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Zinc in PDB 5ly1: JMJD2A/ KDM4A Complexed with Ni(II) and Macrocyclic Peptide Inhibitor CP2 (13-Mer)

Protein crystallography data

The structure of JMJD2A/ KDM4A Complexed with Ni(II) and Macrocyclic Peptide Inhibitor CP2 (13-Mer), PDB code: 5ly1 was solved by O.N.F.King, R.Chowdhury, A.Kawamura, C.J.Schofield, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.34 / 2.50
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 57.265, 101.482, 140.330, 90.00, 99.56, 90.00
R / Rfree (%) 17.8 / 20.5

Other elements in 5ly1:

The structure of JMJD2A/ KDM4A Complexed with Ni(II) and Macrocyclic Peptide Inhibitor CP2 (13-Mer) also contains other interesting chemical elements:

Nickel (Ni) 4 atoms
Chlorine (Cl) 3 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the JMJD2A/ KDM4A Complexed with Ni(II) and Macrocyclic Peptide Inhibitor CP2 (13-Mer) (pdb code 5ly1). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the JMJD2A/ KDM4A Complexed with Ni(II) and Macrocyclic Peptide Inhibitor CP2 (13-Mer), PDB code: 5ly1:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 5ly1

Go back to Zinc Binding Sites List in 5ly1
Zinc binding site 1 out of 4 in the JMJD2A/ KDM4A Complexed with Ni(II) and Macrocyclic Peptide Inhibitor CP2 (13-Mer)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of JMJD2A/ KDM4A Complexed with Ni(II) and Macrocyclic Peptide Inhibitor CP2 (13-Mer) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn502

b:50.5
occ:1.00
NE2 A:HIS240 2.1 42.0 1.0
SG A:CYS306 2.2 37.5 1.0
SG A:CYS234 2.3 50.8 1.0
SG A:CYS308 2.3 53.5 1.0
CE1 A:HIS240 3.1 43.0 1.0
CD2 A:HIS240 3.1 41.6 1.0
CB A:CYS234 3.1 54.3 1.0
CB A:CYS306 3.5 37.8 1.0
CB A:CYS308 3.5 58.5 1.0
N A:CYS308 3.7 70.4 1.0
CA A:CYS306 3.9 44.0 1.0
CA A:CYS308 4.1 62.8 1.0
N A:SER307 4.2 77.0 1.0
ND1 A:HIS240 4.2 43.7 1.0
CG A:HIS240 4.2 41.8 1.0
C A:CYS306 4.4 56.9 1.0
N A:ARG309 4.4 70.4 1.0
CA A:CYS234 4.5 60.3 1.0
O A:ALA236 4.5 41.2 1.0
CD A:ARG309 4.5 67.0 1.0
C A:CYS308 4.6 63.4 1.0
CG A:ARG309 4.6 70.2 1.0
NE A:ARG309 4.7 64.3 1.0
C A:SER307 4.8 86.5 1.0
CA A:PHE237 4.8 42.4 1.0
C A:ALA236 4.9 43.5 1.0

Zinc binding site 2 out of 4 in 5ly1

Go back to Zinc Binding Sites List in 5ly1
Zinc binding site 2 out of 4 in the JMJD2A/ KDM4A Complexed with Ni(II) and Macrocyclic Peptide Inhibitor CP2 (13-Mer)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of JMJD2A/ KDM4A Complexed with Ni(II) and Macrocyclic Peptide Inhibitor CP2 (13-Mer) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn502

b:50.4
occ:1.00
NE2 B:HIS240 2.1 40.8 1.0
SG B:CYS234 2.2 49.0 1.0
SG B:CYS308 2.3 48.1 1.0
SG B:CYS306 2.3 46.2 1.0
CE1 B:HIS240 3.0 40.7 1.0
CB B:CYS234 3.1 51.1 1.0
CD2 B:HIS240 3.2 39.9 1.0
CB B:CYS308 3.5 50.9 1.0
CB B:CYS306 3.5 47.0 1.0
N B:CYS308 3.6 61.5 1.0
CA B:CYS308 4.0 57.5 1.0
CA B:CYS306 4.0 50.9 1.0
N B:SER307 4.1 63.3 1.0
ND1 B:HIS240 4.2 40.6 1.0
CG B:HIS240 4.3 40.3 1.0
C B:CYS306 4.3 56.3 1.0
CA B:CYS234 4.4 55.7 1.0
N B:ARG309 4.4 73.1 1.0
C B:CYS308 4.4 62.0 1.0
CD B:ARG309 4.5 75.7 1.0
CG B:ARG309 4.6 77.7 1.0
O B:ALA236 4.6 44.6 1.0
NE B:ARG309 4.7 74.2 1.0
C B:SER307 4.8 68.9 1.0
CA B:PHE237 4.8 48.0 1.0
C B:ALA236 5.0 46.4 1.0

Zinc binding site 3 out of 4 in 5ly1

Go back to Zinc Binding Sites List in 5ly1
Zinc binding site 3 out of 4 in the JMJD2A/ KDM4A Complexed with Ni(II) and Macrocyclic Peptide Inhibitor CP2 (13-Mer)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of JMJD2A/ KDM4A Complexed with Ni(II) and Macrocyclic Peptide Inhibitor CP2 (13-Mer) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn403

b:38.6
occ:1.00
NE2 C:HIS240 2.2 34.1 1.0
SG C:CYS234 2.2 41.1 1.0
SG C:CYS308 2.3 48.2 1.0
SG C:CYS306 2.3 35.6 1.0
CE1 C:HIS240 3.1 34.6 1.0
CD2 C:HIS240 3.2 34.0 1.0
CB C:CYS234 3.2 42.8 1.0
CB C:CYS306 3.4 37.0 1.0
CB C:CYS308 3.8 50.8 1.0
N C:CYS308 3.8 63.2 1.0
CA C:CYS306 3.9 40.0 1.0
N C:SER307 4.1 69.0 1.0
C C:CYS306 4.2 48.5 1.0
ND1 C:HIS240 4.2 35.0 1.0
CG C:HIS240 4.3 34.5 1.0
CA C:CYS308 4.3 54.8 1.0
CZ2 E:TRP9 4.3 53.8 1.0
O C:ALA236 4.5 36.6 1.0
CA C:CYS234 4.6 46.5 1.0
CH2 E:TRP9 4.8 56.7 1.0
CA C:PHE237 4.8 32.3 1.0
N C:ARG309 4.8 68.5 1.0
C C:SER307 4.8 80.4 1.0
C C:CYS308 4.9 57.7 1.0
C C:ALA236 4.9 36.5 1.0

Zinc binding site 4 out of 4 in 5ly1

Go back to Zinc Binding Sites List in 5ly1
Zinc binding site 4 out of 4 in the JMJD2A/ KDM4A Complexed with Ni(II) and Macrocyclic Peptide Inhibitor CP2 (13-Mer)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of JMJD2A/ KDM4A Complexed with Ni(II) and Macrocyclic Peptide Inhibitor CP2 (13-Mer) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn502

b:46.0
occ:1.00
NE2 D:HIS240 2.1 43.2 1.0
SG D:CYS306 2.2 46.8 1.0
SG D:CYS234 2.3 41.8 1.0
SG D:CYS308 2.3 44.5 1.0
CE1 D:HIS240 3.0 42.8 1.0
CD2 D:HIS240 3.1 42.1 1.0
CB D:CYS234 3.1 45.1 1.0
CB D:CYS308 3.5 47.9 1.0
CB D:CYS306 3.5 48.4 1.0
N D:CYS308 3.7 57.4 1.0
CA D:CYS306 3.9 51.4 1.0
CA D:CYS308 4.1 53.0 1.0
ND1 D:HIS240 4.1 42.7 1.0
N D:SER307 4.1 64.9 1.0
CG D:HIS240 4.2 41.7 1.0
C D:CYS306 4.3 58.0 1.0
O D:ALA236 4.5 39.7 1.0
CA D:CYS234 4.5 50.1 1.0
C D:CYS308 4.5 57.0 1.0
N D:ARG309 4.5 64.9 1.0
CA D:PHE237 4.6 39.1 1.0
CD D:ARG309 4.8 65.3 1.0
CG D:ARG309 4.8 68.0 1.0
C D:ALA236 4.8 39.6 1.0
C D:SER307 4.8 69.3 1.0
N D:PHE237 4.9 39.9 1.0
NE D:ARG309 4.9 61.3 1.0
O D:HOH603 4.9 49.5 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: Wed Dec 16 06:31:06 2020

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