Zinc in PDB 9ch3: Structure of the Alpha-N-Methyltransferase (Sonm) and Ripp Precursor (Sona-L63D) Heteromeric Complex (Bound to Sah)

The structure of Structure of the Alpha-N-Methyltransferase (Sonm) and Ripp Precursor (Sona-L63D) Heteromeric Complex (Bound to Sah), PDB code: 9ch3 was solved by K.K.Crone, J.W.Labonte, M.Elias, M.F.Freeman, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.94 / 2.30
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	52, 108.4, 59, 90, 93.7, 90.2
R / Rfree (%)	27.6 / 29.9

The binding sites of Zinc atom in the Structure of the Alpha-N-Methyltransferase (Sonm) and Ripp Precursor (Sona-L63D) Heteromeric Complex (Bound to Sah) (pdb code 9ch3). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Structure of the Alpha-N-Methyltransferase (Sonm) and Ripp Precursor (Sona-L63D) Heteromeric Complex (Bound to Sah), PDB code: 9ch3:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Structure of the Alpha-N-Methyltransferase (Sonm) and Ripp Precursor (Sona-L63D) Heteromeric Complex (Bound to Sah)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of the Alpha-N-Methyltransferase (Sonm) and Ripp Precursor (Sona-L63D) Heteromeric Complex (Bound to Sah) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:69.9 occ:1.00 OE2 C:GLU126 2.1 43.2 1.0 CE1 C:HIS142 2.3 39.1 1.0 OE2 A:GLU126 2.3 43.0 1.0 OE1 A:GLU126 2.4 41.9 1.0 CE1 A:HIS142 2.5 29.4 1.0 ND1 C:HIS142 2.6 36.1 1.0 CD A:GLU126 2.7 35.0 1.0 CD C:GLU126 2.9 34.6 1.0 OE1 C:GLU126 3.3 33.0 1.0 ND1 A:HIS142 3.3 26.3 1.0 NE2 A:HIS142 3.5 25.6 1.0 NE2 C:HIS142 3.6 33.2 1.0 CG C:HIS142 3.9 36.8 1.0 CG C:GLU126 4.2 34.2 1.0 CG A:GLU126 4.2 30.1 1.0 CD2 C:HIS142 4.4 33.2 1.0 OG A:SER144 4.5 27.5 1.0 CG A:HIS142 4.5 24.6 1.0 CD2 A:HIS142 4.6 24.1 1.0 NE1 C:TRP130 4.7 17.2 1.0 CZ2 C:TRP130 4.7 16.8 1.0 CB C:HIS142 5.0 34.5 1.0

Zinc binding site 2 out of 2 in the Structure of the Alpha-N-Methyltransferase (Sonm) and Ripp Precursor (Sona-L63D) Heteromeric Complex (Bound to Sah)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of the Alpha-N-Methyltransferase (Sonm) and Ripp Precursor (Sona-L63D) Heteromeric Complex (Bound to Sah) within 5.0Å range: probe atom residue distance (Å) B Occ H:Zn302 b:73.3 occ:1.00 OE2 H:GLU126 2.0 49.7 1.0 OE2 J:GLU126 2.2 38.2 1.0 OE1 H:GLU126 2.6 38.3 1.0 CD H:GLU126 2.6 34.0 1.0 ND1 J:HIS142 2.7 49.9 1.0 ND1 H:HIS142 2.7 25.8 1.0 CD J:GLU126 2.9 36.6 1.0 CE1 J:HIS142 3.0 47.3 1.0 OE1 J:GLU126 3.0 39.2 1.0 CE1 H:HIS142 3.0 26.3 1.0 CG J:HIS142 3.9 51.2 1.0 CG H:HIS142 4.0 24.6 1.0 CG H:GLU126 4.1 30.1 1.0 NE2 J:HIS142 4.2 50.2 1.0 CG J:GLU126 4.3 34.4 1.0 NE2 H:HIS142 4.3 28.4 1.0 CD2 J:HIS142 4.6 51.9 1.0 CB J:HIS142 4.7 44.8 1.0 CD2 H:HIS142 4.8 25.7 1.0 OG H:SER144 4.9 30.1 1.0 CB H:HIS142 4.9 22.7 1.0

K.K.Crone, J.W.Labonte, M.H.Elias, M.F.Freeman. Alpha-N-Methyltransferase Regiospecificity Is Mediated By Proximal, Redundant Enzyme-Substrate Interactions. Protein Sci. V. 34 70021 2025.
ISSN: ESSN 1469-896X
PubMed: 39840790
DOI: 10.1002/PRO.70021