Iron in PDB 7uva: Crystal Structure of KDM2A Histone Demethylase Catalytic Domain in Complex with An H3C36 Peptide Modified By UNC8015

All present enzymatic activity of Crystal Structure of KDM2A Histone Demethylase Catalytic Domain in Complex with An H3C36 Peptide Modified By UNC8015:
1.14.11.27;

The structure of Crystal Structure of KDM2A Histone Demethylase Catalytic Domain in Complex with An H3C36 Peptide Modified By UNC8015, PDB code: 7uva was solved by G.R.Budziszewski, D.N.Azzam, C.J.Spangler, A.Skrajna, C.A.Foley, L.I.James, S.V.Frye, R.K.Mcginty, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	88.09 / 1.98
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	54.903, 87.054, 176.177, 90, 90, 90
R / Rfree (%)	18.3 / 23.7

The binding sites of Iron atom in the Crystal Structure of KDM2A Histone Demethylase Catalytic Domain in Complex with An H3C36 Peptide Modified By UNC8015 (pdb code 7uva). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 2 binding sites of Iron where determined in the Crystal Structure of KDM2A Histone Demethylase Catalytic Domain in Complex with An H3C36 Peptide Modified By UNC8015, PDB code: 7uva:
Jump to Iron binding site number: 1; 2;

Iron binding site 1 out of 2 in the Crystal Structure of KDM2A Histone Demethylase Catalytic Domain in Complex with An H3C36 Peptide Modified By UNC8015


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Crystal Structure of KDM2A Histone Demethylase Catalytic Domain in Complex with An H3C36 Peptide Modified By UNC8015 within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe401 b:25.6 occ:1.00 O A:OH0402 2.0 30.2 1.0 OD1 A:ASP214 2.2 23.9 1.0 O3 A:OH0402 2.2 35.1 1.0 NE2 A:HIS212 2.2 23.6 1.0 NE2 A:HIS284 2.2 22.7 1.0 C6 A:OH0402 2.8 41.2 1.0 N A:OH0402 2.8 30.7 1.0 CG A:ASP214 3.1 25.0 1.0 CE1 A:HIS284 3.1 20.6 1.0 CD2 A:HIS212 3.2 21.1 1.0 CE1 A:HIS212 3.2 23.9 1.0 CD2 A:HIS284 3.2 23.2 1.0 OD2 A:ASP214 3.3 29.4 1.0 C7 A:OH0402 4.2 34.4 1.0 C5 A:OH0402 4.2 44.6 1.0 ND1 A:HIS284 4.2 26.8 1.0 ND1 A:HIS212 4.3 23.7 1.0 CG A:HIS212 4.3 20.9 1.0 CG A:HIS284 4.3 21.9 1.0 CB A:ASP214 4.5 19.4 1.0 C3 A:OH0402 4.7 44.5 1.0 C4 A:OH0402 4.7 46.6 1.0 CA A:ASP214 4.8 19.2 1.0 N A:ASP214 4.9 19.4 1.0 C8 A:OH0402 4.9 31.8 1.0

Iron binding site 2 out of 2 in the Crystal Structure of KDM2A Histone Demethylase Catalytic Domain in Complex with An H3C36 Peptide Modified By UNC8015


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Crystal Structure of KDM2A Histone Demethylase Catalytic Domain in Complex with An H3C36 Peptide Modified By UNC8015 within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe401 b:28.3 occ:1.00 O D:OH0402 2.1 31.1 1.0 OD1 D:ASP214 2.1 24.8 1.0 O3 D:OH0402 2.2 30.5 1.0 NE2 D:HIS284 2.2 24.2 1.0 NE2 D:HIS212 2.3 24.6 1.0 C6 D:OH0402 2.8 40.2 1.0 N D:OH0402 2.8 36.7 1.0 CG D:ASP214 3.0 24.6 1.0 CE1 D:HIS284 3.1 22.4 1.0 OD2 D:ASP214 3.2 30.2 1.0 CE1 D:HIS212 3.2 22.7 1.0 CD2 D:HIS284 3.2 24.6 1.0 CD2 D:HIS212 3.3 22.2 1.0 C5 D:OH0402 4.0 46.6 1.0 C4 D:OH0402 4.2 44.0 1.0 C7 D:OH0402 4.3 36.6 1.0 ND1 D:HIS284 4.3 28.1 1.0 ND1 D:HIS212 4.3 23.9 1.0 CG D:HIS284 4.4 24.3 1.0 CG D:HIS212 4.4 19.8 1.0 CB D:ASP214 4.4 19.5 1.0 CA D:ASP214 4.8 19.0 1.0 C3 D:OH0402 4.8 48.5 1.0 N D:ASP214 4.9 19.6 1.0

C.J.Spangler, A.Skrajna, C.A.Foley, A.Nguyen, G.R.Budziszewski, D.N.Azzam, E.C.Arteaga, H.C.Simmons, C.B.Smith, E.M.Wilkerson, J.-M.E.Mcpherson, N.A.Wesley, D.Kireev, L.I.James, S.V.Frye, D.Goldfarb, R.K.Mcginty. Structural Basis of Paralog-Specific KDM2A/B Nucleosome Recognition Nat.Chem.Biol. 2023.
ISSN: ESSN 1552-4469
DOI: 10.1038/S41589-023-01256-Y