Zinc in PDB 7ef3: Crystal Structure of Maize SHH2 Sawadee Domain in Complex with H3K9ME2 Peptide

The structure of Crystal Structure of Maize SHH2 Sawadee Domain in Complex with H3K9ME2 Peptide, PDB code: 7ef3 was solved by Y.Wang, J.Du, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	34.13 / 2.10
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	64.906, 67.37, 80.251, 90, 90, 90
R / Rfree (%)	21.9 / 26.9

The binding sites of Zinc atom in the Crystal Structure of Maize SHH2 Sawadee Domain in Complex with H3K9ME2 Peptide (pdb code 7ef3). 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 Maize SHH2 Sawadee Domain in Complex with H3K9ME2 Peptide, PDB code: 7ef3:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of Maize SHH2 Sawadee Domain in Complex with H3K9ME2 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 Maize SHH2 Sawadee Domain in Complex with H3K9ME2 Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn501 b:39.7 occ:1.00 NE2 A:HIS232 2.3 46.2 1.0 SG A:CYS239 2.4 42.6 1.0 SG A:CYS198 2.4 40.6 1.0 SG A:CYS237 2.4 37.5 1.0 CB A:CYS198 3.0 40.9 1.0 CD2 A:HIS232 3.3 50.2 1.0 CE1 A:HIS232 3.3 47.1 1.0 CB A:CYS239 3.4 37.1 1.0 CB A:CYS237 3.5 41.4 1.0 O A:HOH640 3.6 48.8 1.0 CA A:CYS237 4.0 44.7 1.0 N A:CYS239 4.0 42.1 1.0 O A:ALA195 4.2 45.8 1.0 N A:ARG238 4.3 47.1 1.0 CA A:CYS239 4.4 46.1 1.0 ND1 A:HIS232 4.4 52.2 1.0 CG A:HIS232 4.4 54.0 1.0 CA A:CYS198 4.5 36.9 1.0 C A:CYS237 4.6 45.5 1.0 O A:ARG230 4.8 59.1 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of Maize SHH2 Sawadee Domain in Complex with H3K9ME2 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 Maize SHH2 Sawadee Domain in Complex with H3K9ME2 Peptide within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn501 b:41.7 occ:1.00 NE2 B:HIS232 2.3 45.4 1.0 SG B:CYS237 2.3 41.1 1.0 SG B:CYS198 2.4 42.7 1.0 SG B:CYS239 2.4 41.9 1.0 CE1 B:HIS232 3.0 44.0 1.0 CB B:CYS198 3.1 38.3 1.0 CB B:CYS239 3.3 42.9 1.0 CD2 B:HIS232 3.3 46.3 1.0 CB B:CYS237 3.4 43.2 1.0 N B:CYS239 3.9 40.0 1.0 CA B:CYS237 3.9 43.6 1.0 ND1 B:HIS232 4.2 44.1 1.0 N B:ARG238 4.2 46.7 1.0 CA B:CYS239 4.2 41.2 1.0 O B:ALA195 4.3 54.0 1.0 CG B:HIS232 4.3 45.4 1.0 C B:CYS237 4.5 45.4 1.0 CA B:CYS198 4.6 37.7 1.0 O B:ARG230 4.7 44.0 1.0

Y.Wang, X.Zhou, J.Luo, S.Lv, R.Liu, X.Du, B.Jia, F.Yuan, H.Zhang, J.Du. Recognition of H3K9ME1 By Maize Rna-Directed Dna Methylation Factor SHH2. J Integr Plant Biol V. 63 1091 2021.
ISSN: ISSN 1744-7909
PubMed: 33913587
DOI: 10.1111/JIPB.13103