Magnesium in PDB 7mdy: Lolcde Nucleotide-Free

The structure of Lolcde Nucleotide-Free also contains other interesting chemical elements:

Vanadium

(V)

2 atoms

The binding sites of Magnesium atom in the Lolcde Nucleotide-Free (pdb code 7mdy). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Lolcde Nucleotide-Free, PDB code: 7mdy:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Lolcde Nucleotide-Free


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Lolcde Nucleotide-Free within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg302 b:37.4 occ:1.00 HB3 D:SER49 1.8 34.5 1.0 O4G D:AOV301 1.9 36.9 1.0 OE1 D:GLN94 2.0 31.5 1.0 CB D:SER49 2.8 34.5 1.0 O1B D:AOV301 2.8 36.9 1.0 CD D:GLN94 3.0 31.5 1.0 HE22 D:GLN94 3.1 31.5 1.0 H D:SER49 3.1 34.5 1.0 HB2 D:SER49 3.3 34.5 1.0 HG D:SER49 3.4 34.5 1.0 NE2 D:GLN94 3.4 31.5 1.0 OG D:SER49 3.5 34.5 1.0 N D:SER49 3.6 34.5 1.0 CA D:SER49 3.6 34.5 1.0 VG D:AOV301 3.6 36.9 1.0 HA D:SER49 3.6 34.5 1.0 OD2 D:ASP170 3.8 32.6 1.0 HB2 D:LYS48 3.8 38.6 1.0 HB2 D:GLN94 4.0 31.5 1.0 PB D:AOV301 4.0 36.9 1.0 O1G D:AOV301 4.1 36.9 1.0 HE21 D:GLN94 4.3 31.5 1.0 CG D:ASP170 4.3 32.6 1.0 HB3 D:ASP170 4.3 32.6 1.0 CG D:GLN94 4.3 31.5 1.0 O3A D:AOV301 4.4 36.9 1.0 O1A D:AOV301 4.4 36.9 1.0 O3B D:AOV301 4.5 36.9 1.0 CB D:GLN94 4.5 31.5 1.0 HB3 D:GLN94 4.5 31.5 1.0 H251 D:AOV301 4.6 36.9 1.0 HG11 D:VAL202 4.6 36.5 1.0 C D:LYS48 4.6 38.6 1.0 HD2 D:LYS48 4.7 38.6 1.0 CB D:LYS48 4.7 38.6 1.0 OD1 D:ASP170 4.8 32.6 1.0 HG3 D:GLN94 4.8 31.5 1.0 CB D:ASP170 4.8 32.6 1.0 HG2 D:GLN94 4.9 31.5 1.0 PA D:AOV301 4.9 36.9 1.0 HG3 D:GLU171 4.9 34.5 1.0 O2A D:AOV301 5.0 36.9 1.0 O3G D:AOV301 5.0 36.9 1.0

Magnesium binding site 2 out of 2 in the Lolcde Nucleotide-Free


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Lolcde Nucleotide-Free within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg302 b:35.9 occ:1.00 HB3 C:SER49 1.8 37.5 1.0 HG C:SER49 2.0 37.5 1.0 O4G C:AOV301 2.0 41.7 1.0 CB C:SER49 2.4 37.5 1.0 OG C:SER49 2.5 37.5 1.0 HB2 C:SER49 2.6 37.5 1.0 OE1 C:GLN94 2.7 31.5 1.0 CD C:GLN94 3.2 31.5 1.0 HE22 C:GLN94 3.3 31.5 1.0 NE2 C:GLN94 3.5 31.5 1.0 O1B C:AOV301 3.7 41.7 1.0 H C:SER49 3.7 37.5 1.0 CA C:SER49 3.8 37.5 1.0 O2A C:AOV301 3.8 41.7 1.0 HB3 C:GLN94 3.9 31.5 1.0 VG C:AOV301 4.1 41.7 1.0 HB2 C:GLN94 4.1 31.5 1.0 H D:GLY148 4.1 34.7 1.0 HE21 C:GLN94 4.1 31.5 1.0 HA C:SER49 4.1 37.5 1.0 O3A C:AOV301 4.1 41.7 1.0 N C:SER49 4.1 37.5 1.0 O1A C:AOV301 4.2 41.7 1.0 CG C:GLN94 4.2 31.5 1.0 HE2 C:PHE95 4.3 30.1 1.0 PA C:AOV301 4.3 41.7 1.0 OD2 C:ASP170 4.3 32.4 1.0 CB C:GLN94 4.3 31.5 1.0 HA3 D:GLY148 4.4 34.7 1.0 HG2 C:GLN94 4.5 31.5 1.0 PB C:AOV301 4.5 41.7 1.0 OG D:SER147 4.5 36.6 1.0 HG D:SER147 4.7 36.6 1.0 N D:GLY148 4.8 34.7 1.0 HE1 C:HIS53 4.8 36.1 1.0 C C:SER49 4.8 37.5 1.0 H C:THR50 5.0 39.9 1.0

S.Sharma, R.Zhou, L.Wan, S.Feng, K.Song, C.Xu, Y.Li, M.Liao. Mechanism of Lolcde As A Molecular Extruder of Bacterial Triacylated Lipoproteins Nat Commun V. 12 4687 2021.
ISSN: ESSN 2041-1723
DOI: 10.1038/S41467-021-24965-1