Zinc in PDB 6a5k: Crystal Structure of Arabidopsis Thaliana SUVH6 in Complex with Sam, Form 1

All present enzymatic activity of Crystal Structure of Arabidopsis Thaliana SUVH6 in Complex with Sam, Form 1:
2.1.1.43;

The structure of Crystal Structure of Arabidopsis Thaliana SUVH6 in Complex with Sam, Form 1, PDB code: 6a5k 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)	47.88 / 1.90
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	77.113, 122.152, 56.315, 90.00, 90.00, 90.00
R / Rfree (%)	18.4 / 21.4

The binding sites of Zinc atom in the Crystal Structure of Arabidopsis Thaliana SUVH6 in Complex with Sam, Form 1 (pdb code 6a5k). 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 1, PDB code: 6a5k:
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 1


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 1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn801 b:33.3 occ:1.00 SG A:CYS569 2.3 27.2 1.0 SG A:CYS599 2.4 28.1 1.0 SG A:CYS553 2.4 30.0 1.0 SG A:CYS595 2.4 22.9 1.0 CB A:CYS553 3.1 29.5 1.0 CB A:CYS595 3.2 22.8 1.0 CB A:CYS569 3.3 24.4 1.0 CB A:CYS599 3.3 31.7 1.0 CA A:CYS595 3.7 22.9 1.0 N A:CYS553 3.7 34.3 1.0 ZN A:ZN803 3.9 34.1 1.0 ZN A:ZN802 3.9 32.5 1.0 CA A:CYS553 4.0 34.2 1.0 SG A:CYS601 4.5 31.0 1.0 CA A:CYS599 4.6 36.2 1.0 SG A:CYS559 4.6 28.6 1.0 CA A:CYS569 4.6 30.0 1.0 N A:GLY596 4.6 25.5 1.0 N A:CYS595 4.7 19.5 1.0 SG A:CYS567 4.7 31.6 1.0 C A:CYS595 4.7 25.7 1.0 O A:HOH1062 4.7 35.5 1.0 N A:CYS569 4.7 27.2 1.0 C A:SER552 4.7 36.8 1.0 C A:CYS553 4.9 39.5 1.0 O A:CYS553 5.0 39.9 1.0

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


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 1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn802 b:32.5 occ:1.00 SG A:CYS601 2.3 31.0 1.0 SG A:CYS559 2.4 28.6 1.0 SG A:CYS605 2.4 22.8 1.0 SG A:CYS595 2.4 22.9 1.0 CB A:CYS601 3.0 28.8 1.0 CB A:CYS595 3.3 22.8 1.0 CB A:CYS605 3.4 24.1 1.0 CB A:CYS559 3.6 28.5 1.0 ZN A:ZN801 3.9 33.3 1.0 ZN A:ZN803 4.0 34.1 1.0 SG A:CYS553 4.1 30.0 1.0 N A:CYS559 4.3 32.8 1.0 CB A:LEU607 4.5 19.1 1.0 CA A:CYS601 4.5 30.6 1.0 CA A:CYS559 4.7 30.6 1.0 CA A:CYS595 4.8 22.9 1.0 NE A:ARG608 4.8 24.4 1.0 CA A:CYS605 4.8 27.5 1.0 CD1 A:LEU607 4.9 32.6 1.0 CB A:CYS599 4.9 31.7 1.0 N A:CYS601 5.0 33.2 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of Arabidopsis Thaliana SUVH6 in Complex with Sam, Form 1


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 1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn803 b:34.1 occ:1.00 SG A:CYS567 2.3 31.6 1.0 SG A:CYS559 2.3 28.6 1.0 SG A:CYS555 2.5 32.2 1.0 SG A:CYS553 2.5 30.0 1.0 CB A:CYS553 3.2 29.5 1.0 CB A:CYS555 3.2 38.1 1.0 CB A:CYS559 3.3 28.5 1.0 CB A:CYS567 3.4 33.9 1.0 ZN A:ZN801 3.9 33.3 1.0 ZN A:ZN802 4.0 32.5 1.0 CA A:CYS567 4.2 42.3 1.0 N A:CYS555 4.3 38.7 1.0 CA A:CYS555 4.4 42.1 1.0 SG A:CYS595 4.4 22.9 1.0 CA A:CYS559 4.5 30.6 1.0 CA A:CYS553 4.6 34.2 1.0 CB A:CYS569 4.7 24.4 1.0 C A:CYS567 4.9 40.3 1.0 SG A:CYS569 4.9 27.2 1.0 C A:CYS553 4.9 39.5 1.0

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


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 1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn804 b:20.8 occ:1.00 SG A:CYS785 2.3 15.5 1.0 SG A:CYS778 2.4 12.1 1.0 SG A:CYS780 2.4 13.5 1.0 SG A:CYS720 2.4 12.7 1.0 CB A:CYS785 3.3 21.3 1.0 CB A:CYS778 3.4 13.3 1.0 CB A:CYS780 3.4 12.8 1.0 CB A:CYS720 3.4 18.4 1.0 CA A:CYS785 3.7 21.7 1.0 N A:CYS720 4.0 12.0 1.0 N A:ARG786 4.0 16.6 1.0 N A:CYS780 4.1 12.7 1.0 O A:HOH1103 4.3 16.3 1.0 CA A:CYS780 4.3 14.6 1.0 C A:CYS785 4.3 21.9 1.0 CA A:CYS720 4.3 13.5 1.0 NE2 A:HIS718 4.4 10.2 1.0 N A:ARG787 4.5 19.6 1.0 CD2 A:HIS718 4.6 8.9 1.0 C A:CYS778 4.6 14.4 1.0 CA A:CYS778 4.6 14.5 1.0 O A:CYS778 4.7 14.0 1.0 N A:GLY781 4.8 14.6 1.0 N A:CYS785 4.9 24.3 1.0 C A:CYS780 4.9 18.1 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