Nickel in PDB 3avr: Catalytic Fragment of Utx/KDM6A Bound with Histone H3K27ME3 Peptide, N-Oxyalylglycine, and Ni(II)

The structure of Catalytic Fragment of Utx/KDM6A Bound with Histone H3K27ME3 Peptide, N-Oxyalylglycine, and Ni(II), PDB code: 3avr was solved by T.Sengoku, S.Yokoyama, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.36 / 1.80
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	78.905, 83.081, 95.057, 90.00, 90.00, 90.00
R / Rfree (%)	16.9 / 19.8

The structure of Catalytic Fragment of Utx/KDM6A Bound with Histone H3K27ME3 Peptide, N-Oxyalylglycine, and Ni(II) also contains other interesting chemical elements:

Zinc	(Zn)	1 atom
Chlorine	(Cl)	2 atoms

The binding sites of Nickel atom in the Catalytic Fragment of Utx/KDM6A Bound with Histone H3K27ME3 Peptide, N-Oxyalylglycine, and Ni(II) (pdb code 3avr). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total only one binding site of Nickel was determined in the Catalytic Fragment of Utx/KDM6A Bound with Histone H3K27ME3 Peptide, N-Oxyalylglycine, and Ni(II), PDB code: 3avr:

Nickel binding site 1 out of 1 in the Catalytic Fragment of Utx/KDM6A Bound with Histone H3K27ME3 Peptide, N-Oxyalylglycine, and Ni(II)


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Catalytic Fragment of Utx/KDM6A Bound with Histone H3K27ME3 Peptide, N-Oxyalylglycine, and Ni(II) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni1503 b:27.3 occ:1.00 OE2 A:GLU1148 2.1 23.5 1.0 NE2 A:HIS1226 2.2 18.0 1.0 NE2 A:HIS1146 2.2 30.9 1.0 O2 A:OGA1501 2.2 24.8 1.0 O2' A:OGA1501 2.2 23.4 1.0 O A:HOH265 2.4 25.0 1.0 C2 A:OGA1501 2.8 33.3 1.0 C1 A:OGA1501 2.9 30.1 1.0 CE1 A:HIS1226 3.0 20.8 1.0 HE1 A:HIS1226 3.1 25.0 1.0 CD2 A:HIS1146 3.1 26.8 1.0 CE1 A:HIS1146 3.2 27.5 1.0 CD A:GLU1148 3.2 19.8 1.0 CD2 A:HIS1226 3.3 19.6 1.0 HD2 A:HIS1146 3.3 32.2 1.0 HE1 A:HIS1146 3.4 33.0 1.0 HM21 B:M3L27 3.5 24.2 1.0 HD2 A:HIS1226 3.5 23.6 1.0 HG A:SER1154 3.6 18.8 0.4 OE1 A:GLU1148 3.7 19.3 1.0 O1 A:OGA1501 4.1 16.6 1.0 ND1 A:HIS1226 4.1 16.0 1.0 HM23 B:M3L27 4.2 24.2 1.0 N1 A:OGA1501 4.2 38.2 1.0 CM2 B:M3L27 4.3 20.1 1.0 ND1 A:HIS1146 4.3 28.0 1.0 CG A:HIS1226 4.3 16.3 1.0 CG A:HIS1146 4.3 22.1 1.0 HG2 A:GLU1148 4.4 19.9 1.0 OG A:SER1154 4.4 15.7 0.4 O A:HOH191 4.4 39.6 1.0 HG13 A:ILE1220 4.4 19.4 1.0 CG A:GLU1148 4.4 16.6 1.0 HB2 A:SER1154 4.5 21.0 0.6 OG A:SER1154 4.6 19.4 0.6 HG23 A:THR1143 4.6 20.5 1.0 HE2 B:M3L27 4.6 26.8 1.0 H4C1 A:OGA1501 4.7 42.9 1.0 HB3 A:SER1154 4.7 18.4 0.4 HZ3 A:TRP1166 4.7 22.5 1.0 HB3 A:SER1154 4.7 21.0 0.6 HB2 A:SER1154 4.8 18.4 0.4 HM22 B:M3L27 4.8 24.2 1.0 CB A:SER1154 4.9 17.5 0.6 HA A:GLU1148 4.9 18.8 1.0 HD1 A:HIS1226 4.9 19.2 1.0 H1 A:OGA1501 4.9 45.8 1.0 HG23 A:ILE1220 4.9 18.3 1.0 CB A:SER1154 4.9 15.4 0.4 C4 A:OGA1501 4.9 35.8 1.0 HG3 A:GLU1148 4.9 19.9 1.0 HM12 B:M3L27 5.0 27.5 1.0 H4C2 A:OGA1501 5.0 42.9 1.0

T.Sengoku, S.Yokoyama. Structural Basis For Histone H3 Lys 27 Demethylation By Utx/KDM6A Genes Dev. V. 25 2266 2011.
ISSN: ISSN 0890-9369
PubMed: 22002947
DOI: 10.1101/GAD.172296.111