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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

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