Zinc in PDB 5znp: Crystal Structure of Ptshl in Complex with An H3K4ME3 Peptide

The structure of Crystal Structure of Ptshl in Complex with An H3K4ME3 Peptide, PDB code: 5znp was solved by X.Lv, J.Du, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.96 / 2.80
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	44.340, 91.909, 114.370, 90.00, 90.00, 90.00
R / Rfree (%)	25 / 29.3

The binding sites of Zinc atom in the Crystal Structure of Ptshl in Complex with An H3K4ME3 Peptide (pdb code 5znp). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of Ptshl in Complex with An H3K4ME3 Peptide, PDB code: 5znp:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of Ptshl in Complex with An H3K4ME3 Peptide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of Ptshl in Complex with An H3K4ME3 Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn501 b:78.1 occ:1.00 SG A:CYS142 2.4 0.1 1.0 ND1 A:HIS165 2.4 85.2 1.0 SG A:CYS168 2.5 0.5 1.0 SG A:CYS144 2.5 73.7 1.0 CB A:CYS142 2.9 61.0 1.0 CB A:CYS168 3.2 92.4 1.0 CG A:HIS165 3.3 85.3 1.0 CB A:HIS165 3.5 83.7 1.0 CE1 A:HIS165 3.5 76.1 1.0 CB A:CYS144 3.6 72.4 1.0 N A:HIS165 3.8 83.4 1.0 N A:CYS144 4.1 75.6 1.0 CA A:HIS165 4.2 84.3 1.0 CA A:CYS142 4.4 70.2 1.0 N A:LYS143 4.5 78.2 1.0 CD2 A:HIS165 4.5 77.7 1.0 CA A:CYS144 4.5 75.0 1.0 NE2 A:HIS165 4.5 75.3 1.0 O A:HIS165 4.7 0.5 1.0 CA A:CYS168 4.7 0.2 1.0 C A:CYS142 4.7 72.4 1.0 O A:TYR141 4.8 64.8 1.0 C A:PHE164 4.9 86.9 1.0 C A:HIS165 4.9 0.3 1.0 CE A:MET154 5.0 0.6 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of Ptshl in Complex with An H3K4ME3 Peptide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of Ptshl in Complex with An H3K4ME3 Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn502 b:0.8 occ:1.00 SG A:CYS184 2.6 1.0 1.0 SG A:CYS187 2.6 0.4 1.0 SG A:CYS157 2.7 0.5 1.0 SG A:CYS160 2.9 0.2 1.0 CB A:CYS160 3.0 0.3 1.0 N A:CYS160 3.0 0.6 1.0 CB A:CYS184 3.3 0.0 1.0 N A:CYS184 3.4 0.7 1.0 CA A:CYS160 3.6 0.0 1.0 CA A:CYS184 3.7 0.4 1.0 O A:CYS184 3.8 0.8 1.0 CB A:CYS157 3.9 0.9 1.0 N A:GLY159 4.0 0.7 1.0 C A:CYS184 4.1 0.0 1.0 C A:GLY159 4.1 0.5 1.0 CB A:CYS187 4.1 0.4 1.0 N A:CYS187 4.1 0.1 1.0 CA A:CYS187 4.3 0.7 1.0 CA A:GLY159 4.3 0.8 1.0 C A:PHE183 4.4 0.5 1.0 N A:SER161 4.5 0.6 1.0 C A:CYS160 4.6 0.5 1.0 N A:GLU158 4.6 0.6 1.0 C A:GLU158 4.7 0.6 1.0 CA A:PHE183 4.8 0.8 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of Ptshl in Complex with An H3K4ME3 Peptide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of Ptshl in Complex with An H3K4ME3 Peptide within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn501 b:87.3 occ:1.00 ND1 B:HIS165 2.2 76.5 1.0 SG B:CYS144 2.5 70.9 1.0 SG B:CYS142 2.6 75.7 1.0 SG B:CYS168 2.8 0.4 1.0 CB B:CYS142 3.0 64.5 1.0 CG B:HIS165 3.0 76.5 1.0 CB B:CYS168 3.2 83.6 1.0 CE1 B:HIS165 3.2 74.8 1.0 CB B:HIS165 3.3 79.4 1.0 CB B:CYS144 3.4 73.3 1.0 N B:HIS165 3.7 78.2 1.0 CA B:HIS165 4.1 79.5 1.0 CD2 B:HIS165 4.2 74.7 1.0 NE2 B:HIS165 4.2 73.4 1.0 N B:CYS144 4.4 77.5 1.0 CA B:CYS142 4.5 64.2 1.0 CA B:CYS144 4.5 75.0 1.0 CE B:MET154 4.6 70.7 1.0 CA B:CYS168 4.7 87.5 1.0 O B:HIS165 4.7 86.6 1.0 C B:PHE164 4.8 71.9 1.0 C B:HIS165 4.9 83.2 1.0 N B:LYS143 5.0 80.8 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of Ptshl in Complex with An H3K4ME3 Peptide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of Ptshl in Complex with An H3K4ME3 Peptide within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn502 b:0.2 occ:1.00 SG B:CYS184 2.3 78.3 1.0 CB B:CYS160 2.4 91.8 1.0 SG B:CYS160 2.5 0.0 1.0 N B:CYS160 2.6 96.6 1.0 SG B:CYS157 2.9 91.4 1.0 CA B:CYS160 3.1 93.6 1.0 SG B:CYS187 3.6 0.8 1.0 CB B:CYS184 3.6 0.4 1.0 CB B:CYS157 3.7 96.4 1.0 C B:GLY159 3.7 97.0 1.0 C B:CYS160 4.0 88.0 1.0 CA B:GLY159 4.1 97.9 1.0 OD1 B:ASN186 4.2 0.4 1.0 N B:SER161 4.3 89.7 1.0 N B:GLY159 4.4 96.8 1.0 O B:GLY159 4.8 97.9 1.0 CZ B:PHE164 4.8 73.3 1.0 CA B:CYS184 4.9 0.3 1.0 CE1 B:PHE164 4.9 73.1 1.0 O B:CYS160 4.9 87.1 1.0 O B:PHE183 5.0 0.5 1.0 N B:GLU185 5.0 0.7 1.0 C B:PHE183 5.0 0.5 1.0

S.Qian, X.Lv, R.N.Scheid, L.Lu, Z.Yang, W.Chen, R.Liu, M.D.Boersma, J.M.Denu, X.Zhong, J.Du. Dual Recognition of H3K4ME3 and H3K27ME3 By A Plant Histone Reader Shl. Nat Commun V. 9 2425 2018.
ISSN: ESSN 2041-1723
PubMed: 29930355
DOI: 10.1038/S41467-018-04836-Y