Zinc in PDB 2q8d: Crystal Structure of JMJ2D2A in Ternary Complex with Histone H3-K36ME2 and Succinate

The structure of Crystal Structure of JMJ2D2A in Ternary Complex with Histone H3-K36ME2 and Succinate, PDB code: 2q8d 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)	37.80 / 2.29
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	100.857, 148.642, 57.346, 90.00, 90.00, 90.00
R / Rfree (%)	20.4 / 25.1

The structure of Crystal Structure of JMJ2D2A in Ternary Complex with Histone H3-K36ME2 and Succinate also contains other interesting chemical elements:

Nickel

(Ni)

2 atoms

The binding sites of Zinc atom in the Crystal Structure of JMJ2D2A in Ternary Complex with Histone H3-K36ME2 and Succinate (pdb code 2q8d). 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 JMJ2D2A in Ternary Complex with Histone H3-K36ME2 and Succinate, PDB code: 2q8d:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of JMJ2D2A in Ternary Complex with Histone H3-K36ME2 and Succinate


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 JMJ2D2A in Ternary Complex with Histone H3-K36ME2 and Succinate within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn505 b:32.1 occ:1.00 NE2 A:HIS240 2.2 32.1 1.0 SG A:CYS306 2.2 37.6 1.0 SG A:CYS234 2.2 37.6 1.0 SG A:CYS308 2.5 39.1 1.0 CE1 A:HIS240 3.1 29.6 1.0 CD2 A:HIS240 3.2 31.5 1.0 CB A:CYS306 3.3 38.1 1.0 CB A:CYS234 3.3 39.3 1.0 N A:CYS308 3.6 42.9 1.0 CB A:CYS308 3.7 43.3 1.0 CA A:CYS306 3.9 37.9 1.0 N A:SER307 3.9 39.5 1.0 CA A:CYS308 4.1 44.1 1.0 C A:CYS306 4.1 38.6 1.0 ND1 A:HIS240 4.2 31.4 1.0 CG A:HIS240 4.3 31.6 1.0 CG A:ARG309 4.3 50.4 1.0 N A:ARG309 4.4 48.0 1.0 C A:CYS308 4.5 45.9 1.0 CA A:CYS234 4.6 39.3 1.0 C A:SER307 4.7 41.9 1.0 CD A:ARG309 4.7 51.0 1.0 CA A:SER307 4.8 41.1 1.0 O A:ALA236 4.8 32.9 1.0 CB A:ARG309 4.9 50.1 1.0 NE A:ARG309 4.9 52.3 1.0 O A:CYS306 5.0 38.3 1.0 CA A:PHE237 5.0 32.9 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of JMJ2D2A in Ternary Complex with Histone H3-K36ME2 and Succinate


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 JMJ2D2A in Ternary Complex with Histone H3-K36ME2 and Succinate within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn506 b:36.7 occ:1.00 NE2 B:HIS240 2.2 29.5 1.0 SG B:CYS234 2.2 38.9 1.0 SG B:CYS306 2.2 37.9 1.0 SG B:CYS308 2.4 42.4 1.0 CE1 B:HIS240 3.2 29.0 1.0 CD2 B:HIS240 3.2 29.9 1.0 CB B:CYS234 3.2 40.1 1.0 CB B:CYS306 3.4 38.9 1.0 CB B:CYS308 3.5 44.6 1.0 N B:CYS308 3.5 44.4 1.0 CA B:CYS306 3.9 39.3 1.0 CA B:CYS308 4.0 45.1 1.0 N B:SER307 4.0 40.9 1.0 C B:CYS306 4.2 39.8 1.0 N B:ARG309 4.2 47.8 1.0 ND1 B:HIS240 4.3 29.2 1.0 CG B:HIS240 4.3 30.3 1.0 C B:CYS308 4.4 46.1 1.0 CA B:CYS234 4.5 40.4 1.0 O B:ALA236 4.6 34.5 1.0 CD B:ARG309 4.6 50.1 1.0 C B:SER307 4.7 43.5 1.0 CG B:ARG309 4.7 49.2 1.0 NE B:ARG309 4.8 50.4 1.0 CB B:ARG309 4.9 49.2 1.0 CA B:PHE237 4.9 32.7 1.0 C B:ALA236 4.9 35.0 1.0 CA B:SER307 4.9 42.6 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