Zinc in PDB 5i3l: DPF3B in Complex with H3K14AC Peptide

The structure of DPF3B in Complex with H3K14AC Peptide, PDB code: 5i3l was solved by W.Tempel, Y.Liu, J.R.Walker, A.Zhao, S.Qin, P.Loppnau, C.Bountra, C.H.Arrowsmith, A.M.Edwards, J.Min, Structural Genomics Consortium(Sgc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.01 / 1.85
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	99.822, 121.641, 56.446, 90.00, 90.00, 90.00
R / Rfree (%)	18.2 / 21.2

The structure of DPF3B in Complex with H3K14AC Peptide also contains other interesting chemical elements:

Sodium

(Na)

1 atom

The binding sites of Zinc atom in the DPF3B in Complex with H3K14AC Peptide (pdb code 5i3l). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the DPF3B in Complex with H3K14AC Peptide, PDB code: 5i3l:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in the DPF3B in Complex with H3K14AC Peptide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of DPF3B in Complex with H3K14AC Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1001 b:23.6 occ:1.00 ND1 A:HIS292 2.1 21.7 1.0 SG A:CYS295 2.3 23.8 1.0 SG A:CYS262 2.3 23.9 1.0 SG A:CYS265 2.3 23.3 1.0 CE1 A:HIS292 3.0 23.4 1.0 CB A:CYS262 3.1 24.0 1.0 CG A:HIS292 3.1 20.5 1.0 CB A:CYS265 3.3 24.4 1.0 CB A:CYS295 3.3 23.3 1.0 CB A:HIS292 3.5 21.0 1.0 ND2 A:ASN272 3.9 22.9 1.0 N A:CYS265 3.9 26.0 1.0 CG A:ASN272 4.0 23.2 1.0 OD1 A:ASN272 4.0 25.2 1.0 N A:HIS292 4.1 20.9 1.0 NE2 A:HIS292 4.1 23.3 1.0 CA A:CYS265 4.2 25.6 1.0 CD2 A:HIS292 4.2 21.3 1.0 CA A:HIS292 4.4 21.9 1.0 CA A:CYS262 4.6 23.7 1.0 CA A:CYS295 4.7 23.0 1.0 CB A:ASN272 4.8 23.4 1.0 CB A:PHE264 4.8 26.3 1.0 CA A:ASN272 4.8 22.4 1.0 C A:PHE264 4.9 28.3 1.0 C A:CYS265 4.9 26.0 1.0

Zinc binding site 2 out of 8 in the DPF3B in Complex with H3K14AC Peptide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of DPF3B in Complex with H3K14AC Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1002 b:35.7 occ:1.00 SG A:CYS284 2.3 33.1 1.0 SG A:CYS313 2.3 35.5 1.0 SG A:CYS316 2.4 37.4 1.0 SG A:CYS287 2.4 37.4 1.0 CB A:CYS284 3.2 33.0 1.0 CB A:CYS316 3.3 36.9 1.0 CB A:CYS313 3.4 32.5 1.0 CB A:CYS287 3.4 38.5 1.0 N A:CYS287 3.9 38.2 1.0 N A:CYS313 3.9 30.9 1.0 N A:CYS316 4.1 35.4 1.0 CA A:CYS287 4.2 38.7 1.0 CA A:CYS313 4.2 32.1 1.0 CA A:CYS316 4.3 37.1 1.0 CB A:ASP286 4.6 43.1 1.0 CD A:ARG289 4.6 34.4 1.0 CB A:ARG289 4.7 32.2 1.0 CA A:CYS284 4.7 32.6 1.0 C A:CYS313 4.8 32.0 1.0 C A:ASP286 4.8 41.7 1.0 C A:CYS287 4.8 40.3 1.0 O A:CYS313 4.8 31.8 1.0 N A:GLY288 4.9 36.6 1.0 N A:ARG289 5.0 31.7 1.0

Zinc binding site 3 out of 8 in the DPF3B in Complex with H3K14AC Peptide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of DPF3B in Complex with H3K14AC Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1003 b:36.8 occ:1.00 ND1 A:HIS342 2.1 38.0 1.0 SG A:CYS319 2.3 31.7 1.0 SG A:CYS345 2.3 36.1 1.0 SG A:CYS322 2.3 37.5 1.0 CE1 A:HIS342 3.1 39.9 1.0 CB A:CYS319 3.1 32.3 1.0 CG A:HIS342 3.1 37.4 1.0 CB A:CYS345 3.3 35.1 1.0 CB A:CYS322 3.3 38.0 1.0 CB A:HIS342 3.4 36.5 1.0 N A:CYS322 3.7 34.9 1.0 CA A:CYS322 4.1 36.9 1.0 N A:HIS342 4.1 31.8 1.0 NE2 A:HIS342 4.2 39.9 1.0 CD2 A:HIS342 4.2 39.1 1.0 CA A:HIS342 4.4 34.3 1.0 CE1 A:TYR344 4.4 46.9 1.0 CA A:CYS319 4.5 30.8 1.0 C A:LEU321 4.7 36.2 1.0 CB A:LEU321 4.7 34.8 1.0 CA A:CYS345 4.7 37.4 1.0 OH A:TYR344 4.8 48.7 1.0 CZ A:TYR344 4.9 46.7 1.0 CA A:LEU321 5.0 34.5 1.0 C A:CYS322 5.0 38.4 1.0 N A:LEU321 5.0 32.7 1.0

Zinc binding site 4 out of 8 in the DPF3B in Complex with H3K14AC Peptide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of DPF3B in Complex with H3K14AC Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1004 b:26.6 occ:1.00 SG A:CYS337 2.3 26.9 1.0 SG A:CYS363 2.3 27.5 1.0 SG A:CYS360 2.3 28.0 1.0 SG A:CYS334 2.4 25.7 1.0 CB A:CYS334 3.2 26.6 1.0 CB A:CYS337 3.3 26.3 1.0 CB A:CYS363 3.3 29.3 1.0 CB A:CYS360 3.5 28.6 1.0 N A:CYS337 3.7 23.9 1.0 N A:CYS360 3.8 28.9 1.0 N A:CYS363 4.1 31.0 1.0 CA A:CYS337 4.1 24.3 1.0 CA A:CYS360 4.2 28.9 1.0 CA A:CYS363 4.3 31.1 1.0 C A:ASP336 4.6 25.4 1.0 CA A:CYS334 4.7 27.2 1.0 O A:CYS360 4.7 29.3 1.0 C A:CYS360 4.7 30.9 1.0 CB A:ASP336 4.7 26.2 1.0 NH1 A:ARG339 4.7 27.0 1.0 C A:CYS337 4.8 24.8 1.0 N A:ASP336 4.9 25.1 1.0 CA A:ASP336 5.0 25.2 1.0 OH A:TYR341 5.0 30.3 1.0 C A:SER359 5.0 30.5 1.0

Zinc binding site 5 out of 8 in the DPF3B in Complex with H3K14AC Peptide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of DPF3B in Complex with H3K14AC Peptide within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1001 b:27.4 occ:1.00 ND1 B:HIS292 2.1 27.7 1.0 SG B:CYS265 2.3 29.8 1.0 SG B:CYS262 2.3 25.9 1.0 SG B:CYS295 2.3 29.9 1.0 CE1 B:HIS292 3.1 28.9 1.0 CG B:HIS292 3.1 27.6 1.0 CB B:CYS262 3.1 26.2 1.0 CB B:CYS265 3.3 30.0 1.0 CB B:CYS295 3.3 28.4 1.0 CB B:HIS292 3.4 27.9 1.0 N B:CYS265 3.8 28.2 1.0 ND2 B:ASN272 4.0 34.3 1.0 CG B:ASN272 4.1 35.9 1.0 OD1 B:ASN272 4.1 37.5 1.0 N B:HIS292 4.1 26.5 1.0 CA B:CYS265 4.2 29.0 1.0 NE2 B:HIS292 4.2 28.2 1.0 CD2 B:HIS292 4.2 27.9 1.0 CA B:HIS292 4.4 26.7 1.0 CB B:PHE264 4.5 28.0 1.0 CA B:CYS262 4.6 26.4 1.0 C B:PHE264 4.7 29.1 1.0 CA B:CYS295 4.7 30.1 1.0 CB B:ASN272 4.9 35.6 1.0 CA B:ASN272 4.9 36.7 1.0 N B:PHE264 4.9 25.2 1.0 C B:CYS265 4.9 27.9 1.0 CA B:PHE264 5.0 27.5 1.0

Zinc binding site 6 out of 8 in the DPF3B in Complex with H3K14AC Peptide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of DPF3B in Complex with H3K14AC Peptide within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1002 b:26.4 occ:1.00 SG B:CYS316 2.3 28.8 1.0 SG B:CYS313 2.3 27.4 1.0 SG B:CYS287 2.3 25.9 1.0 SG B:CYS284 2.4 26.0 1.0 CB B:CYS284 3.2 24.8 1.0 CB B:CYS287 3.2 26.6 1.0 CB B:CYS316 3.3 30.8 1.0 CB B:CYS313 3.5 25.0 1.0 N B:CYS287 3.8 28.2 1.0 N B:CYS313 4.0 26.1 1.0 O B:HOH1151 4.1 39.4 1.0 CA B:CYS287 4.1 27.7 1.0 N B:CYS316 4.1 29.4 1.0 CA B:CYS313 4.3 25.1 1.0 CA B:CYS316 4.4 30.6 1.0 O B:HOH1154 4.4 48.3 1.0 CA B:CYS284 4.7 24.9 1.0 O B:CYS313 4.7 28.5 1.0 CB B:ASP286 4.7 32.2 1.0 C B:CYS313 4.7 26.0 1.0 C B:CYS287 4.8 27.8 1.0 C B:ASP286 4.8 29.9 1.0 CB B:GLU315 4.9 37.6 1.0 N B:GLY288 4.9 26.5 1.0

Zinc binding site 7 out of 8 in the DPF3B in Complex with H3K14AC Peptide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of DPF3B in Complex with H3K14AC Peptide within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1003 b:34.9 occ:1.00 ND1 B:HIS342 2.1 38.5 1.0 SG B:CYS345 2.3 34.5 1.0 SG B:CYS319 2.3 31.0 1.0 SG B:CYS322 2.4 36.4 1.0 CB B:CYS319 3.0 31.1 1.0 CG B:HIS342 3.0 36.0 1.0 CE1 B:HIS342 3.1 40.0 1.0 CB B:CYS322 3.3 37.0 1.0 CB B:CYS345 3.3 32.6 1.0 CB B:HIS342 3.3 34.2 1.0 N B:CYS322 3.7 33.6 1.0 CA B:CYS322 4.0 36.5 1.0 O B:HOH1110 4.1 42.6 1.0 NE2 B:HIS342 4.2 37.6 1.0 CD2 B:HIS342 4.2 37.1 1.0 N B:HIS342 4.2 28.1 1.0 CA B:HIS342 4.4 31.1 1.0 CE1 B:TYR344 4.4 46.5 1.0 CA B:CYS319 4.5 29.5 1.0 CA B:CYS345 4.7 34.4 1.0 CB B:LEU321 4.7 30.6 1.0 OH B:TYR344 4.7 47.0 1.0 CZ B:TYR344 4.8 46.8 1.0 C B:LEU321 4.8 32.9 1.0 C B:CYS322 4.9 37.2 1.0 C B:CYS319 5.0 28.8 1.0 N B:GLY323 5.0 37.9 1.0

Zinc binding site 8 out of 8 in the DPF3B in Complex with H3K14AC Peptide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of DPF3B in Complex with H3K14AC Peptide within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1004 b:25.0 occ:1.00 SG B:CYS334 2.3 23.7 1.0 SG B:CYS360 2.3 24.9 1.0 SG B:CYS363 2.3 24.5 1.0 SG B:CYS337 2.4 23.4 1.0 CB B:CYS334 3.3 23.5 1.0 CB B:CYS337 3.3 23.2 1.0 CB B:CYS363 3.4 24.1 1.0 CB B:CYS360 3.5 23.9 1.0 N B:CYS337 3.8 22.4 1.0 N B:CYS360 3.9 22.1 1.0 N B:CYS363 4.1 21.9 1.0 CA B:CYS337 4.1 23.2 1.0 CA B:CYS360 4.2 24.0 1.0 CA B:CYS363 4.3 22.5 1.0 UNK B:UNX1020 4.4 31.3 1.0 O B:CYS360 4.6 22.4 1.0 C B:ASP336 4.6 26.1 1.0 C B:CYS360 4.6 23.6 1.0 CB B:ASP336 4.7 24.2 1.0 CA B:CYS334 4.7 24.1 1.0 NH1 B:ARG339 4.7 30.1 1.0 OH B:TYR341 4.8 25.4 1.0 C B:CYS337 4.8 24.1 1.0 N B:ASP336 5.0 23.6 1.0 CA B:ASP336 5.0 24.4 1.0

W.Li, A.Zhao, W.Tempel, P.Loppnau, Y.Liu. Crystal Structure of DPF3B in Complex with An Acetylated Histone Peptide. J.Struct.Biol. V. 195 365 2016.
ISSN: ESSN 1095-8657
PubMed: 27402533
DOI: 10.1016/J.JSB.2016.07.001