Zinc in PDB 6vdb: SETD2 in Complex with A H3-Variant Peptide

The structure of SETD2 in Complex with A H3-Variant Peptide, PDB code: 6vdb was solved by S.Beldar, W.Tempel, C.H.Arrowsmith, C.Bountra, A.M.Edwards, A.Jeltsch, J.Min, Structural Genomics Consortium, Structural Genomics Consortium(Sgc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.65 / 2.30
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	60.370, 76.520, 77.610, 90.00, 90.00, 90.00
R / Rfree (%)	21.2 / 26.3

The binding sites of Zinc atom in the SETD2 in Complex with A H3-Variant Peptide (pdb code 6vdb). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the SETD2 in Complex with A H3-Variant Peptide, PDB code: 6vdb:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the SETD2 in Complex with A H3-Variant Peptide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of SETD2 in Complex with A H3-Variant Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1921 b:47.1 occ:1.00 SG A:CYS1499 2.3 49.3 1.0 SG A:CYS1520 2.4 43.8 1.0 SG A:CYS1516 2.5 41.5 1.0 SG A:CYS1501 2.5 45.1 1.0 CB A:CYS1501 3.2 42.8 1.0 CB A:CYS1499 3.2 46.3 1.0 CB A:CYS1516 3.2 38.1 1.0 CB A:CYS1520 3.4 40.1 1.0 CA A:CYS1516 3.7 38.2 1.0 ZN A:ZN1922 3.8 43.9 1.0 CA A:CYS1520 4.0 41.1 1.0 N A:CYS1501 4.2 45.4 1.0 SG A:CYS1529 4.3 41.1 1.0 CA A:CYS1501 4.3 44.3 1.0 N A:CYS1516 4.6 39.0 1.0 CA A:CYS1499 4.6 47.0 1.0 N A:LEU1521 4.7 41.8 1.0 C A:CYS1520 4.8 45.1 1.0 SG A:CYS1533 4.8 42.6 1.0 N A:GLU1500 4.8 47.4 1.0 C A:CYS1516 4.8 40.6 1.0 ND2 A:ASN1535 5.0 52.2 1.0

Zinc binding site 2 out of 3 in the SETD2 in Complex with A H3-Variant Peptide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of SETD2 in Complex with A H3-Variant Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1922 b:43.9 occ:1.00 SG A:CYS1539 2.2 40.4 1.0 SG A:CYS1516 2.3 41.5 1.0 SG A:CYS1533 2.4 42.6 1.0 SG A:CYS1529 2.5 41.1 1.0 CB A:CYS1529 3.1 37.2 1.0 CB A:CYS1516 3.2 38.1 1.0 CB A:CYS1539 3.3 37.4 1.0 CB A:CYS1533 3.5 39.3 1.0 ZN A:ZN1921 3.8 47.1 1.0 SG A:CYS1499 4.2 49.3 1.0 CA A:CYS1539 4.3 36.5 1.0 CB A:ASN1541 4.4 29.8 1.0 CA A:CYS1529 4.6 36.9 1.0 CA A:CYS1516 4.6 38.2 1.0 SG A:CYS1520 4.7 43.8 1.0 CA A:CYS1533 4.8 40.4 1.0 CB A:ASN1535 4.9 43.3 1.0

Zinc binding site 3 out of 3 in the SETD2 in Complex with A H3-Variant Peptide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of SETD2 in Complex with A H3-Variant Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1923 b:47.0 occ:1.00 SG A:CYS1680 2.2 43.8 1.0 SG A:CYS1631 2.4 41.4 1.0 SG A:CYS1678 2.4 41.3 1.0 SG A:CYS1685 2.4 50.3 1.0 CB A:CYS1685 3.3 46.6 1.0 CB A:CYS1678 3.5 37.1 1.0 CB A:CYS1631 3.5 39.0 1.0 CB A:CYS1680 3.5 40.0 1.0 CA A:CYS1685 3.6 46.6 1.0 N A:ARG1686 4.0 45.5 1.0 N A:CYS1631 4.0 40.6 1.0 C A:CYS1685 4.2 49.5 1.0 N A:CYS1680 4.3 37.3 1.0 NE2 A:HIS1629 4.3 40.4 1.0 CA A:CYS1631 4.3 40.2 1.0 CD2 A:HIS1629 4.4 40.6 1.0 CA A:CYS1680 4.4 39.8 1.0 C A:CYS1678 4.6 41.6 1.0 CA A:CYS1678 4.6 37.0 1.0 O A:CYS1678 4.7 42.0 1.0 N A:GLY1687 4.8 39.3 1.0 N A:CYS1685 4.9 48.0 1.0 N A:GLY1681 4.9 50.3 1.0 C A:SER1630 4.9 41.3 1.0

S.Beldar, W.Tempel, C.H.Arrowsmith, C.Bountra, A.M.Edwards, A.Jeltsch, J.Min, Structural Genomics Consortium. SETD2 in Complex with A H3-Variant Peptide To Be Published.