Zinc in PDB 5z8l: Crystal Structure of Arabidopsis Thaliana Ebs in Complex with An H3K27ME3 Peptide

The structure of Crystal Structure of Arabidopsis Thaliana Ebs in Complex with An H3K27ME3 Peptide, PDB code: 5z8l was solved by Z.Yang, J.Du, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.02 / 2.01
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	36.247, 60.299, 98.038, 90.00, 90.00, 90.00
R / Rfree (%)	20.1 / 23

The binding sites of Zinc atom in the Crystal Structure of Arabidopsis Thaliana Ebs in Complex with An H3K27ME3 Peptide (pdb code 5z8l). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of Arabidopsis Thaliana Ebs in Complex with An H3K27ME3 Peptide, PDB code: 5z8l:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of Arabidopsis Thaliana Ebs in Complex with An H3K27ME3 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 Arabidopsis Thaliana Ebs in Complex with An H3K27ME3 Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn501 b:45.9 occ:1.00 ND1 A:HIS172 2.2 32.7 1.0 SG A:CYS175 2.4 34.2 1.0 SG A:CYS149 2.4 32.8 1.0 SG A:CYS151 2.4 37.8 1.0 CG A:HIS172 3.1 31.8 1.0 CE1 A:HIS172 3.2 31.9 1.0 CB A:CYS149 3.2 29.3 1.0 CB A:CYS175 3.3 30.4 1.0 CB A:HIS172 3.4 30.7 1.0 CB A:CYS151 3.4 38.8 1.0 O A:HOH689 3.6 43.8 1.0 N A:CYS151 3.9 49.6 1.0 N A:HIS172 4.1 24.1 1.0 NE2 A:HIS172 4.3 31.8 1.0 CD2 A:HIS172 4.3 31.5 1.0 CA A:CYS151 4.3 44.2 1.0 CA A:HIS172 4.3 26.8 1.0 N A:LYS150 4.5 41.9 1.0 CA A:CYS149 4.6 34.7 1.0 CA A:CYS175 4.8 29.6 1.0 C A:CYS149 4.9 43.2 1.0 O A:HIS172 4.9 26.1 1.0 C A:LYS150 5.0 50.1 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of Arabidopsis Thaliana Ebs in Complex with An H3K27ME3 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 Arabidopsis Thaliana Ebs in Complex with An H3K27ME3 Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn502 b:78.7 occ:1.00 SG A:CYS167 2.2 70.3 1.0 SG A:CYS191 2.3 79.9 1.0 SG A:CYS164 2.5 55.7 1.0 SG A:CYS194 2.9 78.5 1.0 CB A:CYS194 2.9 82.3 1.0 CB A:CYS191 2.9 57.4 1.0 CB A:CYS164 3.4 45.9 1.0 N A:CYS194 3.4 82.2 1.0 CA A:CYS191 3.5 55.2 1.0 N A:CYS191 3.5 57.7 1.0 O A:CYS191 3.5 63.6 1.0 C A:CYS191 3.7 58.3 1.0 CA A:CYS194 3.7 83.7 1.0 CB A:CYS167 3.9 52.0 1.0 N A:CYS167 4.0 63.4 1.0 C A:GLU193 4.2 81.3 1.0 OH A:TYR171 4.3 49.1 1.0 CB A:GLU193 4.4 76.2 1.0 N A:GLU193 4.5 81.7 1.0 CA A:CYS167 4.6 55.5 1.0 CA A:GLU193 4.6 80.1 1.0 N A:ALA192 4.6 84.4 1.0 CE1 A:TYR171 4.7 44.8 1.0 C A:VAL190 4.7 51.9 1.0 CA A:CYS164 4.9 46.0 1.0 C A:GLY166 4.9 66.2 1.0 CA A:GLY166 4.9 62.7 1.0 CG1 A:VAL190 4.9 50.5 1.0 CZ A:TYR171 4.9 44.1 1.0 N A:GLY166 5.0 61.2 1.0

Z.Yang, S.Qian, R.N.Scheid, L.Lu, X.Chen, R.Liu, X.Du, X.Lv, M.D.Boersma, M.Scalf, L.M.Smith, J.M.Denu, J.Du, X.Zhong. Ebs Is A Bivalent Histone Reader That Regulates Floral Phase Transition in Arabidopsis. Nat. Genet. V. 50 1247 2018.
ISSN: ISSN 1546-1718
PubMed: 30082787
DOI: 10.1038/S41588-018-0187-8