Zinc in PDB 2kwo: Solution Structure of the Double Phd (Plant Homeodomain) Fingers of Human Transcriptional Protein DPF3B Bound to A Histone H4 Peptide Containing N-Terminal Acetylation at Serine 1

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 N-Terminal Acetylation at Serine 1 (pdb code 2kwo). 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 N-Terminal Acetylation at Serine 1, PDB code: 2kwo:
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 N-Terminal Acetylation at Serine 1


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 N-Terminal Acetylation at Serine 1 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:CYS265 2.3 0.0 1.0 SG A:CYS295 2.3 0.0 1.0 HD22 A:ASN272 2.5 0.0 1.0 HD21 A:ASN272 2.6 0.0 1.0 HB2 A:HIS292 2.7 0.0 1.0 ND2 A:ASN272 2.8 0.0 1.0 HB2 A:PHE264 2.9 0.0 1.0 CE1 A:HIS292 3.1 0.0 1.0 CG A:HIS292 3.1 0.0 1.0 HB3 A:CYS262 3.2 0.0 1.0 HB2 A:CYS265 3.3 0.0 1.0 CB A:CYS262 3.3 0.0 1.0 HE1 A:HIS292 3.3 0.0 1.0 H A:HIS292 3.3 0.0 1.0 CB A:HIS292 3.4 0.0 1.0 HB2 A:CYS262 3.4 0.0 1.0 CB A:CYS265 3.4 0.0 1.0 HB2 A:CYS295 3.4 0.0 1.0 CB A:CYS295 3.4 0.0 1.0 H A:CYS265 3.5 0.0 1.0 HB3 A:CYS295 3.6 0.0 1.0 N A:CYS265 3.7 0.0 1.0 CB A:PHE264 3.9 0.0 1.0 HA A:ASN272 4.0 0.0 1.0 HB3 A:HIS292 4.1 0.0 1.0 N A:HIS292 4.1 0.0 1.0 CA A:CYS265 4.1 0.0 1.0 CG A:ASN272 4.1 0.0 1.0 C A:PHE264 4.1 0.0 1.0 NE2 A:HIS292 4.2 0.0 1.0 H A:PHE264 4.2 0.0 1.0 CD2 A:HIS292 4.2 0.0 1.0 HB3 A:PHE264 4.2 0.0 1.0 HB3 A:CYS265 4.3 0.0 1.0 CA A:HIS292 4.4 0.0 1.0 HD1 A:PHE264 4.4 0.0 1.0 CA A:PHE264 4.5 0.0 1.0 HD23 A:LEU281 4.5 0.0 1.0 H A:LEU266 4.5 0.0 1.0 H A:CYS295 4.6 0.0 1.0 HG3 A:LYS274 4.6 0.0 1.0 O A:ASN272 4.7 0.0 1.0 CA A:CYS262 4.7 0.0 1.0 N A:PHE264 4.7 0.0 1.0 HB2 A:LYS274 4.8 0.0 1.0 HA A:CYS265 4.8 0.0 1.0 CA A:ASN272 4.8 0.0 1.0 CA A:CYS295 4.8 0.0 1.0 O A:PHE264 4.8 0.0 1.0 CG A:PHE264 4.9 0.0 1.0 OD1 A:ASN272 4.9 0.0 1.0 HA2 A:GLY291 4.9 0.0 1.0 C A:ASN272 4.9 0.0 1.0 H A:LYS274 4.9 0.0 1.0 CD1 A:PHE264 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 N-Terminal Acetylation at Serine 1


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 N-Terminal Acetylation at Serine 1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn601 b:0.0 occ:1.00 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 SG A:CYS284 2.3 0.0 1.0 HB3 A:ASP286 2.8 0.0 1.0 HB2 A:CYS316 3.1 0.0 1.0 HB2 A:CYS287 3.2 0.0 1.0 H A:CYS287 3.3 0.0 1.0 HB3 A:CYS313 3.3 0.0 1.0 H A:CYS313 3.4 0.0 1.0 CB A:CYS316 3.4 0.0 1.0 CB A:CYS287 3.4 0.0 1.0 CB A:CYS313 3.4 0.0 1.0 CB A:CYS284 3.4 0.0 1.0 H A:CYS316 3.5 0.0 1.0 HB3 A:CYS284 3.5 0.0 1.0 HB2 A:CYS284 3.5 0.0 1.0 N A:CYS287 3.8 0.0 1.0 N A:CYS313 3.9 0.0 1.0 CB A:ASP286 3.9 0.0 1.0 HB3 A:CYS316 4.1 0.0 1.0 HB2 A:GLU315 4.1 0.0 1.0 CA A:CYS313 4.1 0.0 1.0 CA A:CYS287 4.2 0.0 1.0 N A:CYS316 4.2 0.0 1.0 HB3 A:CYS287 4.3 0.0 1.0 OD1 A:ASP286 4.3 0.0 1.0 HB2 A:CYS313 4.3 0.0 1.0 O A:CYS313 4.3 0.0 1.0 HB2 A:ASP286 4.4 0.0 1.0 H A:ASP286 4.4 0.0 1.0 CA A:CYS316 4.4 0.0 1.0 C A:ASP286 4.5 0.0 1.0 CG A:ASP286 4.6 0.0 1.0 HA A:GLN312 4.6 0.0 1.0 C A:CYS313 4.6 0.0 1.0 CA A:ASP286 4.7 0.0 1.0 H A:GLY288 4.7 0.0 1.0 HA A:CYS287 4.7 0.0 1.0 C A:GLN312 4.8 0.0 1.0 CA A:CYS284 4.9 0.0 1.0 N A:ASP286 4.9 0.0 1.0 HB3 A:GLN312 5.0 0.0 1.0 HA A:CYS316 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 N-Terminal Acetylation at Serine 1


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 N-Terminal Acetylation at Serine 1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn701 b:0.0 occ:1.00 SG A:CYS363 2.3 0.0 1.0 SG A:CYS337 2.3 0.0 1.0 SG A:CYS360 2.3 0.0 1.0 SG A:CYS334 2.3 0.0 1.0 HH11 A:ARG339 2.6 0.0 1.0 H A:CYS360 3.0 0.0 1.0 HB2 A:CYS363 3.1 0.0 1.0 HB3 A:ASP336 3.2 0.0 1.0 NH1 A:ARG339 3.2 0.0 1.0 HB3 A:CYS360 3.3 0.0 1.0 HB3 A:CYS337 3.3 0.0 1.0 HH12 A:ARG339 3.3 0.0 1.0 HB3 A:CYS334 3.3 0.0 1.0 CB A:CYS363 3.3 0.0 1.0 HB2 A:ARG339 3.4 0.0 1.0 CB A:CYS360 3.4 0.0 1.0 CB A:CYS337 3.4 0.0 1.0 CB A:CYS334 3.4 0.0 1.0 HD2 A:ARG339 3.6 0.0 1.0 H A:CYS363 3.7 0.0 1.0 N A:CYS360 3.8 0.0 1.0 HB2 A:CYS334 3.8 0.0 1.0 H A:ASP338 3.9 0.0 1.0 N A:CYS337 3.9 0.0 1.0 C A:ASP336 4.0 0.0 1.0 H A:ARG339 4.0 0.0 1.0 H A:ASP336 4.1 0.0 1.0 CA A:CYS360 4.1 0.0 1.0 HB3 A:CYS363 4.1 0.0 1.0 HG3 A:ARG339 4.1 0.0 1.0 O A:ASP336 4.2 0.0 1.0 CB A:ASP336 4.2 0.0 1.0 N A:CYS363 4.2 0.0 1.0 H A:CYS337 4.2 0.0 1.0 CA A:CYS337 4.2 0.0 1.0 HB2 A:CYS360 4.3 0.0 1.0 HB2 A:CYS337 4.3 0.0 1.0 CZ A:ARG339 4.3 0.0 1.0 CA A:CYS363 4.3 0.0 1.0 CB A:ARG339 4.4 0.0 1.0 CD A:ARG339 4.4 0.0 1.0 HB2 A:LEU362 4.4 0.0 1.0 O A:CYS334 4.4 0.0 1.0 CG A:ARG339 4.5 0.0 1.0 CA A:ASP336 4.5 0.0 1.0 HA A:SER359 4.6 0.0 1.0 N A:ASP338 4.6 0.0 1.0 HA A:CYS363 4.6 0.0 1.0 N A:ASP336 4.7 0.0 1.0 HB2 A:SER359 4.7 0.0 1.0 N A:ARG339 4.7 0.0 1.0 C A:CYS360 4.7 0.0 1.0 NE A:ARG339 4.8 0.0 1.0 OD2 A:ASP336 4.8 0.0 1.0 HB2 A:ASP336 4.8 0.0 1.0 CA A:CYS334 4.8 0.0 1.0 C A:CYS337 4.8 0.0 1.0 C A:CYS334 4.9 0.0 1.0 C A:SER359 4.9 0.0 1.0 HH A:TYR341 4.9 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 N-Terminal Acetylation at Serine 1


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 N-Terminal Acetylation at Serine 1 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:CYS322 2.3 0.0 1.0 SG A:CYS319 2.3 0.0 1.0 SG A:CYS345 2.3 0.0 1.0 H A:HIS342 2.7 0.0 1.0 HB2 A:LEU321 2.8 0.0 1.0 HB2 A:HIS342 2.8 0.0 1.0 CE1 A:HIS342 3.1 0.0 1.0 CG A:HIS342 3.1 0.0 1.0 HB2 A:CYS319 3.2 0.0 1.0 HB2 A:CYS322 3.2 0.0 1.0 HE1 A:HIS342 3.3 0.0 1.0 CB A:CYS319 3.3 0.0 1.0 CB A:CYS322 3.4 0.0 1.0 CB A:HIS342 3.4 0.0 1.0 CB A:CYS345 3.5 0.0 1.0 HB3 A:CYS319 3.5 0.0 1.0 N A:HIS342 3.6 0.0 1.0 HB3 A:CYS345 3.6 0.0 1.0 HB2 A:CYS345 3.6 0.0 1.0 H A:CYS322 3.8 0.0 1.0 N A:CYS322 3.8 0.0 1.0 CB A:LEU321 3.8 0.0 1.0 HD23 A:LEU331 3.9 0.0 1.0 HD22 A:LEU331 4.0 0.0 1.0 C A:LEU321 4.0 0.0 1.0 CA A:HIS342 4.1 0.0 1.0 HB3 A:LEU321 4.1 0.0 1.0 HA A:TYR341 4.1 0.0 1.0 NE2 A:HIS342 4.2 0.0 1.0 CA A:CYS322 4.2 0.0 1.0 HB3 A:CYS322 4.2 0.0 1.0 CD2 A:HIS342 4.2 0.0 1.0 H A:LEU321 4.3 0.0 1.0 HB3 A:HIS342 4.3 0.0 1.0 CA A:LEU321 4.4 0.0 1.0 CD2 A:LEU331 4.4 0.0 1.0 HG A:LEU321 4.5 0.0 1.0 O A:LEU321 4.5 0.0 1.0 C A:TYR341 4.6 0.0 1.0 H A:ILE320 4.7 0.0 1.0 H A:GLY323 4.7 0.0 1.0 N A:LEU321 4.7 0.0 1.0 CA A:CYS319 4.7 0.0 1.0 HG21 A:THR324 4.7 0.0 1.0 CG A:LEU321 4.8 0.0 1.0 O A:HIS342 4.8 0.0 1.0 HB2 A:GLU326 4.8 0.0 1.0 HA A:CYS322 4.8 0.0 1.0 HD21 A:LEU331 4.9 0.0 1.0 HA A:HIS342 4.9 0.0 1.0 CA A:CYS345 4.9 0.0 1.0 HA A:CYS319 4.9 0.0 1.0 CA A:TYR341 4.9 0.0 1.0 C A:HIS342 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