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Zinc 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

Other elements in 4eyu:

The structure of The Free Structure of the Mouse C-Terminal Domain of KDM6B also contains other interesting chemical elements:

Nickel (Ni) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc 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 Zinc atom.
In total 2 binding sites of Zinc where determined in the The Free Structure of the Mouse C-Terminal Domain of KDM6B, PDB code: 4eyu:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 4eyu

Go back to Zinc Binding Sites List in 4eyu
Zinc 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 Zinc with other atoms in the Zn 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:Zn1702

b:51.7
occ:1.00
SG A:CYS1575 2.2 54.8 1.0
SG A:CYS1602 2.4 57.7 1.0
SG A:CYS1578 2.4 59.7 1.0
SG A:CYS1605 2.5 60.9 1.0
CB A:CYS1575 3.0 51.7 1.0
CB A:CYS1605 3.2 59.4 1.0
CB A:CYS1578 3.3 56.1 1.0
CB A:CYS1602 3.5 50.3 1.0
N A:CYS1578 3.7 57.6 1.0
N A:CYS1602 3.8 53.1 1.0
CA A:CYS1578 4.1 68.4 1.0
CA A:CYS1602 4.2 54.4 1.0
CG1 A:VAL1580 4.2 48.8 1.0
N A:CYS1605 4.3 62.3 1.0
CA A:CYS1605 4.4 61.2 1.0
CA A:CYS1575 4.5 53.9 1.0
CB A:GLU1577 4.6 67.5 1.0
C A:GLU1577 4.7 66.6 1.0
C A:CYS1602 4.8 57.8 1.0
C A:CYS1578 4.8 65.5 1.0
N A:GLU1577 4.9 60.0 1.0
C A:HIS1601 4.9 60.9 1.0
O A:CYS1602 4.9 55.2 1.0
CA A:GLU1577 4.9 64.8 1.0
N A:ASP1579 5.0 62.0 1.0
C A:CYS1575 5.0 53.8 1.0

Zinc binding site 2 out of 2 in 4eyu

Go back to Zinc Binding Sites List in 4eyu
Zinc 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 Zinc with other atoms in the Zn 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:Zn1702

b:49.7
occ:1.00
SG B:CYS1575 2.3 56.9 1.0
SG B:CYS1605 2.4 61.8 1.0
SG B:CYS1602 2.4 57.5 1.0
SG B:CYS1578 2.4 55.4 1.0
CB B:CYS1575 3.1 46.0 1.0
CB B:CYS1605 3.2 59.7 1.0
CB B:CYS1578 3.3 55.1 1.0
CB B:CYS1602 3.5 48.6 1.0
N B:CYS1578 3.6 56.6 1.0
N B:CYS1602 3.8 52.7 1.0
CA B:CYS1578 4.0 67.6 1.0
CA B:CYS1602 4.2 53.1 1.0
CG1 B:VAL1580 4.2 46.3 1.0
N B:CYS1605 4.3 59.6 1.0
CA B:CYS1605 4.3 61.3 1.0
CA B:CYS1575 4.5 54.7 1.0
CB B:GLU1577 4.5 66.5 1.0
C B:GLU1577 4.7 66.8 1.0
C B:CYS1578 4.8 65.9 1.0
C B:CYS1602 4.8 57.0 1.0
N B:GLU1577 4.9 59.2 1.0
CA B:GLU1577 4.9 65.0 1.0
O B:CYS1602 4.9 54.4 1.0
N B:ASP1579 5.0 60.2 1.0
C B:HIS1601 5.0 62.2 1.0
C B:CYS1575 5.0 51.8 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 05:16:33 2020

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