Zinc in PDB 5erc: X-Ray Crystal Structure of BRPF1 Pzp Domain

The structure of X-Ray Crystal Structure of BRPF1 Pzp Domain, PDB code: 5erc was solved by B.J.Klein, F.H.Andrews, T.G.Kutateladze, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	63.97 / 2.05
Space group	P 61 2 2
Cell size a, b, c (Å), α, β, γ (°)	73.870, 73.870, 147.130, 90.00, 90.00, 120.00
R / Rfree (%)	16.2 / 19.3

The structure of X-Ray Crystal Structure of BRPF1 Pzp Domain also contains other interesting chemical elements:

Calcium

(Ca)

1 atom

The binding sites of Zinc atom in the X-Ray Crystal Structure of BRPF1 Pzp Domain (pdb code 5erc). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 5 binding sites of Zinc where determined in the X-Ray Crystal Structure of BRPF1 Pzp Domain, PDB code: 5erc:
Jump to Zinc binding site number: 1; 2; 3; 4; 5;

Zinc binding site 1 out of 5 in the X-Ray Crystal Structure of BRPF1 Pzp Domain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of X-Ray Crystal Structure of BRPF1 Pzp Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn501 b:22.3 occ:0.77 SG A:CYS320 2.2 20.8 1.0 SG A:CYS293 2.3 22.5 1.0 SG A:CYS296 2.4 25.1 1.0 SG A:CYS317 2.4 20.3 1.0 CB A:CYS293 3.2 22.8 1.0 CB A:CYS296 3.2 25.4 1.0 CB A:CYS320 3.3 22.1 1.0 CB A:CYS317 3.5 24.6 1.0 N A:CYS296 3.7 29.6 1.0 N A:CYS317 4.0 20.1 1.0 CA A:CYS296 4.0 30.7 1.0 N A:CYS320 4.1 17.1 1.0 CA A:CYS320 4.3 18.5 1.0 NH2 A:ARG319 4.3 60.2 1.0 CA A:CYS317 4.3 18.6 1.0 NE A:ARG319 4.4 51.2 1.0 CB A:LEU298 4.5 22.1 1.0 CA A:CYS293 4.6 24.7 1.0 C A:CYS296 4.7 29.9 1.0 CB A:MET295 4.8 40.3 1.0 C A:MET295 4.8 39.5 1.0 O A:CYS317 4.8 17.8 1.0 C A:CYS317 4.8 20.1 1.0 CZ A:ARG319 4.9 57.5 1.0 N A:ASN297 5.0 29.3 1.0 O A:HOH694 5.0 19.3 1.0

Zinc binding site 2 out of 5 in the X-Ray Crystal Structure of BRPF1 Pzp Domain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of X-Ray Crystal Structure of BRPF1 Pzp Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn502 b:32.9 occ:0.75 SG A:CYS276 2.2 27.8 1.0 SG A:CYS304 2.2 37.4 1.0 ND1 A:HIS301 2.2 20.0 1.0 SG A:CYS279 2.4 34.4 1.0 CG A:HIS301 3.0 20.0 1.0 CB A:HIS301 3.1 20.0 1.0 CB A:CYS276 3.1 33.5 1.0 CB A:CYS304 3.2 24.5 1.0 CB A:CYS279 3.3 39.1 1.0 CE1 A:HIS301 3.3 20.0 1.0 N A:CYS279 3.8 41.7 1.0 N A:HIS301 4.0 28.7 1.0 CA A:CYS279 4.1 41.0 1.0 CA A:HIS301 4.2 27.5 1.0 CD2 A:HIS301 4.2 20.0 1.0 NE2 A:HIS301 4.4 20.0 1.0 CA A:CYS276 4.6 39.4 1.0 CA A:CYS304 4.6 22.1 1.0 CB A:ILE278 4.7 24.7 1.0 C A:ILE278 4.8 38.0 1.0 C A:CYS279 4.9 38.5 1.0 N A:CYS304 4.9 24.2 1.0 C A:CYS276 5.0 35.2 1.0

Zinc binding site 3 out of 5 in the X-Ray Crystal Structure of BRPF1 Pzp Domain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of X-Ray Crystal Structure of BRPF1 Pzp Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn503 b:12.7 occ:0.82 ND1 A:HIS350 2.1 9.8 1.0 SG A:CYS333 2.3 10.9 1.0 SG A:CYS330 2.3 9.3 1.0 SG A:CYS353 2.3 10.1 1.0 CB A:CYS330 3.0 9.2 1.0 CE1 A:HIS350 3.1 13.7 1.0 CG A:HIS350 3.1 10.2 1.0 CB A:CYS333 3.2 8.6 1.0 CB A:HIS350 3.4 10.7 1.0 CB A:CYS353 3.5 9.7 1.0 N A:CYS333 3.9 12.1 1.0 CG2 A:THR412 4.0 13.1 1.0 N A:HIS350 4.1 9.5 1.0 CA A:CYS333 4.1 10.7 1.0 NE2 A:HIS350 4.2 13.6 1.0 CD2 A:HIS350 4.2 13.3 1.0 OG1 A:THR412 4.3 9.9 1.0 C A:LEU332 4.3 13.2 1.0 CA A:HIS350 4.4 9.9 1.0 CB A:LEU332 4.5 7.5 1.0 CA A:CYS330 4.5 8.8 1.0 N A:LEU332 4.7 7.6 1.0 C A:CYS333 4.7 13.3 1.0 CA A:LEU332 4.7 7.5 1.0 CA A:CYS353 4.8 12.9 1.0 O A:CYS333 4.8 11.2 1.0 CB A:THR412 4.8 12.6 1.0 O A:LEU332 4.9 11.7 1.0 O A:ASN335 5.0 17.2 1.0

Zinc binding site 4 out of 5 in the X-Ray Crystal Structure of BRPF1 Pzp Domain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of X-Ray Crystal Structure of BRPF1 Pzp Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn504 b:16.3 occ:0.82 ND1 A:HIS410 2.2 9.2 1.0 SG A:CYS413 2.2 15.2 1.0 SG A:CYS386 2.3 12.0 1.0 SG A:CYS389 2.4 16.6 1.0 CB A:CYS386 3.1 9.7 1.0 CE1 A:HIS410 3.1 13.9 1.0 CG A:HIS410 3.2 10.3 1.0 CB A:CYS389 3.2 19.4 1.0 CB A:CYS413 3.3 14.5 1.0 CB A:HIS410 3.5 10.8 1.0 N A:CYS389 3.7 17.9 1.0 CA A:CYS389 4.1 20.3 1.0 N A:HIS410 4.1 14.7 1.0 NE2 A:HIS410 4.2 15.3 1.0 CD2 A:HIS410 4.3 10.3 1.0 CA A:HIS410 4.4 12.3 1.0 CG A:PRO334 4.5 19.0 1.0 CA A:CYS386 4.5 15.2 1.0 CD A:PRO334 4.7 17.8 1.0 CA A:CYS413 4.7 14.2 1.0 C A:ILE388 4.8 24.4 1.0 CB A:ILE388 4.8 15.7 1.0 C A:CYS389 4.9 18.7 1.0 O A:HOH718 4.9 34.1 1.0

Zinc binding site 5 out of 5 in the X-Ray Crystal Structure of BRPF1 Pzp Domain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of X-Ray Crystal Structure of BRPF1 Pzp Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn505 b:13.7 occ:0.81 ND1 A:HIS447 2.0 15.8 1.0 SG A:CYS400 2.3 12.7 1.0 SG A:CYS444 2.3 13.1 1.0 SG A:CYS405 2.3 12.9 1.0 CE1 A:HIS447 2.9 17.8 1.0 CB A:CYS400 3.1 11.8 1.0 CG A:HIS447 3.1 14.8 1.0 CB A:CYS405 3.2 13.2 1.0 CB A:CYS444 3.5 14.2 1.0 CB A:HIS447 3.6 14.6 1.0 N A:CYS444 4.0 12.3 1.0 NE2 A:HIS447 4.1 14.9 1.0 CD2 A:HIS447 4.2 15.2 1.0 CA A:CYS444 4.3 12.4 1.0 CB A:LYS402 4.3 16.6 1.0 O A:HOH627 4.4 16.4 1.0 N A:HIS447 4.5 14.8 1.0 CA A:CYS400 4.6 15.1 1.0 CA A:CYS405 4.6 22.9 1.0 CB A:THR407 4.6 18.1 1.0 CA A:HIS447 4.7 22.2 1.0 OG1 A:THR407 4.8 17.8 1.0 O A:HOH728 4.8 28.8 1.0 C A:CYS444 4.8 13.1 1.0 O A:CYS444 4.8 13.7 1.0

B.J.Klein, U.M.Muthurajan, M.E.Lalonde, M.D.Gibson, F.H.Andrews, M.Hepler, S.Machida, K.Yan, H.Kurumizaka, M.G.Poirier, J.Cote, K.Luger, T.G.Kutateladze. Bivalent Interaction of the Pzp Domain of BRPF1 with the Nucleosome Impacts Chromatin Dynamics and Acetylation. Nucleic Acids Res. V. 44 472 2016.
ISSN: ESSN 1362-4962
PubMed: 26626149
DOI: 10.1093/NAR/GKV1321