Zinc in PDB 2kwk: Solution Structures of the Double Phd Fingers of Human Transcriptional Protein DPF3B Bound to A H3 Peptide Wild Type

The binding sites of Zinc atom in the Solution Structures of the Double Phd Fingers of Human Transcriptional Protein DPF3B Bound to A H3 Peptide Wild Type (pdb code 2kwk). 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 Structures of the Double Phd Fingers of Human Transcriptional Protein DPF3B Bound to A H3 Peptide Wild Type, PDB code: 2kwk:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Solution Structures of the Double Phd Fingers of Human Transcriptional Protein DPF3B Bound to A H3 Peptide Wild Type


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Solution Structures of the Double Phd Fingers of Human Transcriptional Protein DPF3B Bound to A H3 Peptide Wild Type 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 H A:CYS265 2.7 0.0 1.0 HB2 A:HIS292 2.7 0.0 1.0 HB3 A:CYS262 3.0 0.0 1.0 CE1 A:HIS292 3.0 0.0 1.0 CG A:HIS292 3.1 0.0 1.0 OD1 A:ASN272 3.2 0.0 1.0 HE1 A:HIS292 3.3 0.0 1.0 CB A:CYS262 3.3 0.0 1.0 HB2 A:CYS295 3.3 0.0 1.0 HB3 A:CYS265 3.4 0.0 1.0 HB2 A:PHE264 3.4 0.0 1.0 CB A:CYS265 3.4 0.0 1.0 CB A:CYS295 3.4 0.0 1.0 CB A:HIS292 3.4 0.0 1.0 H A:LEU266 3.5 0.0 1.0 N A:CYS265 3.6 0.0 1.0 HB3 A:CYS295 3.6 0.0 1.0 HB2 A:CYS262 3.7 0.0 1.0 H A:GLY267 3.7 0.0 1.0 H A:HIS292 3.8 0.0 1.0 HB2 A:LYS274 3.8 0.0 1.0 CG A:ASN272 3.8 0.0 1.0 HD22 A:ASN272 3.9 0.0 1.0 H A:LYS273 4.0 0.0 1.0 CA A:CYS265 4.0 0.0 1.0 HB3 A:HIS292 4.0 0.0 1.0 HG3 A:LYS274 4.1 0.0 1.0 NE2 A:HIS292 4.2 0.0 1.0 ND2 A:ASN272 4.2 0.0 1.0 HA A:ASN272 4.2 0.0 1.0 N A:LEU266 4.2 0.0 1.0 CD2 A:HIS292 4.2 0.0 1.0 HB2 A:CYS265 4.3 0.0 1.0 H A:PHE264 4.3 0.0 1.0 CB A:PHE264 4.4 0.0 1.0 N A:HIS292 4.5 0.0 1.0 HG2 A:LYS274 4.5 0.0 1.0 C A:CYS265 4.5 0.0 1.0 H A:LYS274 4.6 0.0 1.0 CA A:HIS292 4.6 0.0 1.0 CA A:CYS262 4.6 0.0 1.0 H A:CYS262 4.7 0.0 1.0 CG A:LYS274 4.7 0.0 1.0 H A:CYS295 4.7 0.0 1.0 CB A:LYS274 4.7 0.0 1.0 C A:PHE264 4.7 0.0 1.0 N A:GLY267 4.7 0.0 1.0 N A:LYS273 4.8 0.0 1.0 HD1 A:PHE264 4.8 0.0 1.0 HB3 A:PHE264 4.8 0.0 1.0 CA A:CYS295 4.8 0.0 1.0 H A:GLY268 4.8 0.0 1.0 HD22 A:LEU281 4.8 0.0 1.0 O A:CYS262 4.9 0.0 1.0 CB A:ASN272 4.9 0.0 1.0 HA A:CYS265 4.9 0.0 1.0 CA A:PHE264 4.9 0.0 1.0 CA A:ASN272 5.0 0.0 1.0 C A:CYS262 5.0 0.0 1.0 HD23 A:LEU281 5.0 0.0 1.0 N A:PHE264 5.0 0.0 1.0 HD21 A:ASN272 5.0 0.0 1.0

Zinc binding site 2 out of 4 in the Solution Structures of the Double Phd Fingers of Human Transcriptional Protein DPF3B Bound to A H3 Peptide Wild Type


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Solution Structures of the Double Phd Fingers of Human Transcriptional Protein DPF3B Bound to A H3 Peptide Wild Type 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 HB2 A:ASP286 3.0 0.0 1.0 H A:CYS313 3.0 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 CB A:CYS316 3.3 0.0 1.0 HB3 A:CYS313 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 3.5 0.0 1.0 HB2 A:CYS284 3.5 0.0 1.0 HB3 A:CYS284 3.6 0.0 1.0 N A:CYS287 3.6 0.0 1.0 H A:ASP286 3.7 0.0 1.0 HB3 A:CYS316 3.8 0.0 1.0 N A:CYS313 3.8 0.0 1.0 HD2 A:ARG289 3.9 0.0 1.0 O A:CYS313 3.9 0.0 1.0 CB A:ASP286 3.9 0.0 1.0 CA A:CYS313 4.0 0.0 1.0 CA A:CYS287 4.1 0.0 1.0 H A:GLY288 4.1 0.0 1.0 HB3 A:ASP286 4.2 0.0 1.0 C A:ASP286 4.2 0.0 1.0 HB3 A:CYS287 4.3 0.0 1.0 HB2 A:CYS313 4.3 0.0 1.0 N A:ASP286 4.4 0.0 1.0 HG3 A:ARG289 4.4 0.0 1.0 CA A:ASP286 4.4 0.0 1.0 C A:CYS313 4.4 0.0 1.0 H A:ALA285 4.6 0.0 1.0 H A:CYS316 4.6 0.0 1.0 CA A:CYS316 4.6 0.0 1.0 H A:ARG289 4.7 0.0 1.0 HH11 A:ARG289 4.7 0.0 1.0 CD A:ARG289 4.8 0.0 1.0 N A:CYS316 4.8 0.0 1.0 HB2 A:ARG289 4.8 0.0 1.0 HA A:GLN312 4.8 0.0 1.0 HA A:CYS287 4.9 0.0 1.0 CA A:CYS284 4.9 0.0 1.0 NH1 A:ARG289 4.9 0.0 1.0 NE A:ARG289 5.0 0.0 1.0 N A:GLY288 5.0 0.0 1.0 O A:ASP286 5.0 0.0 1.0

Zinc binding site 3 out of 4 in the Solution Structures of the Double Phd Fingers of Human Transcriptional Protein DPF3B Bound to A H3 Peptide Wild Type


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Solution Structures of the Double Phd Fingers of Human Transcriptional Protein DPF3B Bound to A H3 Peptide Wild Type within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn701 b:0.0 occ:1.00 SG A:CYS360 2.3 0.0 1.0 SG A:CYS363 2.3 0.0 1.0 SG A:CYS334 2.3 0.0 1.0 SG A:CYS337 2.3 0.0 1.0 H A:CYS363 2.7 0.0 1.0 H A:CYS360 2.7 0.0 1.0 HB3 A:ASP336 3.1 0.0 1.0 HB2 A:CYS337 3.2 0.0 1.0 HB3 A:CYS363 3.3 0.0 1.0 HB3 A:LEU362 3.4 0.0 1.0 CB A:CYS363 3.4 0.0 1.0 CB A:CYS360 3.4 0.0 1.0 CB A:CYS337 3.4 0.0 1.0 HB2 A:CYS334 3.4 0.0 1.0 CB A:CYS334 3.4 0.0 1.0 HB3 A:CYS360 3.5 0.0 1.0 N A:CYS360 3.5 0.0 1.0 N A:CYS363 3.5 0.0 1.0 HB2 A:ASP336 3.6 0.0 1.0 HB3 A:CYS334 3.7 0.0 1.0 H A:CYS337 3.7 0.0 1.0 N A:CYS337 3.8 0.0 1.0 CB A:ASP336 3.8 0.0 1.0 CA A:CYS360 3.8 0.0 1.0 O A:CYS360 3.9 0.0 1.0 H A:ASP336 3.9 0.0 1.0 C A:CYS360 4.0 0.0 1.0 CA A:CYS363 4.0 0.0 1.0 C A:ASP336 4.0 0.0 1.0 H A:ASP338 4.1 0.0 1.0 H A:LEU362 4.2 0.0 1.0 CA A:CYS337 4.2 0.0 1.0 HD2 A:ARG339 4.2 0.0 1.0 HG3 A:ARG339 4.3 0.0 1.0 HB3 A:CYS337 4.3 0.0 1.0 HB2 A:CYS363 4.3 0.0 1.0 CB A:LEU362 4.3 0.0 1.0 CA A:ASP336 4.3 0.0 1.0 HB2 A:CYS360 4.3 0.0 1.0 HB2 A:ARG339 4.3 0.0 1.0 HA A:SER359 4.3 0.0 1.0 H A:ARG339 4.4 0.0 1.0 N A:ASP336 4.5 0.0 1.0 HA A:CYS363 4.5 0.0 1.0 N A:LEU362 4.5 0.0 1.0 HB2 A:LEU362 4.5 0.0 1.0 C A:LEU362 4.5 0.0 1.0 O A:ASP336 4.6 0.0 1.0 C A:SER359 4.6 0.0 1.0 CA A:LEU362 4.7 0.0 1.0 HB3 A:SER359 4.7 0.0 1.0 HD11 A:LEU362 4.8 0.0 1.0 CA A:CYS334 4.8 0.0 1.0 N A:HIS361 4.8 0.0 1.0 HA A:CYS360 4.9 0.0 1.0 CA A:SER359 4.9 0.0 1.0 H A:TRP364 4.9 0.0 1.0 N A:ASP338 4.9 0.0 1.0 HB2 A:SER359 4.9 0.0 1.0 H A:ASP335 5.0 0.0 1.0

Zinc binding site 4 out of 4 in the Solution Structures of the Double Phd Fingers of Human Transcriptional Protein DPF3B Bound to A H3 Peptide Wild Type


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Solution Structures of the Double Phd Fingers of Human Transcriptional Protein DPF3B Bound to A H3 Peptide Wild Type 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:CYS322 2.3 0.0 1.0 SG A:CYS345 2.3 0.0 1.0 HB2 A:HIS342 2.8 0.0 1.0 H A:HIS342 3.0 0.0 1.0 CE1 A:HIS342 3.1 0.0 1.0 CG A:HIS342 3.1 0.0 1.0 HB2 A:LEU321 3.2 0.0 1.0 HB2 A:CYS322 3.2 0.0 1.0 HB3 A:CYS319 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 3.4 0.0 1.0 HB3 A:CYS345 3.4 0.0 1.0 H A:CYS322 3.5 0.0 1.0 HB2 A:CYS319 3.5 0.0 1.0 HB2 A:CYS345 3.6 0.0 1.0 N A:HIS342 3.8 0.0 1.0 N A:CYS322 3.8 0.0 1.0 CA A:HIS342 4.2 0.0 1.0 NE2 A:HIS342 4.2 0.0 1.0 CD2 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 CB A:LEU321 4.2 0.0 1.0 HB3 A:HIS342 4.3 0.0 1.0 C A:LEU321 4.6 0.0 1.0 HB3 A:LEU321 4.6 0.0 1.0 O A:HIS342 4.6 0.0 1.0 O A:CYS319 4.7 0.0 1.0 CA A:CYS319 4.7 0.0 1.0 HA A:TYR341 4.7 0.0 1.0 HA A:CYS322 4.8 0.0 1.0 CA A:CYS345 4.8 0.0 1.0 HG A:LEU321 4.9 0.0 1.0 CA A:LEU321 4.9 0.0 1.0 HD21 A:ASN327 4.9 0.0 1.0 HG1 A:THR324 4.9 0.0 1.0 H A:LEU321 4.9 0.0 1.0 C A:HIS342 4.9 0.0 1.0 OG1 A:THR324 4.9 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