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

The structure of Catalytic Fragment of Utx/KDM6A Bound with N-Oxyalylglycine, and Ni(II), PDB code: 3avs 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)	30.07 / 1.85
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	78.872, 82.879, 92.923, 90.00, 90.00, 90.00
R / Rfree (%)	18.3 / 21.8

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

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

The binding sites of Nickel atom in the Catalytic Fragment of Utx/KDM6A Bound with N-Oxyalylglycine, and Ni(II) (pdb code 3avs). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 3 binding sites of Nickel where determined in the Catalytic Fragment of Utx/KDM6A Bound with N-Oxyalylglycine, and Ni(II), PDB code: 3avs:
Jump to Nickel binding site number: 1; 2; 3;

Nickel binding site 1 out of 3 in the Catalytic Fragment of Utx/KDM6A Bound with 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 N-Oxyalylglycine, and Ni(II) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni1503 b:27.0 occ:1.00 OE2 A:GLU1148 2.1 27.1 1.0 NE2 A:HIS1226 2.2 24.3 1.0 O A:HOH276 2.2 25.7 1.0 NE2 A:HIS1146 2.2 30.4 1.0 O2 A:OGA1501 2.2 26.8 1.0 O2' A:OGA1501 2.2 24.4 1.0 C1 A:OGA1501 2.9 33.6 1.0 C2 A:OGA1501 2.9 27.0 1.0 CE1 A:HIS1146 3.0 28.3 1.0 HE1 A:HIS1146 3.0 33.9 1.0 CE1 A:HIS1226 3.1 21.1 1.0 CD A:GLU1148 3.2 26.2 1.0 CD2 A:HIS1226 3.2 25.4 1.0 HE1 A:HIS1226 3.3 25.3 1.0 HD2 A:HIS1226 3.4 30.5 1.0 CD2 A:HIS1146 3.4 32.9 1.0 OE1 A:GLU1148 3.6 24.4 1.0 HG A:SER1154 3.7 51.8 1.0 HD2 A:HIS1146 3.7 39.4 1.0 O1 A:OGA1501 4.1 26.3 1.0 ND1 A:HIS1146 4.2 40.5 1.0 O A:HOH331 4.2 51.7 1.0 ND1 A:HIS1226 4.2 21.1 1.0 N1 A:OGA1501 4.3 29.0 1.0 CG A:HIS1226 4.3 22.1 1.0 CG A:HIS1146 4.4 28.5 1.0 HB2 A:SER1154 4.4 27.2 1.0 OG A:SER1154 4.4 43.2 1.0 HG2 A:GLU1148 4.4 23.4 1.0 CG A:GLU1148 4.4 19.6 1.0 HG13 A:ILE1220 4.6 28.0 1.0 HG21 A:THR1143 4.6 30.6 1.0 HB3 A:SER1154 4.6 27.2 1.0 CB A:SER1154 4.7 22.7 1.0 HZ3 A:TRP1166 4.8 19.7 1.0 H4C2 A:OGA1501 4.8 39.4 1.0 HA A:GLU1148 4.9 24.5 1.0 HD1 A:HIS1146 4.9 48.6 1.0 HG21 A:ILE1220 4.9 29.0 1.0 HG3 A:GLU1148 4.9 23.4 1.0 H1 A:OGA1501 4.9 34.7 1.0 H4C1 A:OGA1501 4.9 39.4 1.0 C4 A:OGA1501 5.0 32.9 1.0

Nickel binding site 2 out of 3 in the Catalytic Fragment of Utx/KDM6A Bound with 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 2 of Catalytic Fragment of Utx/KDM6A Bound with N-Oxyalylglycine, and Ni(II) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni1504 b:76.6 occ:1.00 HE2 A:HIS1320 2.3 89.5 1.0 NE2 A:HIS1320 2.7 74.6 1.0 O A:HOH215 3.1 47.8 1.0 HE1 A:HIS1320 3.1 78.1 1.0 CE1 A:HIS1320 3.1 65.1 1.0 OE1 A:GLU1326 3.7 39.3 1.0 CD2 A:HIS1320 3.7 68.4 1.0 OE2 A:GLU1326 3.9 37.9 1.0 CD A:GLU1326 4.1 49.2 1.0 HD2 A:HIS1320 4.1 82.0 1.0 ND1 A:HIS1320 4.2 63.4 1.0 HA A:ARG1322 4.2 54.5 1.0 HE22 A:GLN1377 4.3 28.8 0.5 HE21 A:GLN1377 4.3 28.8 0.5 CG A:HIS1320 4.5 64.2 1.0 O A:GLY1321 4.7 35.1 1.0 NE2 A:GLN1377 4.7 24.0 0.5 HD1 A:HIS1320 4.8 76.0 1.0 HG23 A:THR1323 4.9 76.7 1.0

Nickel binding site 3 out of 3 in the Catalytic Fragment of Utx/KDM6A Bound with 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 3 of Catalytic Fragment of Utx/KDM6A Bound with N-Oxyalylglycine, and Ni(II) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni1505 b:0.8 occ:1.00 HE2 A:HIS1101 2.3 0.3 1.0 HE1 A:HIS1101 2.5 89.0 1.0 NE2 A:HIS1101 2.9 84.4 1.0 CE1 A:HIS1101 3.0 74.2 1.0 CD2 A:HIS1101 4.2 74.6 1.0 ND1 A:HIS1101 4.3 66.5 1.0 HD2 A:HIS1101 4.8 89.5 1.0 HD1 A:HIS1101 4.8 79.8 1.0 CG A:HIS1101 4.9 62.7 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