Zinc in PDB 4nj5: Crystal Structure of SUVH9

All present enzymatic activity of Crystal Structure of SUVH9:
2.1.1.43;

The structure of Crystal Structure of SUVH9, PDB code: 4nj5 was solved by J.Du, D.J.Patel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.68 / 2.40
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	63.679, 84.197, 99.359, 90.00, 90.00, 90.00
R / Rfree (%)	18.7 / 22.3

The binding sites of Zinc atom in the Crystal Structure of SUVH9 (pdb code 4nj5). 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 SUVH9, PDB code: 4nj5:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Crystal Structure of SUVH9


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 SUVH9 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn801 b:32.1 occ:1.00 SG A:CYS446 2.3 23.2 1.0 SG A:CYS434 2.3 25.2 1.0 SG A:CYS472 2.4 23.6 1.0 SG A:CYS476 2.4 24.0 1.0 CB A:CYS472 3.2 21.3 1.0 CB A:CYS476 3.3 29.4 1.0 CB A:CYS446 3.3 22.6 1.0 CB A:CYS434 3.4 25.8 1.0 N A:CYS434 3.7 28.7 1.0 ZN A:ZN802 3.7 28.6 0.9 CA A:CYS472 3.7 23.5 1.0 SG A:CYS440 3.9 25.3 1.0 ZN A:ZN803 4.0 36.2 1.0 CA A:CYS434 4.1 27.9 1.0 SG A:CYS478 4.2 23.3 1.0 CA A:CYS476 4.5 30.1 1.0 N A:CYS472 4.6 26.6 1.0 CA A:CYS446 4.7 23.3 1.0 ND2 A:ASN484 4.8 19.6 1.0 C A:GLY433 4.8 36.2 1.0 C A:CYS434 4.9 29.0 1.0 C A:CYS472 4.9 25.0 1.0 O A:CYS434 5.0 28.1 1.0 N A:CYS446 5.0 24.6 1.0

Zinc binding site 2 out of 3 in the Crystal Structure of SUVH9


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 SUVH9 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn802 b:28.6 occ:0.90 SG A:CYS440 2.3 25.3 1.0 SG A:CYS478 2.3 23.3 1.0 SG A:CYS482 2.4 21.0 1.0 SG A:CYS472 2.4 23.6 1.0 CB A:CYS478 3.2 27.1 1.0 CB A:CYS440 3.5 28.8 1.0 CB A:CYS482 3.5 26.0 1.0 CB A:CYS472 3.5 21.3 1.0 ZN A:ZN801 3.7 32.1 1.0 N A:CYS440 3.9 23.0 1.0 SG A:CYS434 3.9 25.2 1.0 ZN A:ZN803 4.0 36.2 1.0 CB A:ASN484 4.1 19.1 1.0 CA A:CYS440 4.2 26.5 1.0 CA A:CYS478 4.6 32.4 1.0 N A:ASN484 4.8 25.0 1.0 NE A:ARG485 4.8 24.3 1.0 C A:GLY439 4.9 28.4 1.0 CA A:CYS482 4.9 26.6 1.0 CA A:ASN484 4.9 23.1 1.0 CA A:CYS472 4.9 23.5 1.0 CB A:CYS436 4.9 26.1 1.0 ND2 A:ASN484 5.0 19.6 1.0

Zinc binding site 3 out of 3 in the Crystal Structure of SUVH9


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 SUVH9 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn803 b:36.2 occ:1.00 SG A:CYS440 2.3 25.3 1.0 SG A:CYS436 2.3 26.0 1.0 SG A:CYS444 2.4 26.1 1.0 SG A:CYS434 2.6 25.2 1.0 CB A:CYS434 3.1 25.8 1.0 CB A:CYS436 3.3 26.1 1.0 CB A:CYS444 3.3 26.0 1.0 CB A:CYS440 3.4 28.8 1.0 CA A:CYS440 3.7 26.5 1.0 ZN A:ZN802 4.0 28.6 0.9 ZN A:ZN801 4.0 32.1 1.0 N A:CYS436 4.4 32.5 1.0 CA A:CYS436 4.5 32.3 1.0 CB A:CYS446 4.5 22.6 1.0 N A:CYS440 4.5 23.0 1.0 CA A:CYS434 4.6 27.9 1.0 CA A:CYS444 4.8 26.8 1.0 SG A:CYS472 4.8 23.6 1.0 C A:CYS440 4.9 22.8 1.0 SG A:CYS446 4.9 23.2 1.0 N A:ASP435 4.9 30.5 1.0 C A:CYS434 4.9 29.0 1.0 N A:CYS446 5.0 24.6 1.0

L.M.Johnson, J.Du, C.J.Hale, S.Bischof, S.Feng, R.K.Chodavarapu, X.Zhong, G.Marson, M.Pellegrini, D.J.Segal, D.J.Patel, S.E.Jacobsen. Sra- and Set-Domain-Containing Proteins Link Rna Polymerase V Occupancy to Dna Methylation. Nature V. 507 124 2014.
ISSN: ISSN 0028-0836
PubMed: 24463519
DOI: 10.1038/NATURE12931