Chlorine 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
Nickel	(Ni)	1 atom

The binding sites of Chlorine 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 Chlorine atom.
In total 2 binding sites of Chlorine where determined in the Catalytic Fragment of Utx/KDM6A Bound with Histone H3K27ME3 Peptide, N-Oxyalylglycine, and Ni(II), PDB code: 3avr:
Jump to Chlorine binding site number: 1; 2;

Chlorine binding site 1 out of 2 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 Chlorine with other atoms in the Cl 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:Cl1402 b:69.4 occ:1.00 HH22 A:ARG1322 2.9 25.6 0.5 H A:GLU1325 2.9 72.2 1.0 HH12 A:ARG1322 3.1 31.3 0.5 HD2 A:LYS1324 3.1 0.3 1.0 HA A:LYS1324 3.3 0.1 1.0 O A:HOH50 3.5 25.8 1.0 NH2 A:ARG1322 3.7 21.4 0.5 N A:GLU1325 3.7 60.2 1.0 HZ3 A:LYS1324 3.8 0.2 1.0 NH1 A:ARG1322 3.9 26.1 0.5 CD A:LYS1324 3.9 0.4 1.0 HD3 A:LYS1324 4.0 0.3 1.0 CA A:LYS1324 4.2 83.4 1.0 CZ A:ARG1322 4.3 32.6 0.5 HH21 A:ARG1322 4.3 25.6 0.5 HZ1 A:LYS1324 4.4 0.2 1.0 HA A:GLU1325 4.4 67.0 1.0 NZ A:LYS1324 4.4 0.2 1.0 C A:LYS1324 4.5 65.7 1.0 O A:THR1323 4.6 58.5 1.0 HH11 A:ARG1322 4.6 31.3 0.5 CA A:GLU1325 4.7 55.8 1.0 CE A:LYS1324 4.8 0.3 1.0 H A:GLU1326 4.9 42.3 1.0 O A:HOH37 5.0 25.5 1.0 O A:HOH268 5.0 43.9 1.0

Chlorine binding site 2 out of 2 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 Chlorine with other atoms in the Cl binding site number 2 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:Cl1403 b:57.0 occ:1.00 H A:ALA1115 2.4 35.2 1.0 HB2 A:SER1114 3.0 34.6 1.0 HA A:SER1114 3.0 32.1 1.0 N A:ALA1115 3.2 29.3 1.0 HH21 A:ARG1111 3.3 50.8 1.0 O A:HOH310 3.6 39.5 1.0 CA A:SER1114 3.6 26.8 1.0 HB2 A:ALA1115 3.7 44.5 1.0 CB A:SER1114 3.7 28.8 1.0 HB3 A:ALA1115 3.7 44.5 1.0 C A:SER1114 3.9 24.9 1.0 CB A:ALA1115 4.0 37.1 1.0 NH2 A:ARG1111 4.1 42.3 1.0 HB3 A:SER1114 4.1 34.6 1.0 CA A:ALA1115 4.2 28.8 1.0 HH22 A:ARG1111 4.3 50.8 1.0 H A:GLY1116 4.5 28.9 1.0 HO2 A:EDO1 4.6 68.0 1.0 HE A:ARG1111 4.7 54.3 1.0 HB1 A:ALA1108 4.8 28.7 1.0 OG A:SER1114 4.8 35.8 1.0 H21 A:EDO1 4.8 68.1 1.0 HA A:ALA1115 4.8 34.5 1.0 N A:SER1114 4.9 22.0 1.0 HB1 A:ALA1115 5.0 44.5 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