Atomistry » Chlorine » PDB 3avi-3b0n » 3avr
Atomistry »
  Chlorine »
    PDB 3avi-3b0n »
      3avr »

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

Protein crystallography data

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

Other elements in 3avr:

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

Chlorine Binding Sites:

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 3avr

Go back to Chlorine Binding Sites List in 3avr
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 3avr

Go back to Chlorine Binding Sites List in 3avr
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

Reference:

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
Page generated: Fri Jul 11 03:14:37 2025

Last articles

Cl in 3QWC
Cl in 3QWJ
Cl in 3QW4
Cl in 3QVR
Cl in 3QVP
Cl in 3QU6
Cl in 3QU4
Cl in 3QVM
Cl in 3QVJ
Cl in 3QU5
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy