Zinc in PDB 6j9j: Crystal Structure of SESTD2 in Complex with H3.3S31PHK36M Peptide

All present enzymatic activity of Crystal Structure of SESTD2 in Complex with H3.3S31PHK36M Peptide:
2.1.1.43;

The structure of Crystal Structure of SESTD2 in Complex with H3.3S31PHK36M Peptide, PDB code: 6j9j was solved by S.Yang, H.T.Li, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.01 / 1.78
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	61.112, 77.014, 77.412, 90.00, 90.00, 90.00
R / Rfree (%)	18.9 / 20.6

The binding sites of Zinc atom in the Crystal Structure of SESTD2 in Complex with H3.3S31PHK36M Peptide (pdb code 6j9j). 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 SESTD2 in Complex with H3.3S31PHK36M Peptide, PDB code: 6j9j:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Crystal Structure of SESTD2 in Complex with H3.3S31PHK36M 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 SESTD2 in Complex with H3.3S31PHK36M Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1801 b:27.8 occ:1.00 SG A:CYS1499 2.3 29.1 1.0 SG A:CYS1520 2.4 25.6 1.0 SG A:CYS1501 2.4 30.0 1.0 SG A:CYS1516 2.5 25.3 1.0 CB A:CYS1499 3.2 31.4 1.0 CB A:CYS1501 3.3 34.1 1.0 CB A:CYS1520 3.3 26.5 1.0 CB A:CYS1516 3.3 22.9 1.0 CA A:CYS1516 3.8 26.0 1.0 ZN A:ZN1802 3.8 24.8 1.0 CA A:CYS1520 4.0 28.8 1.0 N A:CYS1501 4.2 34.4 1.0 SG A:CYS1529 4.3 24.1 1.0 CA A:CYS1501 4.4 32.8 1.0 CA A:CYS1499 4.6 33.4 1.0 N A:CYS1516 4.7 24.7 1.0 N A:LEU1521 4.7 30.7 1.0 C A:CYS1520 4.7 29.5 1.0 SG A:CYS1533 4.8 25.5 1.0 C A:CYS1516 4.9 28.0 1.0 N A:GLU1500 4.9 35.7 1.0

Zinc binding site 2 out of 3 in the Crystal Structure of SESTD2 in Complex with H3.3S31PHK36M 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 SESTD2 in Complex with H3.3S31PHK36M Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1802 b:24.8 occ:1.00 SG A:CYS1533 2.3 25.5 1.0 SG A:CYS1539 2.3 21.9 1.0 SG A:CYS1516 2.4 25.3 1.0 SG A:CYS1529 2.5 24.1 1.0 CB A:CYS1529 3.2 19.4 1.0 CB A:CYS1539 3.3 23.4 1.0 CB A:CYS1516 3.3 22.9 1.0 CB A:CYS1533 3.4 26.5 1.0 ZN A:ZN1801 3.8 27.8 1.0 O A:HOH1991 4.2 27.6 1.0 CA A:CYS1539 4.2 23.8 1.0 SG A:CYS1499 4.3 29.1 1.0 CB A:ASN1541 4.5 21.3 1.0 CA A:CYS1529 4.7 21.8 1.0 CA A:CYS1533 4.7 27.0 1.0 CA A:CYS1516 4.7 26.0 1.0 SG A:CYS1520 4.8 25.6 1.0 CB A:ASN1535 4.9 26.2 1.0

Zinc binding site 3 out of 3 in the Crystal Structure of SESTD2 in Complex with H3.3S31PHK36M 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 SESTD2 in Complex with H3.3S31PHK36M Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1803 b:22.7 occ:1.00 SG A:CYS1685 2.3 23.8 1.0 SG A:CYS1678 2.3 20.0 1.0 SG A:CYS1680 2.3 24.0 1.0 SG A:CYS1631 2.5 23.5 1.0 CB A:CYS1685 3.3 30.1 1.0 CB A:CYS1678 3.3 21.2 1.0 CB A:CYS1680 3.4 22.6 1.0 CB A:CYS1631 3.4 22.1 1.0 CA A:CYS1685 3.7 27.8 1.0 N A:CYS1631 4.0 21.8 1.0 N A:CYS1680 4.0 19.2 1.0 N A:ARG1686 4.0 24.9 1.0 CA A:CYS1680 4.3 24.5 1.0 O A:HOH1982 4.3 24.9 1.0 CA A:CYS1631 4.4 22.3 1.0 C A:CYS1685 4.4 29.4 1.0 NE2 A:HIS1629 4.4 19.1 1.0 CD2 A:HIS1629 4.5 17.7 1.0 CA A:CYS1678 4.6 22.6 1.0 C A:CYS1678 4.6 22.1 1.0 N A:GLY1687 4.7 23.2 1.0 O A:CYS1678 4.7 23.1 1.0 N A:GLY1681 4.8 28.4 1.0 C A:CYS1680 4.9 23.8 1.0 N A:CYS1685 5.0 34.2 1.0 C A:SER1630 5.0 18.5 1.0

S.Yang, H.Li. Phosphorylation of the Ancestral Histone Variant H3.3 Amplifies Stimulation-Induced Transcription To Be Published.