Zinc in PDB 2dx8: Crystal Structure Analysis of the Phd Domain of the Transcription Coactivator Pygophus

The structure of Crystal Structure Analysis of the Phd Domain of the Transcription Coactivator Pygophus, PDB code: 2dx8 was solved by 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)	20.00 / 2.70
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	60.079, 60.079, 95.242, 90.00, 90.00, 90.00
R / Rfree (%)	19.7 / 25.5

The binding sites of Zinc atom in the Crystal Structure Analysis of the Phd Domain of the Transcription Coactivator Pygophus (pdb code 2dx8). 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 Analysis of the Phd Domain of the Transcription Coactivator Pygophus, PDB code: 2dx8:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure Analysis of the Phd Domain of the Transcription Coactivator Pygophus


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure Analysis of the Phd Domain of the Transcription Coactivator Pygophus within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:61.9 occ:1.00 ND1 A:HIS366 2.2 42.1 1.0 SG A:CYS369 2.4 45.1 1.0 SG A:CYS341 2.5 52.6 1.0 SG A:CYS344 2.6 51.0 1.0 CB A:CYS341 3.0 52.6 1.0 CG A:HIS366 3.2 41.1 1.0 CE1 A:HIS366 3.2 42.0 1.0 CB A:CYS369 3.4 43.8 1.0 CB A:CYS344 3.4 49.3 1.0 CB A:HIS366 3.4 40.8 1.0 N A:CYS344 3.9 50.8 1.0 N A:HIS366 3.9 42.7 1.0 CA A:CYS344 4.2 50.1 1.0 CA A:HIS366 4.3 40.7 1.0 NE2 A:HIS366 4.3 39.2 1.0 CD2 A:HIS366 4.3 41.2 1.0 CA A:CYS341 4.5 53.8 1.0 CA A:CYS369 4.7 44.9 1.0 O A:HIS366 4.8 39.4 1.0 N A:CYS369 4.9 44.9 1.0 C A:ILE343 4.9 51.4 1.0 CB A:ILE343 4.9 51.1 1.0 C A:CYS344 4.9 50.6 1.0 N A:THR345 5.0 50.6 1.0 N A:ILE343 5.0 53.0 1.0 O A:ASN346 5.0 59.1 1.0

Zinc binding site 2 out of 4 in the Crystal Structure Analysis of the Phd Domain of the Transcription Coactivator Pygophus


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure Analysis of the Phd Domain of the Transcription Coactivator Pygophus within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn402 b:77.4 occ:1.00 SG A:CYS357 2.4 52.5 1.0 SG A:CYS393 2.5 77.2 1.0 SG A:CYS361 2.5 64.4 1.0 SG A:CYS390 2.5 60.3 1.0 CB A:CYS393 3.3 77.3 1.0 CB A:CYS357 3.3 52.2 1.0 CB A:CYS390 3.4 59.4 1.0 N A:CYS390 3.8 56.3 1.0 CB A:CYS361 3.8 66.8 1.0 CA A:CYS390 4.1 59.2 1.0 N A:CYS393 4.2 75.2 1.0 N A:CYS361 4.2 67.6 1.0 CA A:CYS393 4.3 77.6 1.0 CZ A:PHE365 4.6 46.6 1.0 CA A:CYS361 4.6 66.9 1.0 CE1 A:PHE365 4.6 49.1 1.0 C A:CYS390 4.7 61.0 1.0 O A:CYS390 4.7 61.2 1.0 CA A:CYS357 4.8 52.1 1.0 C A:GLY389 4.9 53.7 1.0 O A:CYS357 5.0 53.6 1.0

Zinc binding site 3 out of 4 in the Crystal Structure Analysis of the Phd Domain of the Transcription Coactivator Pygophus


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure Analysis of the Phd Domain of the Transcription Coactivator Pygophus within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn403 b:59.8 occ:1.00 ND1 B:HIS366 2.4 33.3 1.0 SG B:CYS341 2.4 44.3 1.0 SG B:CYS369 2.4 43.5 1.0 SG B:CYS344 2.5 45.8 1.0 CB B:CYS341 3.0 43.9 1.0 CG B:HIS366 3.3 35.4 1.0 CE1 B:HIS366 3.3 37.5 1.0 CB B:HIS366 3.5 36.4 1.0 CB B:CYS344 3.5 45.3 1.0 CB B:CYS369 3.6 40.5 1.0 N B:CYS344 4.1 44.8 1.0 N B:HIS366 4.1 38.1 1.0 O B:HOH5 4.2 54.1 1.0 CA B:CYS344 4.3 45.4 1.0 CA B:HIS366 4.4 36.2 1.0 CD2 B:HIS366 4.4 40.1 1.0 NE2 B:HIS366 4.5 38.5 1.0 CA B:CYS341 4.5 45.5 1.0 CA B:CYS369 4.9 40.2 1.0 O B:HIS366 4.9 36.9 1.0 N B:CYS369 5.0 40.4 1.0 CB B:ILE343 5.0 42.4 1.0

Zinc binding site 4 out of 4 in the Crystal Structure Analysis of the Phd Domain of the Transcription Coactivator Pygophus


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure Analysis of the Phd Domain of the Transcription Coactivator Pygophus within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn404 b:66.1 occ:1.00 SG B:CYS393 2.3 55.8 1.0 SG B:CYS361 2.4 43.9 1.0 SG B:CYS357 2.4 40.9 1.0 SG B:CYS390 2.5 42.1 1.0 CB B:CYS357 3.3 39.8 1.0 CB B:CYS390 3.4 44.6 1.0 CB B:CYS393 3.5 56.2 1.0 CB B:CYS361 3.7 43.6 1.0 N B:CYS390 3.8 44.5 1.0 N B:CYS361 3.9 43.6 1.0 CA B:CYS390 4.2 44.5 1.0 N B:CYS393 4.3 53.9 1.0 CA B:CYS361 4.4 43.2 1.0 O B:CYS361 4.5 43.8 1.0 CZ B:PHE365 4.5 38.1 1.0 CA B:CYS393 4.5 55.7 1.0 C B:CYS361 4.7 42.4 1.0 CA B:CYS357 4.7 39.9 1.0 CE1 B:PHE365 4.7 35.4 1.0 O B:CYS390 4.7 46.5 1.0 C B:CYS390 4.7 46.4 1.0 N B:SER360 4.8 46.6 1.0 C B:SER360 4.8 44.2 1.0 CB B:SER360 4.8 47.6 1.0 O B:CYS357 4.9 40.2 1.0 C B:GLY389 5.0 44.6 1.0 CA B:SER360 5.0 46.1 1.0

Y.Nakamura, T.Umehara, H.Hamana, Y.Hayashizaki, M.Inoue, T.Kigawa, M.Shirouzu, T.Terada, A.Tanaka, B.Padmanabhan, S.Yokoyama. Crystal Structure Analysis of the Phd Domain of the Transcription Coactivator Pygopus To Be Published.