Zinc in PDB 5z8n: Crystal Structure of Arabidopsis Thaliana Ebs C-Terminal Deletion Construct in Complex with An H3K4ME2 Peptide

The structure of Crystal Structure of Arabidopsis Thaliana Ebs C-Terminal Deletion Construct in Complex with An H3K4ME2 Peptide, PDB code: 5z8n 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)	40.99 / 3.10
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	73.464, 75.696, 80.357, 90.00, 115.41, 90.00
R / Rfree (%)	21.3 / 25.2

The binding sites of Zinc atom in the Crystal Structure of Arabidopsis Thaliana Ebs C-Terminal Deletion Construct in Complex with An H3K4ME2 Peptide (pdb code 5z8n). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Crystal Structure of Arabidopsis Thaliana Ebs C-Terminal Deletion Construct in Complex with An H3K4ME2 Peptide, PDB code: 5z8n:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in the Crystal Structure of Arabidopsis Thaliana Ebs C-Terminal Deletion Construct in Complex with An H3K4ME2 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 C-Terminal Deletion Construct in Complex with An H3K4ME2 Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:76.4 occ:1.00 ND1 A:HIS172 2.2 64.8 1.0 SG A:CYS151 2.4 56.5 1.0 SG A:CYS175 2.4 88.3 1.0 SG A:CYS149 2.5 87.8 1.0 CB A:CYS149 2.9 71.9 1.0 CE1 A:HIS172 3.1 74.2 1.0 CB A:CYS151 3.1 68.2 1.0 CG A:HIS172 3.2 68.2 1.0 CB A:CYS175 3.2 74.6 1.0 CB A:HIS172 3.5 71.2 1.0 N A:HIS172 4.0 71.1 1.0 N A:CYS151 4.0 58.2 1.0 CA A:CYS151 4.2 64.6 1.0 NE2 A:HIS172 4.2 74.2 1.0 CD2 A:HIS172 4.3 69.8 1.0 CA A:HIS172 4.3 71.3 1.0 CA A:CYS149 4.4 75.3 1.0 CA A:CYS175 4.7 73.2 1.0 N A:LYS150 4.7 75.2 1.0 C A:CYS149 4.9 77.0 1.0 O A:TYR148 5.0 66.6 1.0

Zinc binding site 2 out of 6 in the Crystal Structure of Arabidopsis Thaliana Ebs C-Terminal Deletion Construct in Complex with An H3K4ME2 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 C-Terminal Deletion Construct in Complex with An H3K4ME2 Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:83.8 occ:1.00 SG A:CYS191 2.4 89.1 1.0 SG A:CYS164 2.4 64.6 1.0 SG A:CYS167 2.5 0.6 1.0 SG A:CYS194 2.5 74.2 1.0 CB A:CYS167 2.9 70.2 1.0 N A:CYS167 2.9 76.4 1.0 CB A:CYS164 3.3 63.3 1.0 CA A:CYS167 3.5 73.7 1.0 CB A:CYS191 3.5 65.8 1.0 CB A:CYS194 3.7 75.4 1.0 C A:GLY166 4.0 75.6 1.0 N A:CYS191 4.0 64.7 1.0 CA A:GLY166 4.3 71.7 1.0 CA A:CYS191 4.3 70.4 1.0 N A:GLY166 4.4 70.5 1.0 OH A:TYR171 4.5 81.3 1.0 C A:CYS167 4.6 75.7 1.0 N A:CYS194 4.6 75.7 1.0 N A:LYS168 4.6 77.8 1.0 CA A:CYS194 4.6 77.1 1.0 CA A:CYS164 4.7 73.2 1.0 O A:CYS191 4.7 59.2 1.0 CE1 A:TYR171 4.8 75.6 1.0 C A:CYS191 4.9 70.8 1.0

Zinc binding site 3 out of 6 in the Crystal Structure of Arabidopsis Thaliana Ebs C-Terminal Deletion Construct in Complex with An H3K4ME2 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 Arabidopsis Thaliana Ebs C-Terminal Deletion Construct in Complex with An H3K4ME2 Peptide within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn301 b:65.6 occ:1.00 ND1 B:HIS172 2.3 75.2 1.0 SG B:CYS175 2.3 0.0 1.0 SG B:CYS149 2.4 64.2 1.0 SG B:CYS151 2.4 70.3 1.0 CB B:CYS175 3.1 70.0 1.0 CB B:CYS149 3.2 84.7 1.0 CG B:HIS172 3.2 70.2 1.0 CE1 B:HIS172 3.3 68.5 1.0 CB B:HIS172 3.4 66.8 1.0 CB B:CYS151 3.5 65.2 1.0 N B:CYS151 3.9 63.3 1.0 N B:HIS172 4.0 71.6 1.0 CA B:HIS172 4.3 68.8 1.0 CA B:CYS151 4.4 65.1 1.0 N B:LYS150 4.4 74.6 1.0 CD2 B:HIS172 4.4 69.7 1.0 NE2 B:HIS172 4.4 70.3 1.0 CA B:CYS175 4.6 73.7 1.0 CA B:CYS149 4.6 85.0 1.0 C B:CYS149 4.8 81.1 1.0 O B:HIS172 4.9 75.3 1.0 N B:CYS175 5.0 77.9 1.0

Zinc binding site 4 out of 6 in the Crystal Structure of Arabidopsis Thaliana Ebs C-Terminal Deletion Construct in Complex with An H3K4ME2 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 Arabidopsis Thaliana Ebs C-Terminal Deletion Construct in Complex with An H3K4ME2 Peptide within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn302 b:85.3 occ:1.00 SG B:CYS164 2.3 59.7 1.0 CB B:CYS191 2.4 71.9 1.0 SG B:CYS194 2.4 64.3 1.0 SG B:CYS167 2.4 0.7 1.0 CB B:CYS167 2.8 56.1 1.0 CB B:CYS164 3.0 85.2 1.0 N B:CYS167 3.1 64.6 1.0 N B:CYS191 3.4 73.3 1.0 CA B:CYS191 3.4 73.5 1.0 CA B:CYS167 3.5 65.0 1.0 CB B:CYS194 3.5 76.1 1.0 SG B:CYS191 3.6 96.2 1.0 N B:CYS194 4.3 69.4 1.0 C B:GLY166 4.3 62.5 1.0 C B:CYS191 4.3 81.1 1.0 CA B:CYS194 4.4 71.1 1.0 OH B:TYR171 4.5 92.0 1.0 CA B:CYS164 4.5 78.8 1.0 O B:CYS191 4.5 79.4 1.0 C B:VAL190 4.6 73.2 1.0 CE1 B:TYR171 4.6 68.3 1.0 CA B:GLY166 4.6 59.8 1.0 CG1 B:VAL190 4.8 60.0 1.0 N B:GLY166 4.8 80.9 1.0 C B:CYS167 4.9 70.4 1.0 C B:CYS164 4.9 71.8 1.0 CZ B:TYR171 5.0 76.0 1.0

Zinc binding site 5 out of 6 in the Crystal Structure of Arabidopsis Thaliana Ebs C-Terminal Deletion Construct in Complex with An H3K4ME2 Peptide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of Arabidopsis Thaliana Ebs C-Terminal Deletion Construct in Complex with An H3K4ME2 Peptide within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn301 b:79.4 occ:1.00 SG C:CYS149 2.4 69.6 1.0 SG C:CYS175 2.4 0.9 1.0 ND1 C:HIS172 2.5 73.3 1.0 SG C:CYS151 2.5 88.5 1.0 CB C:CYS149 3.0 75.3 1.0 CB C:CYS175 3.3 66.9 1.0 CE1 C:HIS172 3.4 74.6 1.0 CB C:CYS151 3.4 68.1 1.0 CG C:HIS172 3.5 75.6 1.0 CB C:HIS172 3.7 78.2 1.0 N C:CYS151 3.9 74.9 1.0 N C:HIS172 4.1 75.1 1.0 CA C:CYS151 4.3 70.0 1.0 N C:LYS150 4.4 89.5 1.0 CA C:CYS149 4.5 80.0 1.0 CA C:HIS172 4.5 79.0 1.0 NE2 C:HIS172 4.5 75.9 1.0 CD2 C:HIS172 4.6 76.9 1.0 CA C:CYS175 4.8 70.6 1.0 C C:CYS149 4.9 88.3 1.0 O C:HIS172 5.0 83.7 1.0 C C:LYS150 5.0 80.8 1.0

Zinc binding site 6 out of 6 in the Crystal Structure of Arabidopsis Thaliana Ebs C-Terminal Deletion Construct in Complex with An H3K4ME2 Peptide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of Arabidopsis Thaliana Ebs C-Terminal Deletion Construct in Complex with An H3K4ME2 Peptide within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn302 b:86.1 occ:1.00 SG C:CYS167 2.2 67.2 1.0 SG C:CYS194 2.3 90.6 1.0 SG C:CYS164 2.4 60.8 1.0 CB C:CYS191 2.5 78.9 1.0 CB C:CYS194 2.7 94.2 1.0 SG C:CYS191 3.2 97.0 1.0 N C:CYS167 3.3 77.7 1.0 CB C:CYS164 3.6 67.5 1.0 N C:CYS191 3.6 78.9 1.0 CA C:CYS191 3.6 82.8 1.0 CB C:CYS167 3.7 72.6 1.0 CA C:CYS194 3.8 95.5 1.0 N C:CYS194 4.0 91.2 1.0 CA C:CYS167 4.0 75.2 1.0 C C:GLY166 4.1 75.0 1.0 CA C:GLY166 4.1 73.5 1.0 N C:GLY166 4.3 73.3 1.0 C C:CYS191 4.6 93.5 1.0 C C:VAL190 4.8 79.2 1.0 CG1 C:VAL190 4.8 80.8 1.0 O C:CYS191 4.9 99.5 1.0 CA C:CYS164 4.9 67.0 1.0 OH C:TYR171 5.0 87.2 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