Zinc in PDB 5fpa: Crystal Structure of Human KDM4D in Complex with 3H,4H- Pyrido-3,4-D-Pyrimidin-4-One

The structure of Crystal Structure of Human KDM4D in Complex with 3H,4H- Pyrido-3,4-D-Pyrimidin-4-One, PDB code: 5fpa was solved by C.Chung, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	64.59 / 1.96
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	71.525, 71.525, 150.366, 90.00, 90.00, 90.00
R / Rfree (%)	16.928 / 21.06

The structure of Crystal Structure of Human KDM4D in Complex with 3H,4H- Pyrido-3,4-D-Pyrimidin-4-One also contains other interesting chemical elements:

Cobalt

(Co)

1 atom

The binding sites of Zinc atom in the Crystal Structure of Human KDM4D in Complex with 3H,4H- Pyrido-3,4-D-Pyrimidin-4-One (pdb code 5fpa). 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 Crystal Structure of Human KDM4D in Complex with 3H,4H- Pyrido-3,4-D-Pyrimidin-4-One, PDB code: 5fpa:

Zinc binding site 1 out of 1 in the Crystal Structure of Human KDM4D in Complex with 3H,4H- Pyrido-3,4-D-Pyrimidin-4-One


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of Human KDM4D in Complex with 3H,4H- Pyrido-3,4-D-Pyrimidin-4-One within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn350 b:33.9 occ:1.00 NE2 A:HIS244 2.1 33.7 1.0 SG A:CYS238 2.3 32.9 1.0 SG A:CYS310 2.3 35.6 1.0 SG A:CYS312 2.3 37.2 1.0 CE1 A:HIS244 3.0 32.7 1.0 CD2 A:HIS244 3.1 32.0 1.0 CB A:CYS238 3.2 35.4 1.0 CB A:CYS310 3.4 34.6 1.0 CB A:CYS312 3.4 40.7 1.0 N A:CYS312 3.9 43.3 1.0 CA A:CYS310 4.0 36.6 1.0 ND1 A:HIS244 4.2 32.5 1.0 CA A:CYS312 4.2 43.3 1.0 CG A:HIS244 4.2 31.4 1.0 CB A:GLU314 4.3 58.3 1.0 O A:HOH2465 4.3 44.3 1.0 N A:GLU314 4.4 56.4 1.0 C A:CYS310 4.5 38.0 1.0 N A:SER311 4.5 39.8 1.0 CA A:CYS238 4.5 37.2 1.0 N A:ALA315 4.6 55.0 1.0 N A:GLY313 4.6 48.8 1.0 C A:CYS312 4.6 45.5 1.0 O A:ALA240 4.7 30.4 1.0 O A:HOH2463 4.7 47.9 1.0 CA A:GLU314 4.8 57.7 1.0 CA A:PHE241 4.9 29.2 1.0

S.M.Westaway, A.G.S.Preston, M.D.Barker, F.Brown, J.A.Brown, M.Campbell, C.Chung, H.Diallo, C.Douault, G.Drewes, R.Eagle, L.Gordon, C.Haslam, T.G.Hayhow, P.G.Humphreys, G.Joberty, R.Katso, L.Kruidenier, M.Leveridge, J.Liddle, J.Mosley, M.Muelbaier, R.Randle, I.Rioja, A.Rueger, G.A.Seal, R.J.Sheppard, O.Singh, J.Taylor, P.Thomas, D.Thomson, D.M.Wilson, K.Lee, R.K.Prinjha. Cell Penetrant Inhibitors of the KDM4 and KDM5 Families of Histone Lysine Demethylases. 1. 3-Amino-4-Pyridine Carboxylate Derivatives. J.Med.Chem. V. 59 1357 2016.
ISSN: ISSN 0022-2623
PubMed: 26771107
DOI: 10.1021/ACS.JMEDCHEM.5B01537