Atomistry » Zinc » PDB 3oxk-3p44 » 3oxl
Atomistry »
  Zinc »
    PDB 3oxk-3p44 »
      3oxl »

Zinc in PDB 3oxl: Human Lysine Methyltransferase SMYD3 in Complex with Adohcy (Form II)

Enzymatic activity of Human Lysine Methyltransferase SMYD3 in Complex with Adohcy (Form II)

All present enzymatic activity of Human Lysine Methyltransferase SMYD3 in Complex with Adohcy (Form II):
2.1.1.43;

Protein crystallography data

The structure of Human Lysine Methyltransferase SMYD3 in Complex with Adohcy (Form II), PDB code: 3oxl was solved by S.Xu, J.Wu, B.Sun, C.Zhong, J.Ding, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 3.60
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 55.002, 101.020, 117.290, 90.00, 90.00, 90.00
R / Rfree (%) 24.1 / 28.3

Zinc Binding Sites:

The binding sites of Zinc atom in the Human Lysine Methyltransferase SMYD3 in Complex with Adohcy (Form II) (pdb code 3oxl). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Human Lysine Methyltransferase SMYD3 in Complex with Adohcy (Form II), PDB code: 3oxl:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in 3oxl

Go back to Zinc Binding Sites List in 3oxl
Zinc binding site 1 out of 3 in the Human Lysine Methyltransferase SMYD3 in Complex with Adohcy (Form II)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Human Lysine Methyltransferase SMYD3 in Complex with Adohcy (Form II) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn429

b:98.3
occ:1.00
SG A:CYS263 2.3 0.6 1.0
SG A:CYS266 2.3 0.4 1.0
SG A:CYS261 2.3 0.9 1.0
CB A:CYS266 2.4 0.8 1.0
CB A:CYS261 2.5 0.5 1.0
SG A:CYS208 2.7 95.3 1.0
O A:CYS261 3.3 0.6 1.0
C A:CYS261 3.5 0.6 1.0
CA A:CYS261 3.5 0.1 1.0
CA A:CYS266 3.6 0.7 1.0
CB A:CYS263 3.6 0.8 1.0
N A:CYS266 3.7 1.0 1.0
N A:CYS263 3.8 0.1 1.0
CA A:CYS263 4.2 0.9 1.0
N A:ASP262 4.3 0.1 1.0
CB A:CYS208 4.3 95.5 1.0
O A:CYS263 4.6 0.1 1.0
N A:CYS261 4.6 1.0 1.0
N A:CYS208 4.7 95.5 1.0
C A:CYS266 4.8 0.5 1.0
C A:CYS263 4.9 0.9 1.0
C A:ASP262 4.9 0.3 1.0
NH2 A:ARG249 4.9 0.4 1.0
C A:ARG265 4.9 0.3 1.0
NE A:ARG249 4.9 0.6 1.0

Zinc binding site 2 out of 3 in 3oxl

Go back to Zinc Binding Sites List in 3oxl
Zinc binding site 2 out of 3 in the Human Lysine Methyltransferase SMYD3 in Complex with Adohcy (Form II)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Human Lysine Methyltransferase SMYD3 in Complex with Adohcy (Form II) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn430

b:0.4
occ:1.00
SG A:CYS49 1.8 0.9 1.0
SG A:CYS75 2.4 0.9 1.0
CB A:CYS71 2.5 0.3 1.0
SG A:CYS52 2.7 0.3 1.0
CB A:CYS75 3.0 0.2 1.0
CB A:CYS49 3.3 0.9 1.0
N A:CYS52 3.3 0.4 1.0
SG A:CYS71 3.4 0.5 1.0
CB A:CYS52 3.5 0.6 1.0
CA A:CYS71 3.7 0.4 1.0
N A:CYS71 3.7 0.7 1.0
CA A:CYS52 4.0 0.5 1.0
CB A:ARG51 4.1 0.3 1.0
N A:ARG51 4.1 0.0 1.0
C A:ARG51 4.3 0.3 1.0
CA A:ARG51 4.4 0.3 1.0
CA A:CYS75 4.4 0.2 1.0
CA A:CYS49 4.5 0.8 1.0
N A:LEU53 4.7 0.5 1.0
C A:CYS71 4.7 0.2 1.0
C A:CYS52 4.7 0.5 1.0
N A:SER72 4.8 0.1 1.0
N A:ASP50 4.8 0.8 1.0
C A:CYS49 4.8 0.8 1.0
C A:TYR70 4.9 0.9 1.0

Zinc binding site 3 out of 3 in 3oxl

Go back to Zinc Binding Sites List in 3oxl
Zinc binding site 3 out of 3 in the Human Lysine Methyltransferase SMYD3 in Complex with Adohcy (Form II)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Human Lysine Methyltransferase SMYD3 in Complex with Adohcy (Form II) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn431

b:0.4
occ:1.00
SG A:CYS62 1.7 0.3 1.0
SG A:CYS87 2.2 0.7 1.0
NE2 A:HIS83 2.3 0.8 1.0
CB A:CYS62 3.1 0.8 1.0
CD2 A:HIS83 3.3 0.6 1.0
CE1 A:HIS83 3.3 0.3 1.0
SG A:CYS65 3.4 0.9 1.0
N A:CYS65 3.5 0.4 1.0
CB A:CYS65 3.5 0.9 1.0
CB A:CYS87 3.5 0.7 1.0
N A:GLN64 3.8 0.5 1.0
CA A:CYS62 4.0 0.6 1.0
CA A:CYS65 4.0 0.0 1.0
N A:SER63 4.0 0.7 1.0
C A:CYS62 4.2 0.2 1.0
CA A:CYS87 4.3 0.5 1.0
C A:GLN64 4.3 0.8 1.0
ND1 A:HIS83 4.4 0.2 1.0
CG A:HIS83 4.4 0.6 1.0
CA A:GLN64 4.5 0.2 1.0
N A:ARG66 4.7 0.7 1.0
CB A:GLN64 4.8 0.2 1.0
C A:SER63 4.8 0.9 1.0
CA A:SER63 4.8 0.2 1.0
O A:CYS62 4.8 0.1 1.0
C A:CYS65 4.9 0.9 1.0
CB A:SER63 5.0 0.1 1.0

Reference:

S.Xu, J.Wu, B.Sun, C.Zhong, J.Ding. Structural and Biochemical Studies of Human Lysine Methyltransferase SMYD3 Reveal the Important Functional Roles of Its Post-Set and Tpr Domains and the Regulation of Its Activity By Dna Binding Nucleic Acids Res. V. 39 4438 2011.
ISSN: ISSN 0305-1048
PubMed: 21266482
DOI: 10.1093/NAR/GKR019
Page generated: Sat Oct 26 11:10:41 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