Zinc in PDB 5oy3: The Structural Basis of the Histone Demethylase KDM6B Histone 3 Lysine 27 Specificity

The structure of The Structural Basis of the Histone Demethylase KDM6B Histone 3 Lysine 27 Specificity, PDB code: 5oy3 was solved by S.E.Jones, L.Olsen, M.Gajhede, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.73 / 2.14
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	68.908, 68.908, 228.476, 90.00, 90.00, 90.00
R / Rfree (%)	16.5 / 22.1

The structure of The Structural Basis of the Histone Demethylase KDM6B Histone 3 Lysine 27 Specificity also contains other interesting chemical elements:

Iron

(Fe)

1 atom

The binding sites of Zinc atom in the The Structural Basis of the Histone Demethylase KDM6B Histone 3 Lysine 27 Specificity (pdb code 5oy3). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total only one binding site of Zinc was determined in the The Structural Basis of the Histone Demethylase KDM6B Histone 3 Lysine 27 Specificity, PDB code: 5oy3:

Zinc binding site 1 out of 1 in the The Structural Basis of the Histone Demethylase KDM6B Histone 3 Lysine 27 Specificity


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of The Structural Basis of the Histone Demethylase KDM6B Histone 3 Lysine 27 Specificity within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1702 b:33.2 occ:1.00 SG A:CYS1575 2.3 29.9 1.0 SG A:CYS1578 2.3 31.8 1.0 SG A:CYS1605 2.4 36.4 1.0 SG A:CYS1602 2.5 33.4 1.0 HB2 A:CYS1605 2.8 44.7 1.0 H A:CYS1578 3.0 40.7 1.0 CB A:CYS1605 3.2 37.2 1.0 HB3 A:CYS1575 3.2 37.7 1.0 HB3 A:CYS1578 3.2 39.0 1.0 H A:CYS1602 3.2 27.5 1.0 CB A:CYS1575 3.3 31.4 1.0 HB3 A:CYS1602 3.3 31.9 1.0 HB2 A:CYS1575 3.3 37.7 1.0 CB A:CYS1578 3.4 32.5 1.0 HG22 A:VAL1580 3.5 35.5 1.0 CB A:CYS1602 3.5 26.6 1.0 HB2 A:GLU1577 3.6 51.9 1.0 H A:CYS1605 3.6 58.4 1.0 N A:CYS1578 3.7 34.0 1.0 HB3 A:CYS1605 3.8 44.7 1.0 N A:CYS1602 4.0 22.9 1.0 CA A:CYS1578 4.1 35.5 1.0 HB2 A:CYS1578 4.2 39.0 1.0 N A:CYS1605 4.2 48.6 1.0 HG21 A:VAL1580 4.3 35.5 1.0 HB2 A:CYS1602 4.3 31.9 1.0 CG2 A:VAL1580 4.3 29.6 1.0 CA A:CYS1605 4.3 52.5 1.0 CA A:CYS1602 4.3 37.9 1.0 H A:GLU1577 4.4 44.0 1.0 CB A:GLU1577 4.5 43.2 1.0 H A:VAL1580 4.6 31.2 1.0 HG13 A:VAL1580 4.7 48.0 1.0 H A:ASP1579 4.7 37.4 1.0 HB3 A:HIS1601 4.7 44.2 1.0 CA A:CYS1575 4.7 31.4 1.0 C A:GLU1577 4.8 44.9 1.0 HA A:CYS1605 4.8 63.0 1.0 C A:CYS1578 4.8 30.9 1.0 HG23 A:VAL1580 4.8 35.5 1.0 HG2 A:GLU1577 4.8 71.1 1.0 HA A:HIS1601 4.8 35.2 1.0 C A:CYS1602 4.9 46.8 1.0 HA A:CYS1578 4.9 42.6 1.0 N A:GLU1577 5.0 36.7 1.0

S.E.Jones, L.Olsen, M.Gajhede. Structural Basis of Histone Demethylase KDM6B Histone 3 Lysine 27 Specificity. Biochemistry V. 57 585 2018.
ISSN: ISSN 0006-2960
PubMed: 29220567
DOI: 10.1021/ACS.BIOCHEM.7B01152