Magnesium in PDB 8gkh: Structure of the Spizellomyces Punctatus Fanzor (Spufz) in Complex with Omega Rna and Target Dna

The structure of Structure of the Spizellomyces Punctatus Fanzor (Spufz) in Complex with Omega Rna and Target Dna also contains other interesting chemical elements:

Zinc

(Zn)

1 atom

The binding sites of Magnesium atom in the Structure of the Spizellomyces Punctatus Fanzor (Spufz) in Complex with Omega Rna and Target Dna (pdb code 8gkh). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Structure of the Spizellomyces Punctatus Fanzor (Spufz) in Complex with Omega Rna and Target Dna, PDB code: 8gkh:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Structure of the Spizellomyces Punctatus Fanzor (Spufz) in Complex with Omega Rna and Target Dna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of the Spizellomyces Punctatus Fanzor (Spufz) in Complex with Omega Rna and Target Dna within 5.0Å range: probe atom residue distance (Å) B Occ P:Mg701 b:37.8 occ:1.00 OD1 P:ASN385 1.9 45.8 1.0 OP1 T:DT-19 1.9 47.1 1.0 O T:HOH101 1.9 46.6 1.0 CG P:ASN385 2.9 46.2 1.0 OD1 P:ASP606 2.9 42.8 1.0 OD2 P:ASP383 3.1 41.9 1.0 ND2 P:ASN385 3.3 47.2 1.0 P T:DT-19 3.4 35.9 1.0 CG P:ARG605 3.4 43.4 1.0 CD P:ARG605 3.5 42.5 1.0 OP2 T:DT-19 4.0 39.0 1.0 CG P:ASP383 4.1 39.6 1.0 O5' T:DT-19 4.1 51.9 1.0 CB P:ASN385 4.2 42.6 1.0 CG P:ASP606 4.2 46.0 1.0 OP2 T:DT-18 4.3 61.6 1.0 OD1 P:ASP383 4.4 39.3 1.0 N P:ASP606 4.5 45.5 1.0 CA P:ASP606 4.5 42.5 1.0 C5' T:DT-19 4.5 49.8 1.0 C P:ARG605 4.5 40.2 1.0 CB P:ARG605 4.6 44.5 1.0 MG P:MG702 4.6 37.0 1.0 O P:ARG605 4.6 48.0 1.0 O P:PRO384 4.6 46.5 1.0 O P:HOH801 4.8 37.0 1.0 CB P:ASP606 4.9 46.4 1.0 NE P:ARG605 4.9 46.2 1.0 CB P:SER609 5.0 37.5 1.0

Magnesium binding site 2 out of 2 in the Structure of the Spizellomyces Punctatus Fanzor (Spufz) in Complex with Omega Rna and Target Dna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of the Spizellomyces Punctatus Fanzor (Spufz) in Complex with Omega Rna and Target Dna within 5.0Å range: probe atom residue distance (Å) B Occ P:Mg702 b:37.0 occ:1.00 O P:HOH801 1.9 37.0 1.0 OP2 T:DT-19 1.9 39.0 1.0 OE1 P:GLU541 2.0 58.3 1.0 OD1 P:ASP383 2.2 39.3 1.0 CD P:GLU541 2.6 55.5 1.0 OE2 P:GLU541 3.0 50.9 1.0 CG P:ASP383 3.2 39.6 1.0 P T:DT-19 3.2 35.9 1.0 O P:PRO384 3.3 46.5 1.0 OP1 T:DT-19 3.6 47.1 1.0 OD2 P:ASP383 3.6 41.9 1.0 CG P:GLU541 3.6 52.6 1.0 C5' T:DT-19 4.1 49.8 1.0 CB P:GLU541 4.1 49.1 1.0 O5' T:DT-19 4.1 51.9 1.0 OG P:SER609 4.2 43.4 1.0 O T:HOH101 4.3 46.6 1.0 N P:PRO384 4.4 23.8 1.0 CD P:PRO384 4.4 40.0 1.0 CB P:ASP383 4.4 39.1 1.0 OD1 P:ASN385 4.4 45.8 1.0 C P:PRO384 4.4 34.0 1.0 C P:ASP383 4.5 27.8 1.0 MG P:MG701 4.6 37.8 1.0 CA P:ASP383 4.6 33.1 1.0 CE P:MET613 4.6 40.4 1.0 CG P:PRO384 4.7 35.2 1.0 CB P:TRP507 4.7 41.1 1.0 OG1 P:THR544 4.9 40.9 1.0 CG P:ASN385 4.9 46.2 1.0 ND2 P:ASN385 5.0 47.2 1.0 CA P:PRO384 5.0 26.4 1.0 O P:ASP383 5.0 37.3 1.0

M.Saito, P.Xu, G.Faure, S.Maguire, S.Kannan, H.Altae-Tran, S.Vo, A.Desimone, R.K.Macrae, F.Zhang. Fanzor Is A Eukaryotic Programmable Rna-Guided Endonuclease. Nature 2023.
ISSN: ESSN 1476-4687
PubMed: 37380027
DOI: 10.1038/S41586-023-06356-2