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Chlorine in PDB 5ly2: JMJD2A/ KDM4A Complexed with Ni(II), Nog and Macrocyclic Peptide Inhibitor CP2_R6KME3 (13-Mer)

Protein crystallography data

The structure of JMJD2A/ KDM4A Complexed with Ni(II), Nog and Macrocyclic Peptide Inhibitor CP2_R6KME3 (13-Mer), PDB code: 5ly2 was solved by R.Chowdhury, S.K.Madden, R.Hopkinson, C.J.Schofield, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.67 / 2.43
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 58.306, 103.747, 142.367, 90.00, 99.14, 90.00
R / Rfree (%) 21.9 / 24.5

Other elements in 5ly2:

The structure of JMJD2A/ KDM4A Complexed with Ni(II), Nog and Macrocyclic Peptide Inhibitor CP2_R6KME3 (13-Mer) also contains other interesting chemical elements:

Nickel (Ni) 4 atoms
Zinc (Zn) 4 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the JMJD2A/ KDM4A Complexed with Ni(II), Nog and Macrocyclic Peptide Inhibitor CP2_R6KME3 (13-Mer) (pdb code 5ly2). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 5 binding sites of Chlorine where determined in the JMJD2A/ KDM4A Complexed with Ni(II), Nog and Macrocyclic Peptide Inhibitor CP2_R6KME3 (13-Mer), PDB code: 5ly2:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5;

Chlorine binding site 1 out of 5 in 5ly2

Go back to Chlorine Binding Sites List in 5ly2
Chlorine binding site 1 out of 5 in the JMJD2A/ KDM4A Complexed with Ni(II), Nog and Macrocyclic Peptide Inhibitor CP2_R6KME3 (13-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 Macrocyclic Peptide Inhibitor CP2_R6KME3 (13-Mer) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl401

b:48.1
occ:1.00
 NZ B:LYS105 3.0 52.0 1.0
N A:GLY229 3.7 44.6 1.0
CE B:LYS105 3.8 50.4 1.0
N A:SER230 3.8 47.0 1.0
CA A:PHE227 3.9 43.9 1.0
C A:PHE227 4.0 44.1 1.0
CA A:GLY229 4.0 45.0 1.0
OG A:SER230 4.2 49.4 1.0
CB A:PHE227 4.2 45.5 1.0
N A:PRO228 4.2 45.3 1.0
CD B:LYS105 4.3 53.9 1.0
O A:PHE227 4.4 44.5 1.0
CD A:PRO228 4.4 42.7 1.0
C A:GLY229 4.4 45.7 1.0
CD2 A:PHE227 4.5 44.9 1.0
CB A:SER230 4.7 45.1 1.0
C A:PRO228 4.7 46.4 1.0
CA A:SER230 4.8 44.4 1.0
CG A:PHE227 4.9 46.0 1.0
CG A:PRO228 5.0 43.2 1.0

Chlorine binding site 2 out of 5 in 5ly2

Go back to Chlorine Binding Sites List in 5ly2
Chlorine binding site 2 out of 5 in the JMJD2A/ KDM4A Complexed with Ni(II), Nog and Macrocyclic Peptide Inhibitor CP2_R6KME3 (13-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 Macrocyclic Peptide Inhibitor CP2_R6KME3 (13-Mer) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl404

b:55.7
occ:1.00
 O B:HOH603 3.1 50.0 1.0
N B:GLY229 3.6 51.2 1.0
N B:SER230 3.6 51.6 1.0
OG B:SER230 3.6 51.8 1.0
CA B:PHE227 3.9 50.5 1.0
C B:PHE227 3.9 52.1 1.0
CA B:GLY229 3.9 52.9 1.0
NZ A:LYS105 3.9 44.4 1.0
N B:PRO228 4.1 53.5 1.0
CB B:PHE227 4.1 48.9 1.0
C B:GLY229 4.2 49.9 1.0
O B:PHE227 4.3 49.7 1.0
CE A:LYS105 4.4 43.5 1.0
CD B:PRO228 4.4 49.4 1.0
CB B:SER230 4.4 47.9 1.0
CD1 B:PHE227 4.4 46.1 1.0
C B:PRO228 4.6 51.1 1.0
CA B:SER230 4.6 49.9 1.0
CG B:PHE227 4.8 47.2 1.0
CG B:PRO228 4.9 51.5 1.0
CA B:PRO228 4.9 53.9 1.0

Chlorine binding site 3 out of 5 in 5ly2

Go back to Chlorine Binding Sites List in 5ly2
Chlorine binding site 3 out of 5 in the JMJD2A/ KDM4A Complexed with Ni(II), Nog and Macrocyclic Peptide Inhibitor CP2_R6KME3 (13-Mer)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of JMJD2A/ KDM4A Complexed with Ni(II), Nog and Macrocyclic Peptide Inhibitor CP2_R6KME3 (13-Mer) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl503

b:91.7
occ:1.00
 NH1 C:ARG98 3.1 43.4 0.5
O C:TYR59 3.2 47.2 1.0
NH2 C:ARG98 3.3 44.6 0.5
CZ C:ARG98 3.7 44.0 0.5
CE1 C:PHE202 4.0 37.8 1.0
CB C:TYR59 4.0 41.9 1.0
C C:TYR59 4.1 45.9 1.0
CD1 C:PHE202 4.2 36.5 1.0
CZ C:PHE202 4.2 38.5 1.0
CG C:PHE202 4.5 35.0 1.0
CE2 C:PHE202 4.6 37.6 1.0
CD2 C:PHE202 4.7 33.1 1.0
CA C:TYR59 4.7 44.3 1.0
N C:ASP60 5.0 49.2 1.0
NE C:ARG98 5.0 42.2 0.5
CD1 C:ILE62 5.0 42.3 1.0

Chlorine binding site 4 out of 5 in 5ly2

Go back to Chlorine Binding Sites List in 5ly2
Chlorine binding site 4 out of 5 in the JMJD2A/ KDM4A Complexed with Ni(II), Nog and Macrocyclic Peptide Inhibitor CP2_R6KME3 (13-Mer)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of JMJD2A/ KDM4A Complexed with Ni(II), Nog and Macrocyclic Peptide Inhibitor CP2_R6KME3 (13-Mer) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl401

b:43.7
occ:1.00
 NZ D:LYS105 3.0 58.3 1.0
CA C:PHE227 3.6 38.6 1.0
CE D:LYS105 3.6 60.9 1.0
N C:GLY229 3.8 38.9 1.0
CB C:PHE227 3.8 37.3 1.0
O D:HOH565 3.8 42.6 1.0
C C:PHE227 3.9 39.7 1.0
N C:SER230 4.0 41.7 1.0
CD1 C:PHE227 4.0 39.8 1.0
CD C:PRO228 4.1 43.1 1.0
N C:PRO228 4.1 41.9 1.0
CD D:LYS105 4.1 59.1 1.0
CA C:GLY229 4.2 38.8 1.0
OG C:SER230 4.3 41.1 1.0
CG C:PHE227 4.4 37.6 1.0
O C:PHE227 4.5 39.2 1.0
C C:GLY229 4.6 41.8 1.0
O C:PHE226 4.7 41.0 1.0
C C:PRO228 4.8 38.2 1.0
CB C:SER230 4.9 36.9 1.0
N C:PHE227 4.9 37.7 1.0

Chlorine binding site 5 out of 5 in 5ly2

Go back to Chlorine Binding Sites List in 5ly2
Chlorine binding site 5 out of 5 in the JMJD2A/ KDM4A Complexed with Ni(II), Nog and Macrocyclic Peptide Inhibitor CP2_R6KME3 (13-Mer)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of JMJD2A/ KDM4A Complexed with Ni(II), Nog and Macrocyclic Peptide Inhibitor CP2_R6KME3 (13-Mer) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl404

b:55.0
occ:1.00
 N D:GLY229 3.3 45.4 1.0
OG D:SER230 3.4 46.1 1.0
N D:SER230 3.5 49.5 1.0
C D:PHE227 3.6 47.8 1.0
CA D:PHE227 3.6 46.2 1.0
N D:PRO228 3.8 47.0 1.0
CA D:GLY229 3.8 48.2 1.0
CB D:PHE227 4.1 44.4 1.0
O D:PHE227 4.1 48.7 1.0
C D:GLY229 4.1 50.0 1.0
CD D:PRO228 4.1 45.7 1.0
C D:PRO228 4.3 47.5 1.0
CB D:SER230 4.4 44.3 1.0
CD1 D:PHE227 4.4 43.7 1.0
CA D:SER230 4.6 47.2 1.0
CA D:PRO228 4.6 48.6 1.0
CG D:PRO228 4.7 47.1 1.0
CG D:PHE227 4.8 43.4 1.0
N D:PHE227 4.9 45.4 1.0
O D:PHE226 4.9 47.0 1.0

Reference:

A.Kawamura, M.Munzel, T.Kojima, C.Yapp, B.Bhushan, Y.Goto, A.Tumber, T.Katoh, O.N.King, T.Passioura, L.J.Walport, S.B.Hatch, S.Madden, S.Muller, P.E.Brennan, R.Chowdhury, R.J.Hopkinson, H.Suga, C.J.Schofield. Highly Selective Inhibition of Histone Demethylases By De Novo Macrocyclic Peptides. Nat Commun V. 8 14773 2017.
ISSN: ESSN 2041-1723
PubMed: 28382930
DOI: 10.1038/NCOMMS14773
Page generated: Sat Jul 12 05:12:45 2025

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