Zinc in PDB 6a5m: Crystal Structure of Arabidopsis Thaliana SUVH6 in Complex with Sam, Form 2

All present enzymatic activity of Crystal Structure of Arabidopsis Thaliana SUVH6 in Complex with Sam, Form 2:
2.1.1.43;

The structure of Crystal Structure of Arabidopsis Thaliana SUVH6 in Complex with Sam, Form 2, PDB code: 6a5m was solved by X.Li, J.Du, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	38.55 / 2.30
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	57.546, 77.098, 66.820, 90.00, 110.63, 90.00
R / Rfree (%)	17.8 / 22.3

The binding sites of Zinc atom in the Crystal Structure of Arabidopsis Thaliana SUVH6 in Complex with Sam, Form 2 (pdb code 6a5m). 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 Arabidopsis Thaliana SUVH6 in Complex with Sam, Form 2, PDB code: 6a5m:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of Arabidopsis Thaliana SUVH6 in Complex with Sam, Form 2


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 SUVH6 in Complex with Sam, Form 2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn801 b:38.1 occ:1.00 SG A:CYS569 2.3 37.3 1.0 SG A:CYS599 2.4 36.4 1.0 CB A:CYS553 2.4 58.0 1.0 SG A:CYS595 2.5 37.1 1.0 SG A:CYS553 2.6 44.2 1.0 CB A:CYS595 3.2 26.9 1.0 CB A:CYS599 3.3 39.5 1.0 CB A:CYS569 3.3 36.8 1.0 CA A:CYS595 3.7 27.0 1.0 CA A:CYS553 3.7 56.4 1.0 ZN A:ZN802 3.9 36.3 1.0 ZN A:ZN803 4.0 39.8 1.0 N A:CYS553 4.2 56.7 1.0 SG A:CYS601 4.3 0.4 1.0 CA A:CYS599 4.5 43.8 1.0 SG A:CYS559 4.5 44.1 1.0 C A:SER552 4.6 54.1 1.0 SG A:CYS567 4.6 43.8 1.0 CA A:CYS569 4.6 38.0 1.0 N A:GLY596 4.6 30.8 1.0 N A:CYS595 4.7 28.1 1.0 C A:CYS595 4.7 27.4 1.0 N A:CYS569 4.7 41.0 1.0 O A:SER552 4.9 56.8 1.0 C A:CYS553 4.9 57.7 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of Arabidopsis Thaliana SUVH6 in Complex with Sam, Form 2


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 SUVH6 in Complex with Sam, Form 2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn802 b:36.3 occ:1.00 SG A:CYS601 2.2 0.4 1.0 SG A:CYS595 2.3 37.1 1.0 SG A:CYS605 2.3 37.4 1.0 SG A:CYS559 2.5 44.1 1.0 CB A:CYS601 3.0 29.1 1.0 CB A:CYS595 3.3 26.9 1.0 CB A:CYS605 3.4 37.5 1.0 CB A:CYS559 3.5 43.8 1.0 ZN A:ZN801 3.9 38.1 1.0 ZN A:ZN803 4.0 39.8 1.0 N A:CYS559 4.1 46.5 1.0 CB A:LEU607 4.4 34.7 1.0 CA A:CYS559 4.4 46.8 1.0 SG A:CYS553 4.4 44.2 1.0 CA A:CYS601 4.5 39.5 1.0 CA A:CYS595 4.7 27.0 1.0 NE A:ARG608 4.7 33.2 1.0 CA A:CYS605 4.8 35.7 1.0 CB A:CYS599 4.9 39.5 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of Arabidopsis Thaliana SUVH6 in Complex with Sam, Form 2


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 SUVH6 in Complex with Sam, Form 2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn803 b:39.8 occ:1.00 SG A:CYS559 2.1 44.1 1.0 SG A:CYS553 2.1 44.2 1.0 SG A:CYS567 2.2 43.8 1.0 SG A:CYS555 2.4 50.4 1.0 CB A:CYS567 3.3 49.9 1.0 CB A:CYS555 3.4 62.8 1.0 CB A:CYS559 3.4 43.8 1.0 CB A:CYS553 3.9 58.0 1.0 SG A:CYS601 3.9 0.4 1.0 ZN A:ZN801 4.0 38.1 1.0 ZN A:ZN802 4.0 36.3 1.0 CA A:CYS567 4.1 51.5 1.0 CA A:CYS559 4.4 46.8 1.0 SG A:CYS595 4.4 37.1 1.0 N A:CYS555 4.5 67.3 1.0 CA A:CYS555 4.6 65.6 1.0 N A:CYS554 4.7 62.5 1.0 C A:CYS567 4.8 46.4 1.0 CA A:CYS553 4.8 56.4 1.0 C A:CYS554 4.9 70.3 1.0 CB A:CYS569 4.9 36.8 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of Arabidopsis Thaliana SUVH6 in Complex with Sam, Form 2


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 SUVH6 in Complex with Sam, Form 2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn804 b:31.8 occ:1.00 SG A:CYS778 2.2 25.3 1.0 SG A:CYS780 2.4 30.2 1.0 SG A:CYS720 2.4 27.9 1.0 SG A:CYS785 2.4 31.1 1.0 CB A:CYS780 3.3 23.6 1.0 CB A:CYS720 3.3 32.0 1.0 CB A:CYS785 3.3 27.9 1.0 CB A:CYS778 3.4 29.7 1.0 CA A:CYS785 3.8 32.4 1.0 N A:CYS720 3.9 28.2 1.0 N A:CYS780 4.0 26.9 1.0 N A:ARG786 4.1 28.9 1.0 CA A:CYS720 4.2 31.6 1.0 CA A:CYS780 4.2 25.9 1.0 NE2 A:HIS718 4.3 23.9 1.0 C A:CYS785 4.4 34.2 1.0 N A:ARG787 4.5 28.9 1.0 CD2 A:HIS718 4.5 23.8 1.0 C A:CYS778 4.6 32.3 1.0 CA A:CYS778 4.6 31.8 1.0 O A:CYS778 4.7 31.8 1.0 O A:HOH1024 4.7 38.2 1.0 C A:CYS780 4.9 30.1 1.0 C A:SER719 4.9 26.6 1.0 N A:GLY781 4.9 28.5 1.0 N A:PHE779 5.0 30.8 1.0

X.Li, C.J.Harris, Z.Zhong, W.Chen, R.Liu, B.Jia, Z.Wang, S.Li, S.E.Jacobsen, J.Du. Mechanistic Insights Into Plant Suvh Family H3K9 Methyltransferases and Their Binding to Context-Biased Non-Cg Dna Methylation. Proc. Natl. Acad. Sci. V. 115 E8793 2018U.S.A..
ISSN: ESSN 1091-6490
PubMed: 30150382
DOI: 10.1073/PNAS.1809841115