Zinc in PDB 4fmu: Crystal Structure of Methyltransferase Domain of Human Set Domain- Containing Protein 2 Compound: Pr-Snf

All present enzymatic activity of Crystal Structure of Methyltransferase Domain of Human Set Domain- Containing Protein 2 Compound: Pr-Snf:
2.1.1.43;

The structure of Crystal Structure of Methyltransferase Domain of Human Set Domain- Containing Protein 2 Compound: Pr-Snf, PDB code: 4fmu was solved by A.Dong, H.Zeng, G.Ibanez, W.Zheng, W.Tempel, C.Bountra, C.H.Arrowsmith, A.M.Edwards, P.J.Brown, J.Min, M.Luo, H.Wu, Structural Genomicsconsortium (Sgc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	35.12 / 2.10
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	51.547, 77.277, 78.864, 90.00, 90.00, 90.00
R / Rfree (%)	19.4 / 23.5

The binding sites of Zinc atom in the Crystal Structure of Methyltransferase Domain of Human Set Domain- Containing Protein 2 Compound: Pr-Snf (pdb code 4fmu). 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 Methyltransferase Domain of Human Set Domain- Containing Protein 2 Compound: Pr-Snf, PDB code: 4fmu:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Crystal Structure of Methyltransferase Domain of Human Set Domain- Containing Protein 2 Compound: Pr-Snf


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 Methyltransferase Domain of Human Set Domain- Containing Protein 2 Compound: Pr-Snf within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1801 b:45.7 occ:1.00 SG A:CYS1499 2.2 44.8 1.0 SG A:CYS1501 2.3 47.7 1.0 SG A:CYS1516 2.4 41.4 1.0 SG A:CYS1520 2.5 41.7 1.0 CB A:CYS1499 3.2 42.8 1.0 CB A:CYS1501 3.2 45.4 1.0 CB A:CYS1520 3.3 38.8 1.0 CB A:CYS1516 3.3 38.0 1.0 ZN A:ZN1802 3.7 40.2 1.0 CA A:CYS1516 3.8 39.0 1.0 CA A:CYS1520 4.0 39.9 1.0 O A:HOH1926 4.1 45.3 1.0 SG A:CYS1529 4.2 37.9 1.0 N A:CYS1501 4.2 48.1 1.0 CA A:CYS1501 4.3 46.9 1.0 CA A:CYS1499 4.6 44.7 1.0 N A:CYS1516 4.7 39.7 1.0 C A:CYS1520 4.8 45.6 1.0 SG A:CYS1533 4.8 39.9 1.0 N A:LEU1521 4.8 45.2 1.0 C A:CYS1516 4.9 45.4 1.0 N A:GLU1500 4.9 47.4 1.0 ND2 A:ASN1535 5.0 40.2 1.0 C A:CYS1499 5.0 50.3 1.0

Zinc binding site 2 out of 3 in the Crystal Structure of Methyltransferase Domain of Human Set Domain- Containing Protein 2 Compound: Pr-Snf


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 Methyltransferase Domain of Human Set Domain- Containing Protein 2 Compound: Pr-Snf within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1802 b:40.2 occ:1.00 SG A:CYS1516 2.3 41.4 1.0 SG A:CYS1533 2.3 39.9 1.0 SG A:CYS1539 2.3 38.4 1.0 SG A:CYS1529 2.4 37.9 1.0 CB A:CYS1529 3.1 34.0 1.0 CB A:CYS1516 3.3 38.0 1.0 CB A:CYS1539 3.3 34.4 1.0 CB A:CYS1533 3.4 36.5 1.0 ZN A:ZN1801 3.7 45.7 1.0 SG A:CYS1499 4.2 44.8 1.0 O A:HOH1906 4.2 38.6 1.0 CA A:CYS1539 4.3 34.6 1.0 CB A:ASN1541 4.4 30.8 1.0 CA A:CYS1529 4.6 34.4 1.0 CA A:CYS1533 4.6 37.5 1.0 CA A:CYS1516 4.7 39.0 1.0 SG A:CYS1520 4.8 41.7 1.0 CB A:ASN1535 4.9 46.0 1.0

Zinc binding site 3 out of 3 in the Crystal Structure of Methyltransferase Domain of Human Set Domain- Containing Protein 2 Compound: Pr-Snf


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 Methyltransferase Domain of Human Set Domain- Containing Protein 2 Compound: Pr-Snf within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1803 b:44.3 occ:1.00 SG A:CYS1680 2.2 40.1 1.0 SG A:CYS1678 2.3 43.3 1.0 SG A:CYS1631 2.4 45.9 1.0 SG A:CYS1685 2.5 51.4 1.0 CB A:CYS1680 3.3 37.5 1.0 CB A:CYS1685 3.4 47.9 1.0 CB A:CYS1631 3.4 42.1 1.0 CB A:CYS1678 3.5 40.0 1.0 CA A:CYS1685 3.7 48.6 1.0 N A:CYS1631 4.0 42.4 1.0 N A:CYS1680 4.0 36.6 1.0 N A:ARG1686 4.1 49.3 1.0 CA A:CYS1680 4.2 37.9 1.0 O A:HOH1955 4.2 47.5 1.0 CA A:CYS1631 4.3 42.1 1.0 C A:CYS1685 4.4 54.0 1.0 CD2 A:HIS1629 4.5 44.8 1.0 NE2 A:HIS1629 4.6 44.9 1.0 C A:CYS1678 4.6 42.9 1.0 N A:GLY1687 4.6 44.1 1.0 O A:CYS1678 4.6 42.7 1.0 CA A:CYS1678 4.6 39.2 1.0 N A:GLY1681 4.9 47.0 1.0 C A:CYS1680 4.9 45.6 1.0 C A:SER1630 4.9 43.6 1.0

W.Zheng, G.Ibanez, H.Wu, G.Blum, H.Zeng, A.Dong, F.Li, T.Hajian, A.Allali-Hassani, M.F.Amaya, A.Siarheyeva, W.Yu, P.J.Brown, M.Schapira, M.Vedadi, J.Min, M.Luo. Sinefungin Derivatives As Inhibitors and Structure Probes of Protein Lysine Methyltransferase SETD2. J.Am.Chem.Soc. V. 134 18004 2012.
ISSN: ISSN 0002-7863
PubMed: 23043551
DOI: 10.1021/JA307060P