Nickel 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:

Zinc

(Zn)

2 atoms

The binding sites of Nickel 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 Nickel atom.
In total 2 binding sites of Nickel where determined in the Crystal Structure of JMJD2A in Ternary Complex with An Histone H3K9ME3 Peptide and 2-Oxoglutarate, PDB code: 2q8c:
Jump to Nickel binding site number: 1; 2;

Nickel 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 Nickel with other atoms in the Ni 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:Ni501 b:29.7 occ:1.00 O2 A:AKG503 1.5 39.6 1.0 O A:HOH609 1.9 39.9 1.0 NE2 A:HIS276 2.0 37.0 1.0 OE1 A:GLU190 2.1 39.2 1.0 NE2 A:HIS188 2.1 37.7 1.0 C1 A:AKG503 2.4 42.5 1.0 O5 A:AKG503 2.5 37.0 1.0 C2 A:AKG503 2.9 37.5 1.0 CE1 A:HIS276 2.9 36.8 1.0 CE1 A:HIS188 3.0 39.3 1.0 CD2 A:HIS276 3.1 35.4 1.0 CD A:GLU190 3.1 39.7 1.0 CD2 A:HIS188 3.2 38.8 1.0 OE2 A:GLU190 3.5 38.4 1.0 O1 A:AKG503 3.6 40.2 1.0 O A:HOH540 4.0 51.7 1.0 ND1 A:HIS276 4.1 37.1 1.0 ND1 A:HIS188 4.1 40.9 1.0 CG A:HIS276 4.2 36.4 1.0 CG A:HIS188 4.3 38.3 1.0 OG A:SER196 4.3 41.0 1.0 O A:HOH550 4.4 40.6 1.0 C3 A:AKG503 4.4 39.5 1.0 CG A:GLU190 4.5 36.2 1.0 CM3 F:M3L9 4.7 51.2 1.0 CG2 A:THR270 4.9 37.5 1.0 CB A:SER196 4.9 37.7 1.0 OG1 A:THR270 4.9 38.2 1.0

Nickel 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 Nickel with other atoms in the Ni 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:Ni502 b:30.1 occ:1.00 O2 B:AKG504 1.8 40.2 1.0 NE2 B:HIS276 2.1 39.8 1.0 O B:HOH600 2.1 48.3 1.0 NE2 B:HIS188 2.1 35.8 1.0 OE1 B:GLU190 2.2 39.1 1.0 O5 B:AKG504 2.4 32.2 1.0 C1 B:AKG504 2.7 40.5 1.0 C2 B:AKG504 2.9 36.8 1.0 CE1 B:HIS188 3.0 38.4 1.0 CE1 B:HIS276 3.0 38.0 1.0 CD2 B:HIS276 3.1 37.6 1.0 CD2 B:HIS188 3.2 37.8 1.0 CD B:GLU190 3.2 39.0 1.0 OE2 B:GLU190 3.5 39.1 1.0 O1 B:AKG504 3.9 43.9 1.0 ND1 B:HIS276 4.1 38.0 1.0 ND1 B:HIS188 4.1 36.9 1.0 CG B:HIS276 4.2 36.1 1.0 CG B:HIS188 4.2 36.4 1.0 OG B:SER196 4.3 40.0 1.0 C3 B:AKG504 4.5 37.9 1.0 CG B:GLU190 4.5 36.8 1.0 O B:HOH579 4.6 46.4 1.0 CM3 G:M3L9 4.6 49.0 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