CA B:HIS366 4.3 26.9 1.0 CD2 B:HIS366 4.3 26.4 1.0 NE2 B:HIS366 4.4 27.1 1.0 CA B:CYS341 4.4 26.8 1.0 CA B:CYS369 4.8 26.8 1.0 C B:CYS344 4.9 29.3 1.0 N B:CYS369 5.0 26.3 1.0 C B:ILE343 5.0 28.8 1.0

Zinc binding site 4 out of 4 in the Structural Analysis of Phd Domain of Pygopus Complexed with Trimethylated Histone H3 Peptide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structural Analysis of Phd Domain of Pygopus Complexed with Trimethylated Histone H3 Peptide within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn404 b:31.8 occ:1.00 SG B:CYS390 2.2 29.7 1.0 SG B:CYS361 2.3 34.8 1.0 SG B:CYS393 2.3 39.4 1.0 SG B:CYS357 2.4 26.3 1.0 CB B:CYS357 3.3 28.8 1.0 CB B:CYS361 3.4 34.1 1.0 CB B:CYS393 3.4 44.5 1.0 CB B:CYS390 3.5 32.9 1.0 N B:CYS361 3.9 37.6 1.0 N B:CYS390 3.9 32.1 1.0 CA B:CYS361 4.1 34.5 1.0 CA B:CYS390 4.3 32.4 1.0 N B:CYS393 4.3 44.9 1.0 O B:HOH45 4.3 48.0 1.0 CZ B:PHE365 4.4 26.6 1.0 CA B:CYS393 4.5 45.8 1.0 O B:HOH59 4.5 76.0 1.0 CE1 B:PHE365 4.5 27.7 1.0 N B:GLN362 4.7 30.2 1.0 CA B:CYS357 4.7 30.4 1.0 C B:CYS361 4.8 33.0 1.0 C B:CYS390 4.9 34.2 1.0 O B:CYS390 4.9 33.6 1.0 C B:SER360 4.9 40.0 1.0 O B:CYS357 5.0 32.4 1.0

Y.Nakamura, T.Umehara, B.Padmanabhan, S.Yokoyama. Structural Analysis of Phd Domain of Pygopus Complexed with Trimethylated Histone H3 Peptide To Be Published.