Magnesium in PDB 7u58: Ycao-Mediated Atp-Dependent Peptidase Activity in Ribosomal Peptide Biosynthesis

The structure of Ycao-Mediated Atp-Dependent Peptidase Activity in Ribosomal Peptide Biosynthesis also contains other interesting chemical elements:

Zinc

(Zn)

2 atoms

The binding sites of Magnesium atom in the Ycao-Mediated Atp-Dependent Peptidase Activity in Ribosomal Peptide Biosynthesis (pdb code 7u58). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Ycao-Mediated Atp-Dependent Peptidase Activity in Ribosomal Peptide Biosynthesis, PDB code: 7u58:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Ycao-Mediated Atp-Dependent Peptidase Activity in Ribosomal Peptide Biosynthesis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Ycao-Mediated Atp-Dependent Peptidase Activity in Ribosomal Peptide Biosynthesis within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg802 b:71.4 occ:1.00 OE1 A:GLU554 2.1 73.1 1.0 OE2 A:GLU554 2.2 73.1 1.0 CD A:GLU554 2.4 73.1 1.0 O A:ASP538 3.0 73.7 1.0 O A:SER535 3.6 73.1 1.0 OE2 A:GLU433 3.7 82.0 1.0 CG A:GLU554 4.0 73.1 1.0 C A:ASP538 4.2 73.7 1.0 OE1 A:GLU433 4.3 82.0 1.0 NH2 A:ARG558 4.4 71.2 1.0 CD A:GLU433 4.4 82.0 1.0 OG A:SER535 4.6 73.1 1.0 C A:SER535 4.7 73.1 1.0 N A:ASP538 4.7 73.7 1.0 CB A:SER535 4.7 73.1 1.0 CB A:GLU554 4.7 73.1 1.0 CA A:ASP538 4.9 73.7 1.0

Magnesium binding site 2 out of 4 in the Ycao-Mediated Atp-Dependent Peptidase Activity in Ribosomal Peptide Biosynthesis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Ycao-Mediated Atp-Dependent Peptidase Activity in Ribosomal Peptide Biosynthesis within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg803 b:80.0 occ:1.00 OE2 A:GLU430 2.7 97.1 1.0 CD A:GLU430 3.8 97.1 1.0 CG A:GLU430 4.4 97.1 1.0 OE1 A:GLU430 4.9 97.1 1.0

Magnesium binding site 3 out of 4 in the Ycao-Mediated Atp-Dependent Peptidase Activity in Ribosomal Peptide Biosynthesis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Ycao-Mediated Atp-Dependent Peptidase Activity in Ribosomal Peptide Biosynthesis within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg802 b:70.6 occ:1.00 OE1 B:GLU554 2.1 73.0 1.0 OE2 B:GLU554 2.2 73.0 1.0 CD B:GLU554 2.4 73.0 1.0 O B:ASP538 3.0 76.8 1.0 O B:SER535 3.6 72.2 1.0 OE2 B:GLU433 3.8 86.7 1.0 CG B:GLU554 3.9 73.0 1.0 C B:ASP538 4.2 76.8 1.0 OE1 B:GLU433 4.5 86.7 1.0 NH2 B:ARG558 4.5 68.6 1.0 OG B:SER535 4.5 72.2 1.0 CD B:GLU433 4.6 86.7 1.0 CB B:GLU554 4.7 73.0 1.0 C B:SER535 4.7 72.2 1.0 N B:ASP538 4.8 76.8 1.0 CB B:SER535 4.8 72.2 1.0 CA B:ASP538 5.0 76.8 1.0

Magnesium binding site 4 out of 4 in the Ycao-Mediated Atp-Dependent Peptidase Activity in Ribosomal Peptide Biosynthesis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Ycao-Mediated Atp-Dependent Peptidase Activity in Ribosomal Peptide Biosynthesis within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg803 b:71.8 occ:1.00 OE1 B:GLU430 3.7 105.2 1.0 CD B:GLU430 4.8 105.2 1.0

Y.Zheng, S.K.Nair. Ycao-Mediated Atp-Dependent Peptidase Activity in Ribosomal Peptide Biosynthesis. Nat.Chem.Biol. 2022.
ISSN: ESSN 1552-4469
PubMed: 36280794
DOI: 10.1038/S41589-022-01141-0