Nickel 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:

Zinc

(Zn)

2 atoms

The binding sites of Nickel 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 Nickel atom.
In total 2 binding sites of Nickel where determined in the Specificity and Mechanism of JMJD2A, A Trimethyllysine-Specific Histone Demethylase, PDB code: 2q8e:
Jump to Nickel binding site number: 1; 2;

Nickel 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 Nickel with other atoms in the Ni 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:Ni501 b:37.8 occ:1.00 O A:HOH563 1.5 34.0 1.0 NE2 A:HIS276 1.9 40.4 1.0 O2 A:OGA503 2.0 49.5 1.0 OE1 A:GLU190 2.1 47.7 1.0 NE2 A:HIS188 2.1 39.5 1.0 O2' A:OGA503 2.3 46.6 1.0 CE1 A:HIS188 2.8 44.9 1.0 CE1 A:HIS276 2.8 41.9 1.0 C1 A:OGA503 2.9 54.7 1.0 C2 A:OGA503 3.0 53.0 1.0 CD2 A:HIS276 3.0 38.3 1.0 CD A:GLU190 3.2 46.1 1.0 CD2 A:HIS188 3.3 45.6 1.0 OE2 A:GLU190 3.6 44.9 1.0 ND1 A:HIS276 4.0 43.5 1.0 ND1 A:HIS188 4.0 44.7 1.0 O1 A:OGA503 4.1 53.9 1.0 CG A:HIS276 4.1 40.3 1.0 OG A:SER196 4.1 40.6 0.5 CG A:HIS188 4.3 44.0 1.0 N1 A:OGA503 4.3 56.2 1.0 OG A:SER196 4.4 38.4 0.5 CG A:GLU190 4.5 38.9 1.0 O A:HOH580 4.6 58.3 1.0 CB A:SER196 4.7 40.0 1.0 CM3 F:M3L36 4.8 62.9 1.0 CG2 A:THR270 4.8 43.0 1.0 OG1 A:THR270 4.9 43.2 1.0 C4 A:OGA503 5.0 53.7 1.0

Nickel 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 Nickel with other atoms in the Ni 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:Ni502 b:41.2 occ:1.00 O2 B:OGA504 1.8 48.2 1.0 NE2 B:HIS188 2.1 43.7 1.0 NE2 B:HIS276 2.1 45.5 1.0 OE1 B:GLU190 2.2 48.2 1.0 O2' B:OGA504 2.3 40.9 1.0 C1 B:OGA504 2.7 52.0 1.0 CE1 B:HIS188 2.9 44.0 1.0 C2 B:OGA504 2.9 47.9 1.0 CE1 B:HIS276 3.0 45.1 1.0 CD2 B:HIS188 3.2 44.0 1.0 CD B:GLU190 3.2 46.6 1.0 CD2 B:HIS276 3.2 44.3 1.0 OE2 B:GLU190 3.5 44.9 1.0 O1 B:OGA504 3.9 54.1 1.0 ND1 B:HIS188 4.1 42.6 1.0 ND1 B:HIS276 4.1 44.5 1.0 CG B:HIS188 4.2 43.6 1.0 OG B:SER196 4.2 50.5 1.0 N1 B:OGA504 4.3 52.5 1.0 CG B:HIS276 4.3 42.3 1.0 CG B:GLU190 4.5 43.0 1.0 O B:HOH580 4.6 60.3 1.0 CM3 G:M3L36 4.6 61.2 1.0 CG2 B:THR270 4.9 44.5 1.0 OG1 B:THR270 5.0 46.6 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