Zinc in PDB 6a5n: Crystal Structure of Arabidopsis Thaliana SUVH6 in Complex with Methylated Dna

All present enzymatic activity of Crystal Structure of Arabidopsis Thaliana SUVH6 in Complex with Methylated Dna:
2.1.1.43;

The structure of Crystal Structure of Arabidopsis Thaliana SUVH6 in Complex with Methylated Dna, PDB code: 6a5n 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)	33.59 / 2.40
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	74.137, 79.443, 107.845, 90.00, 90.00, 90.00
R / Rfree (%)	23 / 27.9

The binding sites of Zinc atom in the Crystal Structure of Arabidopsis Thaliana SUVH6 in Complex with Methylated Dna (pdb code 6a5n). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Crystal Structure of Arabidopsis Thaliana SUVH6 in Complex with Methylated Dna, PDB code: 6a5n:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Crystal Structure of Arabidopsis Thaliana SUVH6 in Complex with Methylated Dna


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 Methylated Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn801 b:63.6 occ:1.00 SG A:CYS569 2.2 57.0 1.0 SG A:CYS599 2.4 69.7 1.0 SG A:CYS553 2.4 78.2 1.0 SG A:CYS595 2.6 56.1 1.0 CB A:CYS553 3.0 55.0 1.0 CB A:CYS599 3.3 70.4 1.0 N A:CYS553 3.3 63.7 1.0 CB A:CYS595 3.4 56.0 1.0 CB A:CYS569 3.4 64.7 1.0 CA A:CYS595 3.7 60.3 1.0 CA A:CYS553 3.7 66.0 1.0 ZN A:ZN802 3.9 58.7 1.0 ZN A:ZN803 4.2 63.0 1.0 C A:SER552 4.4 74.9 1.0 CA A:CYS599 4.5 64.9 1.0 N A:GLY596 4.5 67.9 1.0 SG A:CYS567 4.5 59.0 1.0 SG A:CYS601 4.6 86.9 1.0 C A:CYS595 4.6 70.3 1.0 SG A:CYS559 4.6 53.6 1.0 C A:CYS553 4.6 69.3 1.0 N A:CYS569 4.6 59.0 1.0 CA A:CYS569 4.6 57.8 1.0 N A:CYS595 4.7 58.0 1.0 O A:CYS553 4.7 73.5 1.0 CA A:SER552 4.7 76.7 1.0

Zinc binding site 2 out of 3 in the Crystal Structure of Arabidopsis Thaliana SUVH6 in Complex with Methylated Dna


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 Methylated Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn802 b:58.7 occ:1.00 SG A:CYS595 2.1 56.1 1.0 SG A:CYS559 2.2 53.6 1.0 SG A:CYS601 2.4 86.9 1.0 SG A:CYS605 2.6 61.9 1.0 CB A:CYS601 3.0 65.6 1.0 CB A:CYS559 3.3 76.4 1.0 CB A:CYS595 3.3 56.0 1.0 CB A:CYS605 3.7 56.2 1.0 SG A:CYS553 3.7 78.2 1.0 ZN A:ZN801 3.9 63.6 1.0 ZN A:ZN803 4.1 63.0 1.0 N A:CYS559 4.2 72.8 1.0 CA A:CYS559 4.3 74.6 1.0 CA A:CYS601 4.5 67.0 1.0 CB A:LEU607 4.5 54.6 1.0 CA A:CYS595 4.7 60.3 1.0 CB A:CYS599 4.9 70.4 1.0 N A:CYS601 4.9 67.3 1.0 NE A:ARG608 5.0 59.0 1.0

Zinc binding site 3 out of 3 in the Crystal Structure of Arabidopsis Thaliana SUVH6 in Complex with Methylated Dna


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 Methylated Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn803 b:63.0 occ:1.00 SG A:CYS567 2.3 59.0 1.0 SG A:CYS555 2.5 72.0 1.0 SG A:CYS559 2.5 53.6 1.0 SG A:CYS553 2.6 78.2 1.0 CB A:CYS567 2.8 58.6 1.0 CB A:CYS553 2.9 55.0 1.0 CB A:CYS555 3.3 72.0 1.0 CB A:CYS559 3.4 76.4 1.0 CA A:CYS567 3.7 61.5 1.0 ZN A:ZN802 4.1 58.7 1.0 ZN A:ZN801 4.2 63.6 1.0 N A:CYS555 4.2 70.8 1.0 CA A:CYS559 4.3 74.6 1.0 CA A:CYS553 4.4 66.0 1.0 C A:CYS567 4.4 63.9 1.0 CA A:CYS555 4.4 70.8 1.0 N A:ALA568 4.6 62.8 1.0 SG A:CYS595 4.6 56.1 1.0 O A:HOH918 4.7 64.3 1.0 N A:CYS554 4.8 66.7 1.0 C A:CYS553 4.8 69.3 1.0 N A:CYS567 4.9 64.3 1.0 N A:CYS569 5.0 59.0 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