Zinc in PDB 5szb: Structure of Human DPF3 Double-Phd Domain Bound to Histone H3 Tail Peptide with Acetylated K14

The structure of Structure of Human DPF3 Double-Phd Domain Bound to Histone H3 Tail Peptide with Acetylated K14, PDB code: 5szb was solved by N.Singh, A.Local, A.Shiau, B.Ren, K.D.Corbett, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	38.00 / 1.20
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	39.321, 39.321, 147.571, 90.00, 90.00, 90.00
R / Rfree (%)	13.8 / 15.5

The binding sites of Zinc atom in the Structure of Human DPF3 Double-Phd Domain Bound to Histone H3 Tail Peptide with Acetylated K14 (pdb code 5szb). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Structure of Human DPF3 Double-Phd Domain Bound to Histone H3 Tail Peptide with Acetylated K14, PDB code: 5szb:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Structure of Human DPF3 Double-Phd Domain Bound to Histone H3 Tail Peptide with Acetylated K14


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of Human DPF3 Double-Phd Domain Bound to Histone H3 Tail Peptide with Acetylated K14 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:8.9 occ:1.00 ND1 A:HIS292 2.1 8.9 1.0 SG A:CYS295 2.3 9.4 1.0 SG A:CYS265 2.3 8.9 1.0 SG A:CYS262 2.3 8.5 1.0 HB2 A:HIS292 2.9 11.0 1.0 HB3 A:CYS262 3.0 10.7 1.0 CE1 A:HIS292 3.0 8.4 1.0 HB3 A:CYS265 3.1 11.1 1.0 CB A:CYS262 3.1 8.9 1.0 HB2 A:CYS262 3.1 10.7 1.0 H A:CYS265 3.1 12.7 1.0 CG A:HIS292 3.1 8.3 1.0 HE1 A:HIS292 3.2 10.0 1.0 HB2 A:CYS295 3.2 11.8 1.0 H A:HIS292 3.2 10.1 1.0 CB A:CYS265 3.3 9.3 1.0 CB A:CYS295 3.3 9.8 1.0 CB A:HIS292 3.5 9.2 1.0 HB3 A:CYS295 3.5 11.8 1.0 HB2 A:PHE264 3.5 15.6 1.0 N A:CYS265 3.7 10.6 1.0 HD21 A:ASN272 3.8 12.7 1.0 OD1 A:ASN272 3.9 10.6 1.0 ND2 A:ASN272 4.0 10.6 1.0 CG A:ASN272 4.0 9.6 1.0 N A:HIS292 4.0 8.4 1.0 HB2 A:CYS265 4.1 11.1 1.0 CA A:CYS265 4.1 9.8 1.0 NE2 A:HIS292 4.2 8.8 1.0 HA A:ASN272 4.2 10.5 1.0 HB3 A:HIS292 4.2 11.0 1.0 CD2 A:HIS292 4.2 8.9 1.0 H A:GLY267 4.3 11.7 1.0 CA A:HIS292 4.4 8.5 1.0 HD22 A:ASN272 4.4 12.7 1.0 H A:PHE264 4.4 13.0 1.0 H A:LYS273 4.4 10.7 1.0 CB A:PHE264 4.5 13.0 1.0 H A:CYS295 4.5 11.5 1.0 O A:HOH619 4.5 20.1 1.0 CA A:CYS262 4.5 8.7 1.0 HD1 A:PHE264 4.6 19.3 1.0 H A:LEU266 4.6 11.9 1.0 H A:LYS274 4.7 13.3 1.0 CA A:CYS295 4.7 10.0 1.0 C A:PHE264 4.7 11.8 1.0 HA2 A:GLY291 4.8 10.6 1.0 C A:CYS265 4.8 10.1 1.0 HB2 A:ASN272 4.8 11.4 1.0 CB A:ASN272 4.8 9.5 1.0 HB3 A:PHE264 4.9 15.6 1.0 HB3 A:LYS274 4.9 17.7 1.0 HA A:CYS265 4.9 11.8 1.0 CA A:ASN272 4.9 8.7 1.0 HE2 A:HIS292 4.9 10.6 1.0 HA A:CYS262 4.9 10.4 1.0 N A:LEU266 4.9 9.9 1.0 N A:PHE264 5.0 10.8 1.0 HA A:CYS295 5.0 12.0 1.0 N A:CYS295 5.0 9.6 1.0

Zinc binding site 2 out of 4 in the Structure of Human DPF3 Double-Phd Domain Bound to Histone H3 Tail Peptide with Acetylated K14


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of Human DPF3 Double-Phd Domain Bound to Histone H3 Tail Peptide with Acetylated K14 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn402 b:10.5 occ:1.00 SG A:CYS287 2.3 11.8 1.0 SG A:CYS316 2.3 12.1 1.0 SG A:CYS313 2.3 10.6 1.0 SG A:CYS284 2.3 9.2 1.0 HB2 A:CYS316 2.9 14.0 1.0 HB3 A:CYS287 3.1 15.4 1.0 CB A:CYS284 3.2 8.6 1.0 HB2 A:CYS284 3.2 10.3 1.0 CB A:CYS316 3.2 11.6 1.0 HB3 A:CYS284 3.2 10.3 1.0 H A:CYS287 3.2 13.6 1.0 H A:CYS313 3.2 9.8 1.0 CB A:CYS287 3.3 12.8 1.0 HB3 A:CYS313 3.3 11.2 1.0 CB A:CYS313 3.4 9.3 1.0 H A:CYS316 3.5 14.4 1.0 N A:CYS287 3.8 11.3 1.0 HB3 A:CYS316 3.8 14.0 1.0 HD2 A:ARG289 3.8 26.9 0.5 HB2 A:ASP286 3.9 16.8 1.0 N A:CYS313 3.9 8.2 1.0 O A:HOH572 4.0 29.4 1.0 HB2 A:CYS287 4.0 15.4 1.0 CA A:CYS287 4.1 12.4 1.0 HD3 A:ARG289 4.1 26.7 0.5 N A:CYS316 4.1 12.0 1.0 HB2 A:ARG289 4.1 16.3 0.5 HB2 A:CYS313 4.2 11.2 1.0 HB2 A:ARG289 4.2 16.2 0.5 CA A:CYS313 4.2 8.8 1.0 CA A:CYS316 4.3 11.5 1.0 H A:ARG289 4.4 11.8 1.0 H A:ASP286 4.4 12.9 1.0 O A:HOH627 4.4 26.6 1.0 HB2 A:GLU315 4.5 18.9 1.0 H A:GLY288 4.6 12.0 1.0 CA A:CYS284 4.6 7.7 1.0 HA A:GLN312 4.7 9.4 1.0 HA A:CYS316 4.7 13.8 1.0 CB A:ASP286 4.7 14.0 1.0 CD A:ARG289 4.8 22.4 0.5 C A:CYS287 4.8 12.4 1.0 C A:ASP286 4.8 12.6 1.0 HB3 A:GLN312 4.8 10.0 1.0 C A:CYS313 4.8 9.0 1.0 CD A:ARG289 4.8 22.3 0.5 HA A:CYS287 4.9 14.9 1.0 O A:CYS313 4.9 9.7 1.0 HG3 A:ARG289 4.9 21.6 0.5 HD2 A:ARG289 4.9 26.7 0.5 N A:GLY288 4.9 10.0 1.0 HA A:CYS284 4.9 9.2 1.0 HG3 A:ARG289 4.9 21.5 0.5 HB3 A:ASP286 5.0 16.8 1.0

Zinc binding site 3 out of 4 in the Structure of Human DPF3 Double-Phd Domain Bound to Histone H3 Tail Peptide with Acetylated K14


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of Human DPF3 Double-Phd Domain Bound to Histone H3 Tail Peptide with Acetylated K14 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn403 b:14.2 occ:1.00 ND1 A:HIS342 2.1 11.9 1.0 SG A:CYS345 2.3 16.8 1.0 SG A:CYS322 2.3 17.0 1.0 SG A:CYS319 2.3 11.7 1.0 HB2 A:HIS342 2.7 15.0 1.0 HB3 A:CYS319 2.9 14.1 1.0 CB A:CYS319 3.0 11.7 1.0 HB3 A:CYS322 3.0 23.5 1.0 HB2 A:CYS319 3.1 14.1 1.0 CG A:HIS342 3.1 11.6 1.0 CE1 A:HIS342 3.1 12.0 1.0 H A:CYS322 3.1 22.9 1.0 HB2 A:CYS345 3.2 20.3 1.0 CB A:CYS322 3.2 19.6 1.0 H A:HIS342 3.3 13.1 1.0 HE1 A:HIS342 3.3 14.4 1.0 CB A:CYS345 3.3 16.9 1.0 CB A:HIS342 3.4 12.5 1.0 HB3 A:CYS345 3.6 20.3 1.0 N A:CYS322 3.7 19.1 1.0 HB2 A:LEU321 3.8 23.2 1.0 HE1 A:TYR344 3.9 20.1 1.0 HB2 A:CYS322 4.0 23.5 1.0 N A:HIS342 4.0 10.9 1.0 HB3 A:HIS342 4.0 15.0 1.0 CA A:CYS322 4.1 19.3 1.0 NE2 A:HIS342 4.2 12.5 1.0 CD2 A:HIS342 4.2 12.3 1.0 CA A:HIS342 4.3 11.0 1.0 H A:LEU321 4.4 20.7 1.0 CE1 A:TYR344 4.4 16.7 1.0 CA A:CYS319 4.5 11.5 1.0 H A:THR324 4.5 20.7 1.0 O A:HOH518 4.5 18.1 1.0 H A:GLY323 4.6 22.7 1.0 HH A:TYR344 4.6 20.3 1.0 CA A:CYS345 4.7 19.1 1.0 H A:CYS345 4.7 22.1 1.0 CB A:LEU321 4.7 19.3 1.0 C A:LEU321 4.7 20.6 1.0 O A:HOH641 4.7 30.6 1.0 C A:CYS322 4.8 20.2 1.0 HA A:CYS322 4.9 23.2 1.0 HA A:TYR341 4.9 11.9 1.0 HA A:CYS319 4.9 13.8 1.0 HA A:CYS345 4.9 23.0 1.0 N A:GLY323 4.9 18.9 1.0 HD1 A:TYR344 4.9 20.4 1.0 N A:CYS345 5.0 18.4 1.0 OG1 A:THR324 5.0 18.3 1.0 HA A:HIS342 5.0 13.2 1.0 CD1 A:TYR344 5.0 17.0 1.0 HE2 A:HIS342 5.0 15.0 1.0 H A:CYS319 5.0 13.0 1.0 CZ A:TYR344 5.0 16.2 1.0

Zinc binding site 4 out of 4 in the Structure of Human DPF3 Double-Phd Domain Bound to Histone H3 Tail Peptide with Acetylated K14


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure of Human DPF3 Double-Phd Domain Bound to Histone H3 Tail Peptide with Acetylated K14 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn404 b:9.2 occ:1.00 SG A:CYS363 2.3 10.2 1.0 SG A:CYS337 2.3 9.6 1.0 SG A:CYS360 2.3 10.6 1.0 SG A:CYS334 2.3 8.5 1.0 HB3 A:CYS337 3.1 11.2 1.0 H A:CYS360 3.1 12.7 1.0 HB2 A:CYS363 3.1 12.9 1.0 HB3 A:CYS334 3.2 10.2 1.0 CB A:CYS334 3.2 8.5 1.0 HB2 A:CYS334 3.2 10.2 1.0 CB A:CYS337 3.3 9.3 1.0 H A:CYS337 3.3 10.8 1.0 CB A:CYS363 3.3 10.8 1.0 HB3 A:CYS360 3.4 12.9 1.0 H A:CYS363 3.4 14.2 1.0 CB A:CYS360 3.5 10.7 1.0 N A:CYS337 3.7 9.0 1.0 N A:CYS360 3.9 10.6 1.0 HH11 A:ARG339 3.9 15.7 1.0 HB2 A:ASP336 3.9 10.1 1.0 HB3 A:CYS363 4.0 12.9 1.0 N A:CYS363 4.1 11.8 1.0 HB2 A:CYS337 4.1 11.2 1.0 CA A:CYS337 4.1 9.3 1.0 HB2 A:ARG339 4.1 11.5 1.0 HB2 A:LEU362 4.1 17.1 1.0 CA A:CYS360 4.2 10.6 1.0 HD2 A:ARG339 4.2 12.9 1.0 H A:ASP336 4.2 10.8 1.0 HH A:TYR341 4.2 16.3 1.0 HB2 A:CYS360 4.3 12.9 1.0 H A:ARG339 4.3 10.2 1.0 HE1 A:TYR341 4.3 13.6 1.0 CA A:CYS363 4.3 11.7 1.0 HB3 A:SER359 4.4 15.2 1.0 O A:HOH609 4.5 25.0 1.0 C A:ASP336 4.6 10.3 1.0 O A:CYS360 4.6 11.8 1.0 H A:ASP338 4.6 9.8 1.0 CA A:CYS334 4.6 8.5 1.0 CB A:ASP336 4.6 8.4 1.0 NH1 A:ARG339 4.6 13.1 1.0 C A:CYS360 4.7 11.2 1.0 HA A:CYS363 4.7 14.0 1.0 HA A:SER359 4.7 13.4 1.0 HB3 A:ASP336 4.7 10.1 1.0 C A:CYS337 4.8 8.4 1.0 HH12 A:ARG339 4.8 15.7 1.0 HA A:CYS337 4.9 11.2 1.0 N A:ASP336 4.9 9.0 1.0 CA A:ASP336 4.9 9.2 1.0 N A:ASP338 4.9 8.1 1.0 H A:LEU362 4.9 17.1 1.0 HA A:CYS334 4.9 10.2 1.0 OH A:TYR341 5.0 13.6 1.0

A.Local, H.Huang, C.P.Albuquerque, N.Singh, A.Y.Lee, W.Wang, C.Wang, J.E.Hsia, A.K.Shiau, K.Ge, K.D.Corbett, D.Wang, H.Zhou, B.Ren. Identification of H3K4ME1-Associated Proteins at Mammalian Enhancers. Nat. Genet. V. 50 73 2018.
ISSN: ISSN 1546-1718
PubMed: 29255264
DOI: 10.1038/S41588-017-0015-6