Zinc in PDB 2q8c: Crystal Structure of JMJD2A in Ternary Complex with An Histone H3K9ME3 Peptide and 2-Oxoglutarate

The structure of Crystal Structure of JMJD2A in Ternary Complex with An Histone H3K9ME3 Peptide and 2-Oxoglutarate, PDB code: 2q8c was solved by J.-F.Couture, E.Collazo, P.Ortiz-Tello, J.S.Brunzelle, R.C.Trievel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	28.90 / 2.05
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	100.887, 149.121, 57.056, 90.00, 90.00, 90.00
R / Rfree (%)	20.1 / 23.6

The structure of Crystal Structure of JMJD2A in Ternary Complex with An Histone H3K9ME3 Peptide and 2-Oxoglutarate also contains other interesting chemical elements:

Nickel

(Ni)

2 atoms

The binding sites of Zinc atom in the Crystal Structure of JMJD2A in Ternary Complex with An Histone H3K9ME3 Peptide and 2-Oxoglutarate (pdb code 2q8c). 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 JMJD2A in Ternary Complex with An Histone H3K9ME3 Peptide and 2-Oxoglutarate, PDB code: 2q8c:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of JMJD2A in Ternary Complex with An Histone H3K9ME3 Peptide and 2-Oxoglutarate


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 JMJD2A in Ternary Complex with An Histone H3K9ME3 Peptide and 2-Oxoglutarate within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn505 b:12.9 occ:1.00 SG A:CYS306 1.8 53.5 1.0 NE2 A:HIS240 2.1 45.5 1.0 SG A:CYS234 2.2 50.2 1.0 SG A:CYS308 2.5 57.5 1.0 CE1 A:HIS240 3.0 44.2 1.0 CD2 A:HIS240 3.1 43.8 1.0 CB A:CYS234 3.2 50.9 1.0 CB A:CYS306 3.3 52.7 1.0 CB A:CYS308 3.8 59.6 1.0 N A:CYS308 3.8 58.8 1.0 CA A:CYS306 3.9 52.7 1.0 N A:SER307 3.9 55.7 1.0 ND1 A:HIS240 4.1 42.8 1.0 C A:CYS306 4.2 54.2 1.0 CG A:HIS240 4.2 41.2 1.0 CA A:CYS308 4.3 59.8 1.0 O A:HOH594 4.4 49.3 1.0 CG A:ARG309 4.5 64.3 1.0 N A:ARG309 4.5 62.0 1.0 CA A:CYS234 4.5 50.5 1.0 C A:CYS308 4.6 61.1 1.0 CD A:ARG309 4.8 65.1 1.0 C A:SER307 4.8 57.9 1.0 O A:ALA236 4.8 41.1 1.0 CA A:PHE237 4.9 39.9 1.0 CA A:SER307 4.9 57.2 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of JMJD2A in Ternary Complex with An Histone H3K9ME3 Peptide and 2-Oxoglutarate


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 JMJD2A in Ternary Complex with An Histone H3K9ME3 Peptide and 2-Oxoglutarate within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn506 b:12.8 occ:1.00 SG B:CYS306 1.8 52.9 1.0 NE2 B:HIS240 2.0 44.4 1.0 SG B:CYS234 2.2 51.5 1.0 SG B:CYS308 2.3 58.0 1.0 CE1 B:HIS240 2.9 44.5 1.0 CD2 B:HIS240 3.1 42.9 1.0 CB B:CYS234 3.2 52.7 1.0 CB B:CYS306 3.3 52.9 1.0 N B:CYS308 3.7 57.4 1.0 CB B:CYS308 3.7 58.3 1.0 N B:SER307 3.9 54.8 1.0 CA B:CYS306 4.0 52.7 1.0 ND1 B:HIS240 4.0 45.0 1.0 CA B:CYS308 4.1 58.3 1.0 CG B:HIS240 4.2 41.9 1.0 C B:CYS306 4.3 53.7 1.0 N B:ARG309 4.4 59.9 1.0 CA B:CYS234 4.5 52.5 1.0 C B:CYS308 4.6 59.0 1.0 O B:ALA236 4.7 42.7 1.0 C B:SER307 4.8 56.5 1.0 CG B:ARG309 4.8 60.0 0.5 CE B:MET312 4.8 64.1 1.0 CA B:SER307 4.9 55.8 1.0 CA B:PHE237 5.0 41.8 1.0

J.F.Couture, E.Collazo, P.A.Ortiz-Tello, J.S.Brunzelle, R.C.Trievel. Specificity and Mechanism of JMJD2A, A Trimethyllysine-Specific Histone Demethylase. Nat.Struct.Mol.Biol. V. 14 689 2007.
ISSN: ISSN 1545-9993
PubMed: 17589523
DOI: 10.1038/NSMB1273