Atomistry » Zinc » PDB 6a57-6agg » 6a5n
Atomistry »
  Zinc »
    PDB 6a57-6agg »
      6a5n »

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

Enzymatic activity of 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;

Protein crystallography data

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

Zinc Binding Sites:

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 6a5n

Go back to Zinc Binding Sites List in 6a5n
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 6a5n

Go back to Zinc Binding Sites List in 6a5n
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 6a5n

Go back to Zinc Binding Sites List in 6a5n
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

Reference:

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
Page generated: Mon Oct 28 17:18:15 2024

Last articles

Zn in 9MJ5
Zn in 9HNW
Zn in 9G0L
Zn in 9FNE
Zn in 9DZN
Zn in 9E0I
Zn in 9D32
Zn in 9DAK
Zn in 8ZXC
Zn in 8ZUF
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy