Zinc in PDB 4c1q: Crystal Structure of the PRDM9 Set Domain in Complex with H3K4ME2 and Adohcy.

All present enzymatic activity of Crystal Structure of the PRDM9 Set Domain in Complex with H3K4ME2 and Adohcy.:
2.1.1.43;

The structure of Crystal Structure of the PRDM9 Set Domain in Complex with H3K4ME2 and Adohcy., PDB code: 4c1q was solved by N.Mathioudakis, S.Cusack, J.Kadlec, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.54 / 2.30
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	55.730, 78.180, 107.610, 90.00, 90.00, 90.00
R / Rfree (%)	20.806 / 25.223

The binding sites of Zinc atom in the Crystal Structure of the PRDM9 Set Domain in Complex with H3K4ME2 and Adohcy. (pdb code 4c1q). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of the PRDM9 Set Domain in Complex with H3K4ME2 and Adohcy., PDB code: 4c1q:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of the PRDM9 Set Domain in Complex with H3K4ME2 and Adohcy.


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 the PRDM9 Set Domain in Complex with H3K4ME2 and Adohcy. within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn493 b:58.3 occ:1.00 SG A:CYS205 2.2 51.8 1.0 SG A:CYS208 2.2 79.9 1.0 SG A:CYS216 2.3 57.9 1.0 ND1 A:HIS219 2.5 80.6 1.0 CB A:CYS208 3.0 65.2 1.0 CB A:CYS205 3.1 52.5 1.0 CE1 A:HIS219 3.3 83.2 1.0 CG A:HIS219 3.3 74.3 1.0 CB A:CYS216 3.4 56.2 1.0 CB A:HIS219 3.7 66.3 1.0 N A:CYS208 3.7 66.6 1.0 CA A:CYS208 4.0 64.8 1.0 N A:HIS219 4.1 65.9 1.0 CB A:ASN218 4.2 70.6 1.0 NE2 A:HIS219 4.3 82.6 1.0 CD2 A:HIS219 4.3 81.8 1.0 ND2 A:ASN218 4.5 75.9 1.0 CA A:HIS219 4.5 62.8 1.0 CA A:CYS205 4.5 51.2 1.0 CB A:LYS207 4.7 72.8 1.0 C A:LYS207 4.7 69.3 1.0 CA A:CYS216 4.8 54.6 1.0 C A:ASN218 4.9 67.0 1.0 C A:CYS205 4.9 53.7 1.0 ND2 A:ASN210 4.9 73.4 1.0 O A:CYS205 4.9 51.2 1.0 CA A:ASN218 4.9 69.2 1.0 CG A:ASN218 5.0 72.7 1.0 N A:ASN218 5.0 66.5 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of the PRDM9 Set Domain in Complex with H3K4ME2 and Adohcy.


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 the PRDM9 Set Domain in Complex with H3K4ME2 and Adohcy. within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn493 b:70.1 occ:1.00 SG B:CYS205 2.2 60.8 1.0 SG B:CYS208 2.3 79.9 1.0 ND1 B:HIS219 2.3 70.7 1.0 SG B:CYS216 2.3 63.2 1.0 CG B:HIS219 3.1 66.0 1.0 CE1 B:HIS219 3.2 70.0 1.0 CB B:CYS205 3.2 62.0 1.0 CB B:CYS208 3.3 73.9 1.0 CB B:CYS216 3.4 58.5 1.0 CB B:HIS219 3.4 62.2 1.0 N B:HIS219 3.9 63.9 1.0 N B:CYS208 3.9 76.0 1.0 CD2 B:HIS219 4.1 68.7 1.0 NE2 B:HIS219 4.1 70.9 1.0 CB B:ASN218 4.2 67.1 1.0 CA B:CYS208 4.2 71.5 1.0 CA B:HIS219 4.3 61.1 1.0 CB B:LYS207 4.6 84.5 1.0 CA B:CYS205 4.6 61.6 1.0 ND2 B:ASN218 4.7 69.5 1.0 C B:ASN218 4.7 62.8 1.0 CA B:CYS216 4.8 58.7 1.0 C B:LYS207 4.8 80.6 1.0 CA B:ASN218 4.9 66.2 1.0 N B:ASN218 4.9 67.8 1.0

H.Wu, N.Mathioudakis, B.Diagouraga, A.Dong, L.Dombrovski, F.Baudat, S.Cusack, B.De Massy, J.Kadlec. Molecular Basis For the Regulation of the H3K4 Methyltransferase Activity of PRDM9. Cell Rep. V. 5 13 2013.
ISSN: ISSN 2211-1247
PubMed: 24095733
DOI: 10.1016/J.CELREP.2013.08.035