Zinc in PDB 8q5p: Structure of the Lysine Methyltransferase SETD2 in Complex with A Peptide Derived From Human Tyrosine Kinase ACK1

Enzymatic activity of Structure of the Lysine Methyltransferase SETD2 in Complex with A Peptide Derived From Human Tyrosine Kinase ACK1

All present enzymatic activity of Structure of the Lysine Methyltransferase SETD2 in Complex with A Peptide Derived From Human Tyrosine Kinase ACK1:
2.1.1.43; 2.7.10.2; 2.7.11.1;

Protein crystallography data

The structure of Structure of the Lysine Methyltransferase SETD2 in Complex with A Peptide Derived From Human Tyrosine Kinase ACK1, PDB code: 8q5p was solved by A.Mechaly, L.Le Coadou, J.M.Dupret, A.Haouz, F.Rodrigues Lima, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.56 / 1.81
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 60.94, 76.33, 77.41, 90, 90, 90
R / Rfree (%) 21.6 / 24.6

Zinc Binding Sites:

The binding sites of Zinc atom in the Structure of the Lysine Methyltransferase SETD2 in Complex with A Peptide Derived From Human Tyrosine Kinase ACK1 (pdb code 8q5p). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Structure of the Lysine Methyltransferase SETD2 in Complex with A Peptide Derived From Human Tyrosine Kinase ACK1, PDB code: 8q5p:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in 8q5p

Go back to Zinc Binding Sites List in 8q5p
Zinc binding site 1 out of 3 in the Structure of the Lysine Methyltransferase SETD2 in Complex with A Peptide Derived From Human Tyrosine Kinase ACK1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of the Lysine Methyltransferase SETD2 in Complex with A Peptide Derived From Human Tyrosine Kinase ACK1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1801

b:47.3
occ:1.00
 SG A:CYS1499 2.2 51.9 1.0
SG A:CYS1520 2.4 52.0 1.0
SG A:CYS1516 2.4 50.7 1.0
SG A:CYS1501 2.5 59.2 1.0
CB A:CYS1499 3.2 57.1 1.0
CB A:CYS1520 3.2 56.1 1.0
CB A:CYS1516 3.3 56.0 1.0
CB A:CYS1501 3.3 58.7 1.0
ZN A:ZN1802 3.8 40.4 1.0
CA A:CYS1516 3.8 58.0 1.0
CA A:CYS1520 4.0 57.7 1.0
O A:HOH2010 4.0 56.8 1.0
SG A:CYS1529 4.2 38.8 1.0
N A:CYS1501 4.3 58.2 1.0
CA A:CYS1501 4.4 58.7 1.0
CA A:CYS1499 4.6 58.2 1.0
N A:LEU1521 4.6 56.2 1.0
C A:CYS1520 4.7 57.3 1.0
N A:CYS1516 4.8 59.2 1.0
SG A:CYS1533 4.9 42.9 1.0
O A:HOH2006 4.9 45.7 1.0
C A:CYS1516 4.9 58.8 1.0
C A:CYS1499 5.0 58.1 1.0
N A:GLU1500 5.0 57.6 1.0

Zinc binding site 2 out of 3 in 8q5p

Go back to Zinc Binding Sites List in 8q5p
Zinc binding site 2 out of 3 in the Structure of the Lysine Methyltransferase SETD2 in Complex with A Peptide Derived From Human Tyrosine Kinase ACK1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of the Lysine Methyltransferase SETD2 in Complex with A Peptide Derived From Human Tyrosine Kinase ACK1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1802

b:40.4
occ:1.00
 SG A:CYS1533 2.3 42.9 1.0
SG A:CYS1539 2.4 38.5 1.0
SG A:CYS1516 2.4 50.7 1.0
SG A:CYS1529 2.4 38.8 1.0
CB A:CYS1529 3.1 36.2 1.0
CB A:CYS1516 3.3 56.0 1.0
CB A:CYS1539 3.3 39.7 1.0
CB A:CYS1533 3.4 40.7 1.0
ZN A:ZN1801 3.8 47.3 1.0
O A:HOH2006 4.1 45.7 1.0
SG A:CYS1499 4.2 51.9 1.0
CA A:CYS1539 4.3 41.0 1.0
CB A:ASN1541 4.4 37.0 1.0
CA A:CYS1529 4.6 35.4 1.0
CA A:CYS1533 4.7 42.0 1.0
CA A:CYS1516 4.7 58.0 1.0
SG A:CYS1520 4.8 52.0 1.0
CB A:ASN1535 4.9 49.1 1.0
ND2 A:ASN1535 4.9 51.8 1.0
ND2 A:ASN1541 5.0 38.4 1.0

Zinc binding site 3 out of 3 in 8q5p

Go back to Zinc Binding Sites List in 8q5p
Zinc binding site 3 out of 3 in the Structure of the Lysine Methyltransferase SETD2 in Complex with A Peptide Derived From Human Tyrosine Kinase ACK1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of the Lysine Methyltransferase SETD2 in Complex with A Peptide Derived From Human Tyrosine Kinase ACK1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1803

b:36.0
occ:1.00
 SG A:CYS1678 2.3 33.9 1.0
SG A:CYS1685 2.3 40.4 1.0
SG A:CYS1680 2.4 37.5 1.0
SG A:CYS1631 2.4 38.4 1.0
CB A:CYS1685 3.2 43.9 1.0
CB A:CYS1678 3.3 34.3 1.0
CB A:CYS1680 3.4 36.5 1.0
CB A:CYS1631 3.5 37.7 1.0
CA A:CYS1685 3.7 45.3 1.0
N A:CYS1631 4.0 35.7 1.0
N A:CYS1680 4.0 35.0 1.0
N A:ARG1686 4.0 44.4 1.0
CA A:CYS1680 4.2 36.5 1.0
O A:HOH1993 4.3 41.6 1.0
C A:CYS1685 4.3 45.2 1.0
CA A:CYS1631 4.3 37.6 1.0
NE2 A:HIS1629 4.5 33.4 1.0
CD2 A:HIS1629 4.5 32.6 1.0
CA A:CYS1678 4.5 34.3 1.0
C A:CYS1678 4.6 34.9 1.0
N A:GLY1687 4.7 41.8 1.0
O A:CYS1678 4.7 35.1 1.0
N A:CYS1685 4.9 46.4 1.0
N A:GLY1681 4.9 41.2 1.0
OG A:SER1682 4.9 54.8 1.0
C A:CYS1680 5.0 39.4 1.0
C A:SER1630 5.0 34.5 1.0

Reference:

L.Le Coadou, J.Berthelet, A.E.Mechaly, C.Michail, L.C.Bui, J.Dairou, A.Haouz, J.M.Dupret, F.Rodrigues Lima. Structural and Enzymatic Evidence For the Methylation of the ACK1 Tyrosine Kinase By the Histone Lysine Methyltransferase SETD2. Biochem.Biophys.Res.Commun. V. 695 49400 2024.
ISSN: ESSN 1090-2104
PubMed: 38160530
DOI: 10.1016/J.BBRC.2023.149400
Page generated: Thu Oct 31 09:57:08 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