Zinc in PDB 5jlb: Crystal Structure of SETD2 Bound to Histone H3.3 K36I Peptide

All present enzymatic activity of Crystal Structure of SETD2 Bound to Histone H3.3 K36I Peptide:
2.1.1.43;

The structure of Crystal Structure of SETD2 Bound to Histone H3.3 K36I Peptide, PDB code: 5jlb was solved by H.Li, S.Yang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	34.52 / 1.50
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	60.593, 76.844, 77.264, 90.00, 90.00, 90.00
R / Rfree (%)	16.4 / 19

The binding sites of Zinc atom in the Crystal Structure of SETD2 Bound to Histone H3.3 K36I Peptide (pdb code 5jlb). 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 SETD2 Bound to Histone H3.3 K36I Peptide, PDB code: 5jlb:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Crystal Structure of SETD2 Bound to Histone H3.3 K36I Peptide


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 SETD2 Bound to Histone H3.3 K36I Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1807 b:23.8 occ:1.00 SG A:CYS1520 2.3 21.4 1.0 SG A:CYS1499 2.3 27.0 1.0 SG A:CYS1516 2.4 20.5 1.0 SG A:CYS1501 2.4 26.1 1.0 CB A:CYS1499 3.2 27.2 1.0 CB A:CYS1520 3.2 23.9 1.0 CB A:CYS1516 3.2 19.7 1.0 CB A:CYS1501 3.3 27.9 1.0 CA A:CYS1516 3.8 21.8 1.0 ZN A:ZN1808 3.8 19.8 1.0 CA A:CYS1520 4.0 23.2 1.0 O A:HOH2075 4.0 28.5 1.0 SG A:CYS1529 4.2 19.4 1.0 N A:CYS1501 4.2 31.1 1.0 CA A:CYS1501 4.4 30.1 1.0 CA A:CYS1499 4.6 27.5 1.0 N A:CYS1516 4.6 22.1 1.0 C A:CYS1520 4.7 23.3 1.0 N A:LEU1521 4.8 24.7 1.0 SG A:CYS1533 4.8 22.3 1.0 C A:CYS1516 4.9 22.5 1.0 N A:GLU1500 4.9 29.8 1.0 O A:HOH2080 5.0 22.6 1.0

Zinc binding site 2 out of 3 in the Crystal Structure of SETD2 Bound to Histone H3.3 K36I Peptide


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 SETD2 Bound to Histone H3.3 K36I Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1808 b:19.8 occ:1.00 SG A:CYS1533 2.2 22.3 1.0 SG A:CYS1539 2.3 17.9 1.0 SG A:CYS1516 2.4 20.5 1.0 SG A:CYS1529 2.4 19.4 1.0 CB A:CYS1529 3.1 17.0 1.0 CB A:CYS1516 3.3 19.7 1.0 CB A:CYS1539 3.3 17.1 1.0 CB A:CYS1533 3.4 22.6 1.0 ZN A:ZN1807 3.8 23.8 1.0 O A:HOH2080 4.1 22.6 1.0 SG A:CYS1499 4.2 27.0 1.0 CA A:CYS1539 4.3 16.7 1.0 CB A:ASN1541 4.5 18.1 1.0 CA A:CYS1529 4.6 15.5 1.0 CA A:CYS1533 4.6 20.7 1.0 CA A:CYS1516 4.7 21.8 1.0 SG A:CYS1520 4.8 21.4 1.0 CB A:ASN1535 4.9 21.9 1.0

Zinc binding site 3 out of 3 in the Crystal Structure of SETD2 Bound to Histone H3.3 K36I Peptide


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 SETD2 Bound to Histone H3.3 K36I Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1809 b:18.1 occ:1.00 SG A:CYS1685 2.3 20.4 1.0 SG A:CYS1678 2.3 16.7 1.0 SG A:CYS1680 2.4 18.8 1.0 SG A:CYS1631 2.4 18.8 1.0 CB A:CYS1678 3.3 18.9 1.0 CB A:CYS1685 3.3 19.8 1.0 CB A:CYS1680 3.4 17.4 1.0 CB A:CYS1631 3.5 19.1 1.0 CA A:CYS1685 3.7 19.4 1.0 N A:CYS1631 4.0 17.1 1.0 N A:ARG1686 4.1 20.7 1.0 N A:CYS1680 4.1 16.6 1.0 CA A:CYS1680 4.3 18.0 1.0 O A:HOH2007 4.3 21.3 1.0 C A:CYS1685 4.3 22.7 1.0 CA A:CYS1631 4.4 17.7 1.0 NE2 A:HIS1629 4.4 16.4 1.0 CD2 A:HIS1629 4.5 16.4 1.0 CA A:CYS1678 4.6 16.7 1.0 C A:CYS1678 4.6 16.5 1.0 N A:GLY1687 4.7 21.5 1.0 O A:CYS1678 4.7 19.1 1.0 N A:GLY1681 4.9 19.6 1.0 N A:CYS1685 4.9 23.9 1.0 C A:CYS1680 4.9 20.1 1.0 C A:SER1630 5.0 15.4 1.0

S.Yang, X.Zheng, C.Lu, G.M.Li, C.D.Allis, H.Li. Molecular Basis For Oncohistone H3 Recognition By SETD2 Methyltransferase Genes Dev. V. 30 1611 2016.
ISSN: ISSN 0890-9369
PubMed: 27474439
DOI: 10.1101/GAD.284323.116