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Nickel in PDB 4eyu: The Free Structure of the Mouse C-Terminal Domain of KDM6B

Protein crystallography data

The structure of The Free Structure of the Mouse C-Terminal Domain of KDM6B, PDB code: 4eyu 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) 38.45 / 2.30
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 82.977, 102.284, 145.302, 90.00, 90.00, 90.00
R / Rfree (%) 23 / 26.8

Nickel Binding Sites:

The binding sites of Nickel atom in the The Free Structure of the Mouse C-Terminal Domain of KDM6B (pdb code 4eyu). 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 Free Structure of the Mouse C-Terminal Domain of KDM6B, PDB code: 4eyu:
Jump to Nickel binding site number: 1; 2;

Nickel binding site 1 out of 2 in 4eyu

Go back to Nickel Binding Sites List in 4eyu
Nickel binding site 1 out of 2 in the The Free Structure of the Mouse C-Terminal Domain of KDM6B


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of The Free Structure of the Mouse C-Terminal Domain of KDM6B within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni1701

b:34.0
occ:1.00
OE2 A:GLU1392 1.8 42.3 1.0
O2 A:OGA1700 2.1 27.9 1.0
O2' A:OGA1700 2.1 38.8 1.0
O A:HOH1827 2.1 26.9 1.0
NE2 A:HIS1390 2.2 39.4 1.0
NE2 A:HIS1470 2.2 38.8 1.0
CE1 A:HIS1470 2.6 44.6 1.0
C2 A:OGA1700 2.8 44.7 1.0
C1 A:OGA1700 2.8 36.0 1.0
CD A:GLU1392 3.0 39.9 1.0
CE1 A:HIS1390 3.1 36.9 1.0
CD2 A:HIS1390 3.1 40.7 1.0
CD2 A:HIS1470 3.3 55.7 1.0
OE1 A:GLU1392 3.7 41.4 1.0
ND1 A:HIS1470 3.7 55.7 1.0
O1 A:OGA1700 4.0 30.0 1.0
N1 A:OGA1700 4.0 45.1 1.0
CG A:HIS1470 4.1 30.2 1.0
ND1 A:HIS1390 4.2 45.6 1.0
CG A:GLU1392 4.2 37.3 1.0
CG A:HIS1390 4.2 47.6 1.0
O A:HOH1841 4.2 58.9 1.0
OG A:SER1398 4.6 46.5 1.0
C4 A:OGA1700 4.8 51.4 1.0
CB A:SER1398 4.9 47.4 1.0

Nickel binding site 2 out of 2 in 4eyu

Go back to Nickel Binding Sites List in 4eyu
Nickel binding site 2 out of 2 in the The Free Structure of the Mouse C-Terminal Domain of KDM6B


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of The Free Structure of the Mouse C-Terminal Domain of KDM6B within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ni1701

b:36.4
occ:1.00
OE2 B:GLU1392 1.9 43.4 1.0
O2 B:OGA1700 2.0 40.8 1.0
O2' B:OGA1700 2.2 44.2 1.0
NE2 B:HIS1390 2.2 41.4 1.0
O B:HOH1832 2.3 38.6 1.0
NE2 B:HIS1470 2.3 41.7 1.0
CE1 B:HIS1470 2.6 46.2 1.0
C1 B:OGA1700 2.7 42.4 1.0
C2 B:OGA1700 2.8 47.2 1.0
CD B:GLU1392 3.0 41.8 1.0
CE1 B:HIS1390 3.1 41.4 1.0
CD2 B:HIS1390 3.2 41.4 1.0
CD2 B:HIS1470 3.4 59.3 1.0
OE1 B:GLU1392 3.6 42.8 1.0
ND1 B:HIS1470 3.7 57.9 1.0
O1 B:OGA1700 3.9 31.3 1.0
N1 B:OGA1700 4.1 48.4 1.0
CG B:HIS1470 4.1 42.0 1.0
ND1 B:HIS1390 4.2 47.1 1.0
CG B:GLU1392 4.2 41.9 1.0
CG B:HIS1390 4.3 47.1 1.0
OG B:SER1398 4.6 49.9 1.0
C4 B:OGA1700 4.8 44.5 1.0
CB B:SER1398 4.9 49.9 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: Fri Sep 25 08:41:54 2020
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