Zinc in PDB 2f6n: Crystal Structure of Phd Finger-Linker-Bromodomain Fragment of Human Bptf in the Free Form

The structure of Crystal Structure of Phd Finger-Linker-Bromodomain Fragment of Human Bptf in the Free Form, PDB code: 2f6n was solved by H.Li, D.J.Patel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 2.00
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	85.144, 144.894, 38.315, 90.00, 90.00, 90.00
R / Rfree (%)	21.7 / 23.4

The binding sites of Zinc atom in the Crystal Structure of Phd Finger-Linker-Bromodomain Fragment of Human Bptf in the Free Form (pdb code 2f6n). 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 Phd Finger-Linker-Bromodomain Fragment of Human Bptf in the Free Form, PDB code: 2f6n:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of Phd Finger-Linker-Bromodomain Fragment of Human Bptf in the Free Form


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 Phd Finger-Linker-Bromodomain Fragment of Human Bptf in the Free Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1001 b:19.1 occ:1.00 ND1 A:HIS34 2.2 16.8 1.0 SG A:CYS37 2.3 18.4 1.0 SG A:CYS13 2.3 17.6 1.0 SG A:CYS11 2.4 17.9 1.0 CG A:HIS34 3.1 17.4 1.0 CE1 A:HIS34 3.2 17.2 1.0 CB A:CYS11 3.2 20.5 1.0 CB A:CYS37 3.2 20.0 1.0 CB A:HIS34 3.3 19.5 1.0 CB A:CYS13 3.5 22.5 1.0 N A:CYS13 4.0 23.4 1.0 N A:HIS34 4.1 21.4 1.0 CD2 A:HIS34 4.2 15.9 1.0 NE2 A:HIS34 4.3 17.8 1.0 CA A:HIS34 4.3 20.0 1.0 CA A:CYS13 4.4 21.7 1.0 O A:HOH1152 4.5 39.2 1.0 N A:ILE12 4.6 23.5 1.0 CA A:CYS11 4.6 22.3 1.0 CA A:CYS37 4.6 20.6 1.0 O A:HOH1146 4.8 40.0 1.0 C A:CYS11 4.9 22.5 1.0 OG1 A:THR15 4.9 25.2 1.0 O A:HIS34 5.0 20.2 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of Phd Finger-Linker-Bromodomain Fragment of Human Bptf in the Free Form


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 Phd Finger-Linker-Bromodomain Fragment of Human Bptf in the Free Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1002 b:14.1 occ:1.00 SG A:CYS29 2.2 15.4 1.0 SG A:CYS26 2.3 12.9 1.0 SG A:CYS56 2.3 14.0 1.0 SG A:CYS53 2.4 15.7 1.0 CB A:CYS26 3.2 17.0 1.0 CB A:CYS29 3.2 15.0 1.0 CB A:CYS56 3.3 12.9 1.0 CB A:CYS53 3.5 16.9 1.0 N A:CYS29 3.6 12.3 1.0 N A:CYS53 4.0 17.5 1.0 OH A:TYR33 4.0 24.6 1.0 CA A:CYS29 4.0 14.6 1.0 N A:CYS56 4.3 16.6 1.0 CA A:CYS53 4.3 17.6 1.0 O A:HOH1117 4.3 17.1 1.0 CA A:CYS56 4.4 15.7 1.0 CB A:ARG28 4.4 14.5 1.0 CE1 A:TYR33 4.6 19.4 1.0 CA A:CYS26 4.6 14.8 1.0 C A:ARG28 4.7 13.5 1.0 CZ A:TYR33 4.7 21.2 1.0 O A:HOH1095 4.7 26.7 1.0 O A:CYS53 4.8 18.0 1.0 C A:CYS53 4.9 18.1 1.0 C A:CYS29 4.9 15.1 1.0 CA A:ARG28 5.0 13.9 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of Phd Finger-Linker-Bromodomain Fragment of Human Bptf in the Free Form


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 Phd Finger-Linker-Bromodomain Fragment of Human Bptf in the Free Form within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1003 b:25.5 occ:1.00 SG B:CYS37 2.1 25.5 1.0 ND1 B:HIS34 2.2 24.7 1.0 SG B:CYS13 2.3 25.1 1.0 SG B:CYS11 2.3 23.5 1.0 CE1 B:HIS34 3.2 24.3 1.0 CB B:CYS37 3.2 30.2 1.0 CG B:HIS34 3.2 23.3 1.0 CB B:CYS11 3.3 24.4 1.0 CB B:CYS13 3.4 28.7 1.0 CB B:HIS34 3.5 23.9 1.0 O B:HOH1121 3.9 36.3 1.0 N B:CYS13 3.9 30.7 1.0 N B:HIS34 4.1 23.0 1.0 NE2 B:HIS34 4.3 25.1 1.0 CA B:CYS13 4.3 29.6 1.0 CD2 B:HIS34 4.3 22.4 1.0 CA B:HIS34 4.4 23.1 1.0 N B:ILE12 4.5 30.0 1.0 CA B:CYS37 4.5 31.7 1.0 CA B:CYS11 4.6 26.8 1.0 C B:CYS11 4.8 28.4 1.0 N B:CYS37 4.9 32.4 1.0 O B:HOH1053 4.9 40.8 1.0 O B:HIS34 4.9 24.5 1.0 OG1 B:THR15 5.0 26.0 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of Phd Finger-Linker-Bromodomain Fragment of Human Bptf in the Free Form


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 Phd Finger-Linker-Bromodomain Fragment of Human Bptf in the Free Form within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1004 b:25.0 occ:1.00 SG B:CYS26 2.2 25.5 1.0 SG B:CYS53 2.3 25.0 1.0 SG B:CYS29 2.3 30.7 1.0 SG B:CYS56 2.3 24.6 1.0 CB B:CYS26 3.2 28.8 1.0 CB B:CYS56 3.2 25.2 1.0 CB B:CYS29 3.3 31.2 1.0 CB B:CYS53 3.4 24.7 1.0 N B:CYS29 3.7 33.1 1.0 N B:CYS53 3.9 25.7 1.0 CA B:CYS29 4.1 31.9 1.0 OH B:TYR33 4.1 26.4 1.0 O B:HOH1102 4.2 48.5 1.0 CA B:CYS53 4.2 25.2 1.0 CA B:CYS56 4.4 25.2 1.0 N B:CYS56 4.4 25.6 1.0 CB B:ARG28 4.4 37.7 1.0 CA B:CYS26 4.6 28.8 1.0 O B:CYS26 4.7 31.2 1.0 CE1 B:TYR33 4.8 25.1 1.0 C B:ARG28 4.8 35.5 1.0 O B:CYS53 4.8 25.5 1.0 CZ B:TYR33 4.9 24.6 1.0 C B:CYS53 4.9 27.1 1.0 C B:CYS26 4.9 31.1 1.0 C B:CYS29 5.0 30.9 1.0

H.Li, S.Ilin, W.Wang, E.M.Duncan, J.Wysocka, C.D.Allis, D.J.Patel. Molecular Basis For Site-Specific Read-Out of Histone H3K4ME3 By the Bptf Phd Finger of Nurf. Nature V. 442 91 2006.
ISSN: ISSN 0028-0836
PubMed: 16728978
DOI: 10.1038/NATURE04802