Zinc in PDB 2q8e: Specificity and Mechanism of JMJD2A, A Trimethyllysine-Specific Histone Demethylase

The structure of Specificity and Mechanism of JMJD2A, A Trimethyllysine-Specific Histone Demethylase, PDB code: 2q8e 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)	29.97 / 2.05
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	100.294, 148.964, 56.810, 90.00, 90.00, 90.00
R / Rfree (%)	21.3 / 26

The structure of Specificity and Mechanism of JMJD2A, A Trimethyllysine-Specific Histone Demethylase also contains other interesting chemical elements:

Nickel

(Ni)

2 atoms

The binding sites of Zinc atom in the Specificity and Mechanism of JMJD2A, A Trimethyllysine-Specific Histone Demethylase (pdb code 2q8e). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Specificity and Mechanism of JMJD2A, A Trimethyllysine-Specific Histone Demethylase, PDB code: 2q8e:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Specificity and Mechanism of JMJD2A, A Trimethyllysine-Specific Histone Demethylase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Specificity and Mechanism of JMJD2A, A Trimethyllysine-Specific Histone Demethylase within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn505 b:10.7 occ:1.00 SG A:CYS306 1.7 52.2 1.0 NE2 A:HIS240 2.1 46.0 1.0 SG A:CYS234 2.1 53.1 1.0 SG A:CYS308 2.3 54.4 1.0 CE1 A:HIS240 2.9 45.3 1.0 CB A:CYS306 3.1 52.7 1.0 CD2 A:HIS240 3.2 46.5 1.0 CB A:CYS234 3.3 54.1 1.0 CB A:CYS308 3.7 59.2 1.0 CA A:CYS306 3.8 53.1 1.0 N A:CYS308 3.8 59.3 1.0 N A:SER307 3.9 56.4 1.0 C A:CYS306 4.1 54.6 1.0 ND1 A:HIS240 4.1 45.4 1.0 CA A:CYS308 4.2 60.3 1.0 CG A:HIS240 4.2 42.1 1.0 N A:ARG309 4.3 64.3 1.0 CA A:CYS234 4.5 54.2 1.0 C A:CYS308 4.6 62.4 1.0 CG A:ARG309 4.6 66.2 1.0 O A:ALA236 4.8 45.2 1.0 C A:SER307 4.8 59.1 1.0 CD A:ARG309 4.8 67.6 1.0 CA A:SER307 4.9 58.4 1.0 CA A:PHE237 4.9 43.7 1.0 O A:CYS306 4.9 55.4 1.0 C A:ALA236 4.9 45.2 1.0 O A:HOH542 4.9 57.8 1.0

Zinc binding site 2 out of 2 in the Specificity and Mechanism of JMJD2A, A Trimethyllysine-Specific Histone Demethylase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Specificity and Mechanism of JMJD2A, A Trimethyllysine-Specific Histone Demethylase within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn506 b:17.2 occ:1.00 SG B:CYS306 1.6 50.4 1.0 NE2 B:HIS240 2.0 48.0 1.0 SG B:CYS234 2.1 53.5 1.0 SG B:CYS308 2.3 61.3 1.0 CE1 B:HIS240 2.9 46.5 1.0 CD2 B:HIS240 3.1 45.3 1.0 CB B:CYS234 3.1 54.7 1.0 CB B:CYS306 3.2 53.4 1.0 CB B:CYS308 3.6 60.8 1.0 N B:CYS308 3.8 60.1 1.0 CA B:CYS306 3.9 53.3 1.0 N B:SER307 4.0 56.2 1.0 ND1 B:HIS240 4.1 47.2 1.0 CA B:CYS308 4.2 61.2 1.0 CG B:HIS240 4.2 43.9 1.0 C B:CYS306 4.3 54.8 1.0 N B:ARG309 4.4 63.1 1.0 CA B:CYS234 4.4 54.3 1.0 O B:ALA236 4.6 45.5 1.0 C B:CYS308 4.6 62.2 1.0 CG B:ARG309 4.8 63.3 1.0 CA B:PHE237 4.8 44.0 1.0 CD B:ARG309 4.8 62.5 1.0 C B:SER307 4.9 59.2 1.0 NE B:ARG309 4.9 59.2 1.0 C B:ALA236 4.9 45.8 1.0 O B:HOH525 5.0 64.0 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