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Nickel in PDB 4ezh: The Crystal Structure of KDM6B Bound with H3K27ME3 Peptide

Protein crystallography data

The structure of The Crystal Structure of KDM6B Bound with H3K27ME3 Peptide, PDB code: 4ezh was solved by Z.J.Cheng, D.J.Patel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.00 / 2.52
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 83.682, 102.413, 143.200, 90.00, 90.00, 90.00
R / Rfree (%) 21.3 / 25.4

Other elements in 4ezh:

The structure of The Crystal Structure of KDM6B Bound with H3K27ME3 Peptide also contains other interesting chemical elements:

Zinc (Zn) 2 atoms

Nickel Binding Sites:

The binding sites of Nickel atom in the The Crystal Structure of KDM6B Bound with H3K27ME3 Peptide (pdb code 4ezh). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 2 binding sites of Nickel where determined in the The Crystal Structure of KDM6B Bound with H3K27ME3 Peptide, PDB code: 4ezh:
Jump to Nickel binding site number: 1; 2;

Nickel binding site 1 out of 2 in 4ezh

Go back to Nickel Binding Sites List in 4ezh
Nickel binding site 1 out of 2 in the The Crystal Structure of KDM6B Bound with H3K27ME3 Peptide


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of The Crystal Structure of KDM6B Bound with H3K27ME3 Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni1701

b:34.0
occ:1.00
NE2 A:HIS1470 1.9 34.4 1.0
O2' A:OGA1703 2.1 20.0 1.0
OE2 A:GLU1392 2.1 55.5 1.0
NE2 A:HIS1390 2.2 42.6 1.0
O2 A:OGA1703 2.2 20.0 1.0
O A:HOH1813 2.3 32.8 1.0
C2 A:OGA1703 2.7 20.0 1.0
C1 A:OGA1703 2.8 20.0 1.0
CE1 A:HIS1470 2.8 39.0 1.0
CE1 A:HIS1390 2.9 49.6 1.0
CD2 A:HIS1470 3.0 33.9 1.0
CD A:GLU1392 3.2 43.1 1.0
CD2 A:HIS1390 3.2 42.6 1.0
OE1 A:GLU1392 3.6 33.8 1.0
ND1 A:HIS1470 3.9 36.4 1.0
O1 A:OGA1703 4.0 20.0 1.0
N1 A:OGA1703 4.0 20.0 1.0
ND1 A:HIS1390 4.0 56.6 1.0
CG A:HIS1470 4.0 26.4 1.0
CG A:HIS1390 4.2 53.0 1.0
CM3 C:M3L27 4.3 62.5 1.0
CG A:GLU1392 4.5 47.4 1.0
OG A:SER1398 4.7 43.1 1.0
C4 A:OGA1703 4.8 20.0 1.0

Nickel binding site 2 out of 2 in 4ezh

Go back to Nickel Binding Sites List in 4ezh
Nickel binding site 2 out of 2 in the The Crystal Structure of KDM6B Bound with H3K27ME3 Peptide


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of The Crystal Structure of KDM6B Bound with H3K27ME3 Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ni1701

b:40.6
occ:1.00
NE2 B:HIS1470 1.9 36.5 1.0
OE2 B:GLU1392 2.1 57.6 1.0
O2 B:OGA1703 2.1 20.0 1.0
O2' B:OGA1703 2.2 20.0 1.0
NE2 B:HIS1390 2.2 42.2 1.0
O B:HOH1811 2.2 30.8 1.0
C1 B:OGA1703 2.5 20.0 1.0
C2 B:OGA1703 2.5 20.0 1.0
CE1 B:HIS1390 2.8 49.8 1.0
CE1 B:HIS1470 2.8 40.2 1.0
CD2 B:HIS1470 2.9 36.8 1.0
CD B:GLU1392 3.2 45.0 1.0
CD2 B:HIS1390 3.3 42.6 1.0
OE1 B:GLU1392 3.6 38.7 1.0
O1 B:OGA1703 3.7 20.0 1.0
N1 B:OGA1703 3.8 20.0 1.0
ND1 B:HIS1470 3.9 38.0 1.0
ND1 B:HIS1390 3.9 57.9 1.0
CG B:HIS1470 4.0 36.8 1.0
CG B:HIS1390 4.2 54.5 1.0
CG B:GLU1392 4.4 47.8 1.0
CM3 D:M3L27 4.5 72.8 1.0
OG B:SER1398 4.7 44.5 1.0
C4 B:OGA1703 4.7 20.0 1.0

Reference:

L.Kruidenier, C.W.Chung, Z.Cheng, J.Liddle, K.Che, G.Joberty, M.Bantscheff, C.Bountra, A.Bridges, H.Diallo, D.Eberhard, S.Hutchinson, E.Jones, R.Katso, M.Leveridge, P.K.Mander, J.Mosley, C.Ramirez-Molina, P.Rowland, C.J.Schofield, R.J.Sheppard, J.E.Smith, C.Swales, R.Tanner, P.Thomas, A.Tumber, G.Drewes, U.Oppermann, D.J.Patel, K.Lee, D.M.Wilson. A Selective Jumonji H3K27 Demethylase Inhibitor Modulates the Proinflammatory Macrophage Response. Nature V. 488 404 2012.
ISSN: ISSN 0028-0836
PubMed: 22842901
DOI: 10.1038/NATURE11262
Page generated: Wed Dec 16 01:30:11 2020

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