Zinc in PDB 2f6j: Crystal Structure of Phd Finger-Linker-Bromodomain Fragment of Human Bptf in the H3(1-15)K4ME3 Bound State

The structure of Crystal Structure of Phd Finger-Linker-Bromodomain Fragment of Human Bptf in the H3(1-15)K4ME3 Bound State, PDB code: 2f6j 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)	N/A / 2.00
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	38.579, 84.987, 109.385, 90.00, 99.23, 90.00
R / Rfree (%)	19.8 / 22.7

The binding sites of Zinc atom in the Crystal Structure of Phd Finger-Linker-Bromodomain Fragment of Human Bptf in the H3(1-15)K4ME3 Bound State (pdb code 2f6j). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Crystal Structure of Phd Finger-Linker-Bromodomain Fragment of Human Bptf in the H3(1-15)K4ME3 Bound State, PDB code: 2f6j:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in the Crystal Structure of Phd Finger-Linker-Bromodomain Fragment of Human Bptf in the H3(1-15)K4ME3 Bound State


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 H3(1-15)K4ME3 Bound State within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1001 b:25.0 occ:1.00 ND1 A:HIS34 2.2 19.6 1.0 SG A:CYS37 2.2 22.8 1.0 SG A:CYS13 2.3 24.0 1.0 SG A:CYS11 2.3 17.5 1.0 CG A:HIS34 3.1 18.1 1.0 CB A:CYS11 3.2 18.6 1.0 CE1 A:HIS34 3.2 20.2 1.0 CB A:CYS37 3.3 21.2 1.0 CB A:HIS34 3.3 18.4 1.0 CB A:CYS13 3.5 26.0 1.0 N A:CYS13 4.1 24.3 1.0 N A:HIS34 4.2 18.3 1.0 O A:HOH1151 4.2 38.2 1.0 CD2 A:HIS34 4.3 20.4 1.0 NE2 A:HIS34 4.3 20.1 1.0 CA A:HIS34 4.4 19.2 1.0 CA A:CYS13 4.4 25.5 1.0 CA A:CYS11 4.6 20.1 1.0 N A:ILE12 4.6 20.5 1.0 CA A:CYS37 4.7 22.1 1.0 CG1 A:ILE12 4.8 31.9 1.0 O A:HOH1110 4.9 39.8 1.0 OG1 A:THR15 4.9 26.0 1.0 C A:CYS11 4.9 21.6 1.0 N A:CYS37 5.0 21.4 1.0

Zinc binding site 2 out of 6 in the Crystal Structure of Phd Finger-Linker-Bromodomain Fragment of Human Bptf in the H3(1-15)K4ME3 Bound State


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 H3(1-15)K4ME3 Bound State within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1002 b:21.4 occ:1.00 SG A:CYS26 2.3 16.1 1.0 SG A:CYS56 2.3 17.3 1.0 SG A:CYS29 2.4 16.8 1.0 SG A:CYS53 2.4 16.7 1.0 CB A:CYS26 3.2 18.8 1.0 CB A:CYS56 3.3 17.1 1.0 CB A:CYS29 3.3 19.2 1.0 CB A:CYS53 3.6 16.6 1.0 N A:CYS29 3.6 20.9 1.0 OH A:TYR33 4.0 17.2 1.0 N A:CYS53 4.0 19.1 1.0 CA A:CYS29 4.1 17.9 1.0 O A:HOH1084 4.1 26.1 1.0 CE1 A:TYR33 4.3 12.5 1.0 CB A:ARG28 4.3 25.9 1.0 CA A:CYS53 4.3 18.0 1.0 N A:CYS56 4.3 16.1 1.0 CA A:CYS56 4.4 18.1 1.0 CZ A:TYR33 4.5 17.8 1.0 C A:ARG28 4.6 22.2 1.0 CA A:CYS26 4.6 19.5 1.0 CA A:ARG28 4.8 23.5 1.0 O A:CYS53 4.9 19.1 1.0 N A:ARG28 4.9 23.5 1.0 C A:CYS53 4.9 18.4 1.0 C A:CYS29 5.0 16.9 1.0

Zinc binding site 3 out of 6 in the Crystal Structure of Phd Finger-Linker-Bromodomain Fragment of Human Bptf in the H3(1-15)K4ME3 Bound State


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 H3(1-15)K4ME3 Bound State within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1003 b:27.3 occ:1.00 ND1 B:HIS34 2.2 26.8 1.0 SG B:CYS13 2.2 24.9 1.0 SG B:CYS37 2.3 25.1 1.0 SG B:CYS11 2.4 23.8 1.0 CG B:HIS34 3.1 25.2 1.0 CE1 B:HIS34 3.1 27.5 1.0 CB B:CYS11 3.2 21.9 1.0 CB B:CYS37 3.2 26.3 1.0 CB B:HIS34 3.4 25.4 1.0 CB B:CYS13 3.4 28.6 1.0 N B:CYS13 4.0 28.4 1.0 N B:HIS34 4.2 25.4 1.0 NE2 B:HIS34 4.3 25.6 1.0 CD2 B:HIS34 4.3 25.0 1.0 CA B:CYS13 4.3 28.1 1.0 O B:HOH1121 4.4 35.7 1.0 CA B:HIS34 4.5 25.6 1.0 N B:ILE12 4.5 29.2 1.0 CA B:CYS11 4.6 27.2 1.0 CA B:CYS37 4.7 28.6 1.0 OG1 B:THR15 4.8 26.9 1.0 C B:CYS11 4.9 28.1 1.0

Zinc binding site 4 out of 6 in the Crystal Structure of Phd Finger-Linker-Bromodomain Fragment of Human Bptf in the H3(1-15)K4ME3 Bound State


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 H3(1-15)K4ME3 Bound State within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1004 b:25.2 occ:1.00 SG B:CYS29 2.3 22.3 1.0 SG B:CYS56 2.3 21.1 1.0 SG B:CYS53 2.3 23.4 1.0 SG B:CYS26 2.3 22.1 1.0 CB B:CYS26 3.2 24.4 1.0 CB B:CYS56 3.2 21.2 1.0 CB B:CYS29 3.3 22.7 1.0 CB B:CYS53 3.5 24.1 1.0 N B:CYS29 3.6 20.4 1.0 OH B:TYR33 4.0 22.6 1.0 N B:CYS53 4.0 24.2 1.0 CA B:CYS29 4.1 21.1 1.0 O B:HOH1075 4.3 25.0 1.0 CA B:CYS53 4.3 24.8 1.0 N B:CYS56 4.3 22.4 1.0 CA B:CYS56 4.4 22.8 1.0 CB B:ARG28 4.4 18.8 1.0 CE1 B:TYR33 4.6 21.0 1.0 CA B:CYS26 4.6 24.3 1.0 CZ B:TYR33 4.7 23.3 1.0 O B:HOH1066 4.7 42.9 1.0 C B:ARG28 4.7 20.7 1.0 O B:CYS53 4.8 26.6 1.0 C B:CYS53 4.9 24.9 1.0 C B:CYS29 4.9 22.3 1.0 CA B:ARG28 4.9 21.9 1.0 N B:ARG28 5.0 22.1 1.0

Zinc binding site 5 out of 6 in the Crystal Structure of Phd Finger-Linker-Bromodomain Fragment of Human Bptf in the H3(1-15)K4ME3 Bound State


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of Phd Finger-Linker-Bromodomain Fragment of Human Bptf in the H3(1-15)K4ME3 Bound State within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn1005 b:37.1 occ:1.00 SG C:CYS37 2.2 37.4 1.0 SG C:CYS13 2.3 38.3 1.0 SG C:CYS11 2.3 31.4 1.0 ND1 C:HIS34 2.4 33.5 1.0 CB C:CYS37 3.1 42.2 1.0 CB C:CYS11 3.1 33.4 1.0 CG C:HIS34 3.2 33.6 1.0 CB C:HIS34 3.4 32.8 1.0 CE1 C:HIS34 3.4 33.6 1.0 CB C:CYS13 3.5 43.2 1.0 N C:CYS13 4.0 44.1 1.0 N C:HIS34 4.2 30.4 1.0 CD2 C:HIS34 4.4 33.0 1.0 CA C:HIS34 4.4 32.1 1.0 CA C:CYS13 4.4 43.1 1.0 NE2 C:HIS34 4.4 34.7 1.0 CA C:CYS11 4.5 37.3 1.0 N C:ILE12 4.6 40.3 1.0 CA C:CYS37 4.6 43.9 1.0 OG1 C:THR15 4.8 38.9 1.0 C C:CYS11 4.8 38.0 1.0 N C:CYS37 4.9 44.7 1.0

Zinc binding site 6 out of 6 in the Crystal Structure of Phd Finger-Linker-Bromodomain Fragment of Human Bptf in the H3(1-15)K4ME3 Bound State


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of Phd Finger-Linker-Bromodomain Fragment of Human Bptf in the H3(1-15)K4ME3 Bound State within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn1006 b:30.5 occ:1.00 SG C:CYS26 2.3 27.2 1.0 SG C:CYS29 2.4 27.8 1.0 SG C:CYS53 2.4 30.1 1.0 SG C:CYS56 2.4 23.6 1.0 CB C:CYS26 3.1 28.2 1.0 CB C:CYS29 3.2 28.3 1.0 CB C:CYS56 3.2 28.2 1.0 CB C:CYS53 3.6 31.9 1.0 N C:CYS29 3.6 26.7 1.0 OH C:TYR33 3.9 36.7 1.0 N C:CYS53 4.0 32.4 1.0 CA C:CYS29 4.0 27.6 1.0 N C:CYS56 4.3 32.2 1.0 CA C:CYS53 4.3 33.0 1.0 CB C:ARG28 4.4 28.1 1.0 CA C:CYS56 4.4 30.5 1.0 CE1 C:TYR33 4.5 34.8 1.0 CA C:CYS26 4.6 29.1 1.0 CZ C:TYR33 4.6 33.9 1.0 C C:ARG28 4.7 27.8 1.0 C C:CYS29 4.9 28.5 1.0 CA C:ARG28 4.9 29.4 1.0 O C:CYS53 4.9 33.9 1.0 C C:CYS53 4.9 34.0 1.0 N C:ARG28 5.0 29.8 1.0 C C:CYS26 5.0 29.7 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