Zinc in PDB 3u4s: Histone Lysine Demethylase JMJD2A in Complex with T11C Peptide Substrate Crosslinked to N-Oxalyl-D-Cysteine

The structure of Histone Lysine Demethylase JMJD2A in Complex with T11C Peptide Substrate Crosslinked to N-Oxalyl-D-Cysteine, PDB code: 3u4s was solved by J.Ma, M.A.Mcdonough, C.J.Schofield, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	37.28 / 2.15
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	99.819, 150.060, 55.917, 90.00, 90.00, 90.00
R / Rfree (%)	18.1 / 22.2

The structure of Histone Lysine Demethylase JMJD2A in Complex with T11C Peptide Substrate Crosslinked to N-Oxalyl-D-Cysteine also contains other interesting chemical elements:

Nickel

(Ni)

2 atoms

The binding sites of Zinc atom in the Histone Lysine Demethylase JMJD2A in Complex with T11C Peptide Substrate Crosslinked to N-Oxalyl-D-Cysteine (pdb code 3u4s). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Histone Lysine Demethylase JMJD2A in Complex with T11C Peptide Substrate Crosslinked to N-Oxalyl-D-Cysteine, PDB code: 3u4s:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Histone Lysine Demethylase JMJD2A in Complex with T11C Peptide Substrate Crosslinked to N-Oxalyl-D-Cysteine


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Histone Lysine Demethylase JMJD2A in Complex with T11C Peptide Substrate Crosslinked to N-Oxalyl-D-Cysteine within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn502 b:32.6 occ:1.00 NE2 A:HIS240 2.1 29.4 1.0 SG A:CYS306 2.3 31.9 1.0 SG A:CYS234 2.3 33.4 1.0 SG A:CYS308 2.3 35.8 1.0 CE1 A:HIS240 3.0 29.6 1.0 CB A:CYS234 3.1 45.2 1.0 CD2 A:HIS240 3.1 28.6 1.0 CB A:CYS306 3.4 37.2 1.0 N A:CYS308 3.6 50.5 1.0 CB A:CYS308 3.6 48.5 1.0 CA A:CYS306 4.0 39.2 1.0 CA A:CYS308 4.1 48.7 1.0 N A:SER307 4.1 51.2 1.0 ND1 A:HIS240 4.1 27.9 1.0 CG A:HIS240 4.2 25.3 1.0 C A:CYS306 4.3 43.3 1.0 N A:ARG309 4.4 46.3 1.0 CG A:ARG309 4.5 48.1 1.0 CA A:CYS234 4.6 44.4 1.0 O A:HOH787 4.6 39.8 1.0 C A:CYS308 4.6 46.1 1.0 O A:HOH726 4.6 34.3 1.0 C A:SER307 4.7 54.8 1.0 CA A:PHE237 4.7 28.5 1.0 O A:ALA236 4.8 26.7 1.0 OG A:SER307 4.9 50.3 1.0 N A:PHE237 4.9 30.3 1.0 CA A:SER307 4.9 56.5 1.0 C A:ALA236 4.9 27.6 1.0

Zinc binding site 2 out of 2 in the Histone Lysine Demethylase JMJD2A in Complex with T11C Peptide Substrate Crosslinked to N-Oxalyl-D-Cysteine


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Histone Lysine Demethylase JMJD2A in Complex with T11C Peptide Substrate Crosslinked to N-Oxalyl-D-Cysteine within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn502 b:42.1 occ:1.00 NE2 B:HIS240 2.1 40.9 1.0 SG B:CYS306 2.2 42.9 1.0 SG B:CYS308 2.4 51.0 1.0 SG B:CYS234 2.4 49.5 1.0 CE1 B:HIS240 3.0 36.5 1.0 CD2 B:HIS240 3.1 39.0 1.0 CB B:CYS234 3.2 56.2 1.0 CB B:CYS306 3.5 51.8 1.0 CB B:CYS308 3.6 65.0 1.0 N B:CYS308 3.7 67.9 1.0 N B:SER307 4.1 61.4 1.0 ND1 B:HIS240 4.1 36.5 1.0 CA B:CYS306 4.2 52.9 1.0 CA B:CYS308 4.2 66.0 1.0 CG B:HIS240 4.2 35.1 1.0 C B:CYS306 4.5 55.5 1.0 O B:HOH776 4.5 46.0 1.0 N B:ARG309 4.5 64.8 1.0 C B:SER307 4.6 70.2 1.0 O B:HOH747 4.6 36.4 1.0 CA B:CYS234 4.7 55.6 1.0 C B:CYS308 4.7 65.6 1.0 CA B:PHE237 4.7 37.8 1.0 O B:HOH770 4.7 43.0 1.0 CG B:ARG309 4.8 65.5 1.0 OG B:SER307 4.9 67.4 1.0 N B:PHE237 4.9 37.5 1.0 CA B:SER307 4.9 68.0 1.0 O B:ALA236 5.0 32.7 1.0 CD B:ARG309 5.0 65.9 1.0 C B:ALA236 5.0 36.4 1.0

E.C.Woon, A.Tumber, A.Kawamura, L.Hillringhaus, W.Ge, N.R.Rose, J.H.Ma, M.C.Chan, L.J.Walport, K.H.Che, S.S.Ng, B.D.Marsden, U.Oppermann, M.A.Mcdonough, C.J.Schofield. Linking of 2-Oxoglutarate and Substrate Binding Sites Enables Potent and Highly Selective Inhibition of Jmjc Histone Demethylases. Angew.Chem.Int.Ed.Engl. V. 51 1631 2012.
ISSN: ISSN 1433-7851
PubMed: 22241642
DOI: 10.1002/ANIE.201107833