Chlorine in PDB 6h8p: JMJD2A/ KDM4A Complexed with Ni(II), Nog and Histone H1.4(18-32)K26ME3 Peptide (15-Mer)

Protein crystallography data

The structure of JMJD2A/ KDM4A Complexed with Ni(II), Nog and Histone H1.4(18-32)K26ME3 Peptide (15-Mer), PDB code: 6h8p was solved by R.Chowdhury, L.J.Walport, C.J.Schofield, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.44 / 1.98
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 100.722, 150.146, 57.601, 90.00, 90.00, 90.00
R / Rfree (%) 19.2 / 21.2

Other elements in 6h8p:

The structure of JMJD2A/ KDM4A Complexed with Ni(II), Nog and Histone H1.4(18-32)K26ME3 Peptide (15-Mer) also contains other interesting chemical elements:

Nickel (Ni) 2 atoms
Zinc (Zn) 2 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the JMJD2A/ KDM4A Complexed with Ni(II), Nog and Histone H1.4(18-32)K26ME3 Peptide (15-Mer) (pdb code 6h8p). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 2 binding sites of Chlorine where determined in the JMJD2A/ KDM4A Complexed with Ni(II), Nog and Histone H1.4(18-32)K26ME3 Peptide (15-Mer), PDB code: 6h8p:
Jump to Chlorine binding site number: 1; 2;

Chlorine binding site 1 out of 2 in 6h8p

Go back to Chlorine Binding Sites List in 6h8p
Chlorine binding site 1 out of 2 in the JMJD2A/ KDM4A Complexed with Ni(II), Nog and Histone H1.4(18-32)K26ME3 Peptide (15-Mer)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of JMJD2A/ KDM4A Complexed with Ni(II), Nog and Histone H1.4(18-32)K26ME3 Peptide (15-Mer) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl503

b:97.7
occ:1.00
H A:GLY229 2.5 64.2 1.0
H A:SER230 2.6 67.7 1.0
HA A:PHE227 2.9 56.6 1.0
N A:GLY229 3.1 53.5 1.0
HA3 A:GLY229 3.2 73.2 1.0
HB3 A:PHE227 3.2 57.1 1.0
N A:SER230 3.4 56.4 1.0
C A:PHE227 3.5 48.4 1.0
CA A:PHE227 3.5 47.1 1.0
CA A:GLY229 3.6 61.0 1.0
HD1 A:PHE227 3.7 59.9 1.0
N A:PRO228 3.7 50.9 1.0
HD2 A:PRO228 3.7 61.0 1.0
CB A:PHE227 3.8 47.5 1.0
OG A:SER230 3.9 48.4 1.0
O A:PHE227 3.9 47.5 1.0
C A:GLY229 4.0 61.4 1.0
HG2 A:PRO228 4.1 64.5 1.0
C A:PRO228 4.2 50.5 1.0
HB2 A:SER230 4.2 54.1 1.0
CD A:PRO228 4.2 50.9 1.0
HG A:SER230 4.2 58.0 1.0
CB A:SER230 4.4 45.0 1.0
CD1 A:PHE227 4.4 49.9 1.0
HA2 A:GLY229 4.5 73.2 1.0
CA A:PRO228 4.5 50.7 1.0
CA A:SER230 4.5 48.5 1.0
HB2 A:PHE227 4.6 57.1 1.0
CG A:PHE227 4.6 47.3 1.0
CG A:PRO228 4.7 53.8 1.0
N A:PHE227 4.8 47.5 1.0
O A:PHE226 4.8 50.9 1.0
HA A:SER230 5.0 58.2 1.0

Chlorine binding site 2 out of 2 in 6h8p

Go back to Chlorine Binding Sites List in 6h8p
Chlorine binding site 2 out of 2 in the JMJD2A/ KDM4A Complexed with Ni(II), Nog and Histone H1.4(18-32)K26ME3 Peptide (15-Mer)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of JMJD2A/ KDM4A Complexed with Ni(II), Nog and Histone H1.4(18-32)K26ME3 Peptide (15-Mer) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl503

b:71.0
occ:1.00
H B:GLY229 2.4 47.1 1.0
H B:SER230 2.7 51.5 1.0
HA B:PHE227 3.0 41.2 1.0
N B:GLY229 3.1 39.2 1.0
HA3 B:GLY229 3.2 54.1 1.0
HD2 B:PRO228 3.4 48.5 1.0
HB3 B:PHE227 3.4 46.4 1.0
N B:SER230 3.4 42.9 1.0
C B:PHE227 3.5 36.8 1.0
CA B:GLY229 3.6 45.1 1.0
HD1 B:PHE227 3.6 60.9 1.0
CA B:PHE227 3.6 34.3 1.0
N B:PRO228 3.8 38.3 1.0
OG B:SER230 3.9 44.5 1.0
O B:PHE227 3.9 41.6 1.0
CB B:PHE227 4.0 38.6 1.0
C B:GLY229 4.0 47.5 1.0
CD B:PRO228 4.0 40.4 1.0
HG B:SER230 4.1 53.4 1.0
C B:PRO228 4.2 41.5 1.0
HG2 B:PRO228 4.3 48.5 1.0
CD1 B:PHE227 4.4 50.7 1.0
HA2 B:GLY229 4.5 54.1 1.0
HB2 B:SER230 4.5 54.9 1.0
CB B:SER230 4.6 45.7 1.0
CA B:SER230 4.6 40.3 1.0
CA B:PRO228 4.6 40.4 1.0
CG B:PHE227 4.7 46.0 1.0
CG B:PRO228 4.7 40.4 1.0
HB2 B:PHE227 4.8 46.4 1.0
HD3 B:PRO228 4.8 48.5 1.0
N B:PHE227 4.9 33.3 1.0
O B:PHE226 5.0 42.8 1.0

Reference:

L.J.Walport, R.J.Hopkinson, R.Chowdhury, Y.Zhang, J.Bonnici, R.Schiller, A.Kawamura, C.J.Schofield. Mechanistic and Structural Studies of Kdm-Catalysed Demethylation of Histone 1 Isotype 4 at Lysine 26. Febs Lett. V. 592 3264 2018.
ISSN: ISSN 1873-3468
PubMed: 30156264
DOI: 10.1002/1873-3468.13231
Page generated: Sat Dec 12 13:04:28 2020

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