Zinc in PDB 2kwn: Solution Structure of the Double Phd (Plant Homeodomain) Fingers of Human Transcriptional Protein DPF3B Bound to A Histone H4 Peptide Containing Acetylation at Lysine 16

The binding sites of Zinc atom in the Solution Structure of the Double Phd (Plant Homeodomain) Fingers of Human Transcriptional Protein DPF3B Bound to A Histone H4 Peptide Containing Acetylation at Lysine 16 (pdb code 2kwn). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Solution Structure of the Double Phd (Plant Homeodomain) Fingers of Human Transcriptional Protein DPF3B Bound to A Histone H4 Peptide Containing Acetylation at Lysine 16, PDB code: 2kwn:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Solution Structure of the Double Phd (Plant Homeodomain) Fingers of Human Transcriptional Protein DPF3B Bound to A Histone H4 Peptide Containing Acetylation at Lysine 16


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Solution Structure of the Double Phd (Plant Homeodomain) Fingers of Human Transcriptional Protein DPF3B Bound to A Histone H4 Peptide Containing Acetylation at Lysine 16 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn501 b:0.0 occ:1.00 ND1 A:HIS292 2.1 0.0 1.0 SG A:CYS262 2.3 0.0 1.0 SG A:CYS295 2.3 0.0 1.0 SG A:CYS265 2.3 0.0 1.0 HB2 A:HIS292 2.5 0.0 1.0 HB2 A:PHE264 2.6 0.0 1.0 CG A:HIS292 3.0 0.0 1.0 CE1 A:HIS292 3.1 0.0 1.0 HB3 A:CYS262 3.2 0.0 1.0 CB A:CYS262 3.2 0.0 1.0 CB A:HIS292 3.3 0.0 1.0 H A:CYS265 3.3 0.0 1.0 HE1 A:HIS292 3.3 0.0 1.0 HB2 A:CYS262 3.4 0.0 1.0 HB2 A:CYS295 3.4 0.0 1.0 CB A:CYS295 3.4 0.0 1.0 HB2 A:CYS265 3.4 0.0 1.0 CB A:CYS265 3.5 0.0 1.0 N A:CYS265 3.6 0.0 1.0 HB3 A:CYS295 3.6 0.0 1.0 H A:HIS292 3.7 0.0 1.0 CB A:PHE264 3.7 0.0 1.0 HB3 A:HIS292 3.9 0.0 1.0 H A:PHE264 4.0 0.0 1.0 HB3 A:PHE264 4.1 0.0 1.0 C A:PHE264 4.1 0.0 1.0 CA A:CYS265 4.1 0.0 1.0 OD1 A:ASN272 4.2 0.0 1.0 NE2 A:HIS292 4.2 0.0 1.0 CD2 A:HIS292 4.2 0.0 1.0 HD22 A:ASN272 4.2 0.0 1.0 N A:HIS292 4.3 0.0 1.0 CA A:PHE264 4.3 0.0 1.0 HB3 A:CYS265 4.4 0.0 1.0 HD1 A:PHE264 4.4 0.0 1.0 CA A:HIS292 4.4 0.0 1.0 CG A:PHE264 4.6 0.0 1.0 H A:LEU266 4.6 0.0 1.0 N A:PHE264 4.6 0.0 1.0 HG3 A:LYS274 4.6 0.0 1.0 HB2 A:LYS274 4.7 0.0 1.0 CA A:CYS262 4.7 0.0 1.0 ND2 A:ASN272 4.7 0.0 1.0 CG A:ASN272 4.7 0.0 1.0 CD1 A:PHE264 4.8 0.0 1.0 CA A:CYS295 4.8 0.0 1.0 HA A:CYS265 4.8 0.0 1.0 O A:PHE264 4.9 0.0 1.0 H A:CYS295 4.9 0.0 1.0 H A:LYS274 5.0 0.0 1.0 H A:LYS273 5.0 0.0 1.0

Zinc binding site 2 out of 4 in the Solution Structure of the Double Phd (Plant Homeodomain) Fingers of Human Transcriptional Protein DPF3B Bound to A Histone H4 Peptide Containing Acetylation at Lysine 16


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Solution Structure of the Double Phd (Plant Homeodomain) Fingers of Human Transcriptional Protein DPF3B Bound to A Histone H4 Peptide Containing Acetylation at Lysine 16 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn601 b:0.0 occ:1.00 SG A:CYS284 2.3 0.0 1.0 SG A:CYS316 2.3 0.0 1.0 SG A:CYS313 2.3 0.0 1.0 SG A:CYS287 2.3 0.0 1.0 H A:CYS287 2.7 0.0 1.0 HB3 A:ASP286 3.1 0.0 1.0 HB2 A:CYS316 3.1 0.0 1.0 HB3 A:CYS313 3.2 0.0 1.0 HB3 A:CYS287 3.3 0.0 1.0 CB A:CYS284 3.3 0.0 1.0 CB A:CYS316 3.3 0.0 1.0 CB A:CYS313 3.4 0.0 1.0 HB3 A:CYS284 3.4 0.0 1.0 CB A:CYS287 3.4 0.0 1.0 H A:CYS313 3.4 0.0 1.0 HB2 A:CYS284 3.4 0.0 1.0 N A:CYS287 3.5 0.0 1.0 H A:GLY288 3.6 0.0 1.0 HG2 A:ARG289 3.6 0.0 1.0 H A:CYS316 3.7 0.0 1.0 HB2 A:GLU315 3.8 0.0 1.0 N A:CYS313 3.9 0.0 1.0 CA A:CYS287 4.0 0.0 1.0 H A:ARG289 4.0 0.0 1.0 N A:CYS316 4.1 0.0 1.0 HB3 A:CYS316 4.1 0.0 1.0 H A:ASP286 4.1 0.0 1.0 CB A:ASP286 4.1 0.0 1.0 CA A:CYS313 4.1 0.0 1.0 HB2 A:CYS313 4.3 0.0 1.0 HB2 A:CYS287 4.3 0.0 1.0 CA A:CYS316 4.3 0.0 1.0 N A:GLY288 4.4 0.0 1.0 O A:CYS313 4.4 0.0 1.0 HE A:ARG289 4.5 0.0 1.0 C A:CYS313 4.6 0.0 1.0 C A:ASP286 4.6 0.0 1.0 OD1 A:ASP286 4.6 0.0 1.0 H A:GLU315 4.6 0.0 1.0 CG A:ARG289 4.7 0.0 1.0 HB2 A:ASP286 4.7 0.0 1.0 HA A:GLN312 4.7 0.0 1.0 CA A:ASP286 4.8 0.0 1.0 C A:CYS287 4.8 0.0 1.0 CA A:CYS284 4.8 0.0 1.0 C A:GLU315 4.8 0.0 1.0 CB A:GLU315 4.8 0.0 1.0 N A:ASP286 4.8 0.0 1.0 CG A:ASP286 4.8 0.0 1.0 HA A:CYS287 4.9 0.0 1.0 HA A:CYS316 4.9 0.0 1.0 C A:GLN312 4.9 0.0 1.0 HB3 A:ARG289 5.0 0.0 1.0 HB3 A:GLN312 5.0 0.0 1.0

Zinc binding site 3 out of 4 in the Solution Structure of the Double Phd (Plant Homeodomain) Fingers of Human Transcriptional Protein DPF3B Bound to A Histone H4 Peptide Containing Acetylation at Lysine 16


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Solution Structure of the Double Phd (Plant Homeodomain) Fingers of Human Transcriptional Protein DPF3B Bound to A Histone H4 Peptide Containing Acetylation at Lysine 16 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn701 b:0.0 occ:1.00 SG A:CYS334 2.3 0.0 1.0 SG A:CYS360 2.3 0.0 1.0 SG A:CYS337 2.3 0.0 1.0 SG A:CYS363 2.3 0.0 1.0 HB3 A:ASP336 3.0 0.0 1.0 HB3 A:CYS360 3.2 0.0 1.0 H A:CYS363 3.2 0.0 1.0 HB3 A:CYS337 3.2 0.0 1.0 O A:SER359 3.2 0.0 1.0 HB3 A:CYS334 3.3 0.0 1.0 HB2 A:CYS363 3.3 0.0 1.0 CB A:CYS360 3.4 0.0 1.0 CB A:CYS334 3.4 0.0 1.0 CB A:CYS337 3.4 0.0 1.0 HB2 A:LEU362 3.4 0.0 1.0 CB A:CYS363 3.5 0.0 1.0 HB2 A:CYS334 3.7 0.0 1.0 HB2 A:ARG339 3.7 0.0 1.0 C A:SER359 3.7 0.0 1.0 C A:ASP336 3.9 0.0 1.0 N A:CYS363 3.9 0.0 1.0 N A:CYS337 4.0 0.0 1.0 O A:ASP336 4.0 0.0 1.0 HA A:SER359 4.0 0.0 1.0 CB A:ASP336 4.1 0.0 1.0 H A:ASP336 4.1 0.0 1.0 HB2 A:CYS360 4.2 0.0 1.0 HG3 A:ARG339 4.2 0.0 1.0 N A:CYS360 4.2 0.0 1.0 HD11 A:LEU362 4.2 0.0 1.0 CA A:CYS337 4.2 0.0 1.0 HB2 A:CYS337 4.2 0.0 1.0 H A:ASP338 4.3 0.0 1.0 HB3 A:CYS363 4.3 0.0 1.0 CA A:CYS363 4.3 0.0 1.0 H A:CYS337 4.3 0.0 1.0 CA A:CYS360 4.3 0.0 1.0 H A:ARG339 4.4 0.0 1.0 CA A:ASP336 4.4 0.0 1.0 CA A:SER359 4.5 0.0 1.0 CB A:LEU362 4.5 0.0 1.0 HB2 A:ASP336 4.6 0.0 1.0 H A:LEU362 4.7 0.0 1.0 HH A:TYR341 4.7 0.0 1.0 N A:ASP336 4.7 0.0 1.0 CB A:ARG339 4.7 0.0 1.0 O A:CYS334 4.7 0.0 1.0 HB3 A:SER359 4.7 0.0 1.0 CA A:CYS334 4.8 0.0 1.0 OD2 A:ASP336 4.8 0.0 1.0 HA A:CYS363 4.8 0.0 1.0 N A:ASP338 4.8 0.0 1.0 C A:CYS360 4.8 0.0 1.0 H A:CYS360 4.9 0.0 1.0 C A:CYS337 4.9 0.0 1.0 CG A:ARG339 4.9 0.0 1.0 HG A:LEU362 5.0 0.0 1.0 C A:CYS334 5.0 0.0 1.0 C A:LEU362 5.0 0.0 1.0 CG A:ASP336 5.0 0.0 1.0

Zinc binding site 4 out of 4 in the Solution Structure of the Double Phd (Plant Homeodomain) Fingers of Human Transcriptional Protein DPF3B Bound to A Histone H4 Peptide Containing Acetylation at Lysine 16


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Solution Structure of the Double Phd (Plant Homeodomain) Fingers of Human Transcriptional Protein DPF3B Bound to A Histone H4 Peptide Containing Acetylation at Lysine 16 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn801 b:0.0 occ:1.00 ND1 A:HIS342 2.1 0.0 1.0 SG A:CYS319 2.3 0.0 1.0 SG A:CYS345 2.3 0.0 1.0 SG A:CYS322 2.3 0.0 1.0 HB2 A:HIS342 2.9 0.0 1.0 H A:HIS342 2.9 0.0 1.0 CE1 A:HIS342 3.0 0.0 1.0 HB2 A:LEU321 3.1 0.0 1.0 CG A:HIS342 3.1 0.0 1.0 H A:CYS322 3.2 0.0 1.0 HB2 A:CYS322 3.2 0.0 1.0 HE1 A:HIS342 3.2 0.0 1.0 CB A:CYS319 3.3 0.0 1.0 HB2 A:CYS319 3.3 0.0 1.0 CB A:CYS322 3.4 0.0 1.0 HB3 A:CYS319 3.4 0.0 1.0 CB A:CYS345 3.4 0.0 1.0 CB A:HIS342 3.4 0.0 1.0 HB3 A:CYS345 3.5 0.0 1.0 HB2 A:CYS345 3.5 0.0 1.0 N A:CYS322 3.8 0.0 1.0 N A:HIS342 3.8 0.0 1.0 HD22 A:LEU331 3.8 0.0 1.0 CB A:LEU321 4.1 0.0 1.0 HD23 A:LEU331 4.1 0.0 1.0 CA A:CYS322 4.1 0.0 1.0 NE2 A:HIS342 4.1 0.0 1.0 CD2 A:HIS342 4.2 0.0 1.0 CA A:HIS342 4.2 0.0 1.0 HB3 A:CYS322 4.2 0.0 1.0 HB3 A:HIS342 4.3 0.0 1.0 HA A:TYR341 4.4 0.0 1.0 HB3 A:LEU321 4.4 0.0 1.0 CD2 A:LEU331 4.5 0.0 1.0 C A:LEU321 4.6 0.0 1.0 HA A:CYS322 4.6 0.0 1.0 HG A:LEU321 4.6 0.0 1.0 H A:GLY323 4.7 0.0 1.0 CA A:CYS319 4.7 0.0 1.0 CA A:CYS345 4.8 0.0 1.0 HG21 A:THR324 4.8 0.0 1.0 C A:TYR341 4.9 0.0 1.0 CA A:LEU321 4.9 0.0 1.0 CG A:LEU321 4.9 0.0 1.0 HD21 A:LEU331 4.9 0.0 1.0 H A:LEU321 5.0 0.0 1.0 O A:HIS342 5.0 0.0 1.0 HA A:HIS342 5.0 0.0 1.0 HD11 A:LEU321 5.0 0.0 1.0

L.Zeng, Q.Zhang, S.Li, A.N.Plotnikov, M.J.Walsh, M.M.Zhou. Mechanism and Regulation of Acetylated Histone Binding By the Tandem Phd Finger of DPF3B. Nature V. 466 258 2010.
ISSN: ISSN 0028-0836
PubMed: 20613843
DOI: 10.1038/NATURE09139