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Nickel 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:

Chlorine (Cl) 3 atoms
Zinc (Zn) 4 atoms

Nickel Binding Sites:

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

Nickel binding site 1 out of 4 in 5ly1

Go back to Nickel Binding Sites List in 5ly1
Nickel 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 Nickel with other atoms in the Ni 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:Ni501

b:62.2
occ:1.00
OE2 A:GLU190 2.3 40.9 1.0
O A:HOH671 2.3 42.3 1.0
NE2 A:HIS276 2.4 37.0 1.0
NE2 A:HIS188 2.4 39.4 1.0
O A:HOH662 2.6 54.8 1.0
CE1 A:HIS188 3.1 38.6 1.0
CD A:GLU190 3.3 40.7 1.0
O A:HOH695 3.3 50.6 1.0
CD2 A:HIS276 3.3 36.4 1.0
CE1 A:HIS276 3.4 37.6 1.0
OE1 A:GLU190 3.5 40.4 1.0
CD2 A:HIS188 3.6 38.5 1.0
O A:HOH647 4.2 49.2 1.0
ND1 A:HIS188 4.3 38.2 1.0
OG A:SER196 4.3 47.6 1.0
ND1 A:HIS276 4.5 37.5 1.0
CG A:HIS276 4.5 36.0 1.0
CG A:HIS188 4.6 37.4 1.0
CG A:GLU190 4.6 39.7 1.0
CB A:SER196 4.8 44.5 1.0
CG2 A:THR270 4.9 37.2 1.0

Nickel binding site 2 out of 4 in 5ly1

Go back to Nickel Binding Sites List in 5ly1
Nickel 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 Nickel with other atoms in the Ni 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:Ni501

b:63.9
occ:1.00
OE2 B:GLU190 2.2 41.7 1.0
NE2 B:HIS188 2.4 41.7 1.0
NE2 B:HIS276 2.4 32.9 1.0
O B:HOH632 2.5 66.4 1.0
O B:HOH670 3.0 51.5 1.0
CE1 B:HIS188 3.1 41.4 1.0
O B:HOH652 3.1 52.4 1.0
CD B:GLU190 3.2 41.6 1.0
CE1 B:HIS276 3.4 33.4 1.0
CD2 B:HIS276 3.4 32.6 1.0
CD2 B:HIS188 3.5 41.3 1.0
OE1 B:GLU190 3.6 42.5 1.0
OG B:SER196 4.3 53.9 1.0
ND1 B:HIS188 4.3 40.5 1.0
ND1 B:HIS276 4.5 35.2 1.0
CG B:GLU190 4.5 41.3 1.0
CG B:HIS276 4.5 33.6 1.0
CG B:HIS188 4.5 39.9 1.0
O1 B:PPI505 4.6 48.2 1.0
CB B:SER196 4.7 51.5 1.0
NZ B:LYS241 4.9 57.0 1.0
OG1 B:THR270 4.9 44.1 1.0

Nickel binding site 3 out of 4 in 5ly1

Go back to Nickel Binding Sites List in 5ly1
Nickel 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 Nickel with other atoms in the Ni 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:Ni402

b:62.6
occ:1.00
OE2 C:GLU190 2.2 36.2 1.0
O C:HOH508 2.3 38.2 1.0
NE2 C:HIS276 2.6 36.4 1.0
NE2 C:HIS188 2.6 35.3 1.0
O C:HOH556 2.6 44.4 1.0
CE1 C:HIS188 3.1 35.5 1.0
O C:HOH624 3.1 57.5 1.0
CD C:GLU190 3.2 33.0 1.0
OE1 C:GLU190 3.4 32.0 1.0
CE1 C:HIS276 3.5 37.7 1.0
CD2 C:HIS276 3.5 36.2 1.0
CD2 C:HIS188 3.7 35.8 1.0
O C:HOH568 4.1 37.5 1.0
OG C:SER196 4.2 43.8 1.0
ND1 C:HIS188 4.3 36.0 1.0
CG C:GLU190 4.6 31.6 1.0
CB C:SER196 4.6 41.0 1.0
ND1 C:HIS276 4.6 38.0 1.0
O C:HOH612 4.6 51.2 1.0
CG C:HIS188 4.7 34.8 1.0
CG C:HIS276 4.7 36.7 1.0
CG2 C:THR270 4.9 35.6 1.0

Nickel binding site 4 out of 4 in 5ly1

Go back to Nickel Binding Sites List in 5ly1
Nickel 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 Nickel with other atoms in the Ni 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:Ni501

b:68.1
occ:1.00
OE2 D:GLU190 2.3 51.5 1.0
NE2 D:HIS276 2.4 33.3 1.0
NE2 D:HIS188 2.4 37.8 1.0
O D:HOH677 2.7 54.3 1.0
O D:HOH694 2.8 54.6 1.0
O D:HOH684 2.8 64.5 1.0
CE1 D:HIS188 3.2 36.3 1.0
CD D:GLU190 3.3 49.7 1.0
CD2 D:HIS276 3.3 32.8 1.0
CE1 D:HIS276 3.4 32.7 1.0
CD2 D:HIS188 3.5 36.9 1.0
OE1 D:GLU190 3.6 50.2 1.0
O D:HOH688 3.8 54.6 1.0
ND1 D:HIS188 4.4 35.6 1.0
CG D:HIS276 4.5 32.2 1.0
OG D:SER196 4.5 51.4 1.0
ND1 D:HIS276 4.5 32.3 1.0
CG D:HIS188 4.5 35.6 1.0
CG D:GLU190 4.6 46.6 1.0
O D:HOH602 4.6 51.5 1.0
CB D:SER196 4.8 47.5 1.0
OG1 D:THR270 4.8 45.0 1.0
CZ3 D:TRP208 5.0 29.1 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 01:41:34 2020

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