Zinc in PDB 6f6d: The Catalytic Domain of KDM6B in Complex with H3(17-33)K18IA21M Peptide

The structure of The Catalytic Domain of KDM6B in Complex with H3(17-33)K18IA21M Peptide, PDB code: 6f6d 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)	57.50 / 1.82
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	68.480, 68.480, 230.000, 90.00, 90.00, 90.00
R / Rfree (%)	16.5 / 21.4

The structure of The Catalytic Domain of KDM6B in Complex with H3(17-33)K18IA21M Peptide also contains other interesting chemical elements:

Iron

(Fe)

1 atom

The binding sites of Zinc atom in the The Catalytic Domain of KDM6B in Complex with H3(17-33)K18IA21M Peptide (pdb code 6f6d). 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 Catalytic Domain of KDM6B in Complex with H3(17-33)K18IA21M Peptide, PDB code: 6f6d:

Zinc binding site 1 out of 1 in the The Catalytic Domain of KDM6B in Complex with H3(17-33)K18IA21M Peptide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of The Catalytic Domain of KDM6B in Complex with H3(17-33)K18IA21M Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1702 b:27.3 occ:1.00 SG A:CYS1605 2.3 30.8 1.0 SG A:CYS1602 2.3 26.5 1.0 SG A:CYS1578 2.3 28.1 1.0 SG A:CYS1575 2.3 25.7 1.0 HB2 A:CYS1605 2.9 42.1 1.0 HB3 A:CYS1578 3.0 35.6 1.0 H A:CYS1602 3.1 26.6 1.0 H A:CYS1578 3.1 33.4 1.0 CB A:CYS1575 3.2 24.3 1.0 HB3 A:CYS1575 3.2 29.2 1.0 HB2 A:CYS1575 3.2 29.2 1.0 CB A:CYS1605 3.2 35.1 1.0 CB A:CYS1578 3.3 29.6 1.0 HB3 A:CYS1602 3.3 30.0 1.0 CB A:CYS1602 3.4 25.0 1.0 H A:CYS1605 3.5 41.0 1.0 HG22 A:VAL1580 3.5 33.5 1.0 HB2 A:GLU1577 3.7 48.0 1.0 N A:CYS1578 3.8 27.8 1.0 HB3 A:CYS1605 3.8 42.1 1.0 N A:CYS1602 3.9 22.2 1.0 O A:HOH1973 4.0 49.0 1.0 HB2 A:CYS1578 4.1 35.6 1.0 CA A:CYS1578 4.1 29.9 1.0 N A:CYS1605 4.2 34.2 1.0 CA A:CYS1602 4.2 24.9 1.0 HB2 A:CYS1602 4.2 30.0 1.0 HG21 A:VAL1580 4.3 33.5 1.0 CA A:CYS1605 4.3 39.1 1.0 CG2 A:VAL1580 4.3 27.9 1.0 H A:GLU1577 4.5 29.0 1.0 H A:VAL1580 4.5 26.2 1.0 O A:HOH2217 4.5 42.0 1.0 CA A:CYS1575 4.6 22.6 1.0 H A:ASP1579 4.7 30.9 1.0 CB A:GLU1577 4.7 40.0 1.0 HG13 A:VAL1580 4.7 43.7 1.0 HA A:CYS1605 4.8 47.0 1.0 HA A:HIS1601 4.8 29.8 1.0 C A:CYS1578 4.8 29.2 1.0 HB3 A:HIS1601 4.8 31.0 1.0 C A:GLU1577 4.8 30.9 1.0 C A:CYS1602 4.8 34.4 1.0 HG23 A:VAL1580 4.8 33.5 1.0 O A:CYS1602 4.9 26.6 1.0 HA A:CYS1575 4.9 27.1 1.0 HA A:CYS1578 4.9 35.8 1.0 N A:ASP1579 5.0 25.8 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 1520-4995
PubMed: 29220567
DOI: 10.1021/ACS.BIOCHEM.7B01152