Zinc in PDB 9dbd: Zn-Bound Structure of A Single-Chain TET4 Variant with An H38E Mutation

The structure of Zn-Bound Structure of A Single-Chain TET4 Variant with An H38E Mutation, PDB code: 9dbd was solved by A.M.Hoffnagle, M.N.Neeley, F.A.Tezcan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	42.22 / 2.60
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	46.04, 46.04, 46.1, 104.25, 104.34, 104.17
R / Rfree (%)	23.8 / 31.1

The binding sites of Zinc atom in the Zn-Bound Structure of A Single-Chain TET4 Variant with An H38E Mutation (pdb code 9dbd). 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 Zn-Bound Structure of A Single-Chain TET4 Variant with An H38E Mutation, PDB code: 9dbd:

Zinc binding site 1 out of 1 in the Zn-Bound Structure of A Single-Chain TET4 Variant with An H38E Mutation


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Zn-Bound Structure of A Single-Chain TET4 Variant with An H38E Mutation within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:83.3 occ:1.00 OE2 A:GLU38 2.2 68.9 1.0 NE2 A:HIS302 2.2 94.8 1.0 O A:HOH503 2.2 92.0 1.0 NE2 A:HIS170 2.2 71.5 1.0 CE1 A:HIS302 2.6 87.9 1.0 CD2 A:HIS170 2.8 75.4 1.0 CD2 A:HIS302 3.2 93.7 1.0 CD A:GLU38 3.2 71.2 1.0 CE1 A:HIS170 3.3 76.5 1.0 ND1 A:HIS302 3.6 91.7 1.0 CG A:GLU38 3.6 64.3 1.0 CG A:HIS302 3.9 86.7 1.0 CG A:HIS170 4.1 72.5 1.0 ND1 A:HIS170 4.3 72.2 1.0 OE1 A:GLU38 4.4 78.5 1.0 O A:HOH525 4.6 38.9 1.0 CE A:MET39 4.9 56.3 1.0

A.M.Hoffnagle, S.Srisantitham, M.Neeley, C.Y.Tsai, F.A.Tezcan. A De Novo Designed Protein with Versatile Metal Binding and Tunable Hydrolytic Activity. Biochemistry 2025.
ISSN: ISSN 0006-2960
PubMed: 40700614
DOI: 10.1021/ACS.BIOCHEM.5C00259