Vanadium in PDB 7mdy: Lolcde Nucleotide-Free

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

Magnesium

(Mg)

2 atoms

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

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


Mono view


Stereo pair view

A full contact list of Vanadium with other atoms in the V binding site number 1 of Lolcde Nucleotide-Free within 5.0Å range: probe atom residue distance (Å) B Occ D:V301 b:36.9 occ:1.00 VG D:AOV301 0.0 36.9 1.0 O4G D:AOV301 2.1 36.9 1.0 O1G D:AOV301 2.1 36.9 1.0 O2G D:AOV301 2.1 36.9 1.0 O3G D:AOV301 2.1 36.9 1.0 O3B D:AOV301 2.1 36.9 1.0 H251 D:AOV301 2.6 36.9 1.0 H3G1 D:AOV301 2.6 36.9 1.0 H2G1 D:AOV301 2.6 36.9 1.0 HE22 D:GLN94 2.6 31.5 1.0 PB D:AOV301 3.1 36.9 1.0 O1B D:AOV301 3.2 36.9 1.0 NE2 D:GLN94 3.4 31.5 1.0 O3A D:AOV301 3.5 36.9 1.0 MG D:MG302 3.6 37.4 1.0 HG C:SER147 3.8 32.9 1.0 HE1 D:HIS204 3.9 39.4 1.0 H C:GLY149 3.9 32.3 1.0 HA3 C:GLY148 3.9 31.4 1.0 HE21 D:GLN94 3.9 31.5 1.0 HA D:SER44 4.0 36.4 1.0 OG C:SER147 4.2 32.9 1.0 H D:GLY45 4.2 37.9 1.0 OE1 D:GLN94 4.2 31.5 1.0 OE2 D:GLU171 4.2 34.5 1.0 CD D:GLN94 4.3 31.5 1.0 N C:GLY149 4.4 32.3 1.0 O2B D:AOV301 4.4 36.9 1.0 CA C:GLY148 4.6 31.4 1.0 N C:GLY148 4.6 31.4 1.0 CE1 D:HIS204 4.6 39.4 1.0 HB2 D:SER44 4.7 36.4 1.0 HZ2 D:LYS48 4.7 38.6 1.0 O C:ASN175 4.7 37.9 1.0 HA3 C:GLY149 4.7 32.3 1.0 HD2 D:LYS48 4.8 38.6 1.0 C C:GLY148 4.8 31.4 1.0 CA D:SER44 4.9 36.4 1.0 OD1 C:ASN175 4.9 37.9 1.0 HB3 D:SER44 4.9 36.4 1.0 PA D:AOV301 5.0 36.9 1.0 HB3 D:SER49 5.0 34.5 1.0 CD D:GLU171 5.0 34.5 1.0

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


Mono view


Stereo pair view

A full contact list of Vanadium with other atoms in the V binding site number 2 of Lolcde Nucleotide-Free within 5.0Å range: probe atom residue distance (Å) B Occ C:V301 b:41.7 occ:1.00 VG C:AOV301 0.0 41.7 1.0 O4G C:AOV301 2.1 41.7 1.0 O1G C:AOV301 2.1 41.7 1.0 O3G C:AOV301 2.1 41.7 1.0 O2G C:AOV301 2.1 41.7 1.0 O3B C:AOV301 2.1 41.7 1.0 H2G1 C:AOV301 2.6 41.7 1.0 H251 C:AOV301 2.6 41.7 1.0 H3G1 C:AOV301 2.6 41.7 1.0 HE22 C:GLN94 2.6 31.5 1.0 PB C:AOV301 3.1 41.7 1.0 O1B C:AOV301 3.2 41.7 1.0 NE2 C:GLN94 3.4 31.5 1.0 O3A C:AOV301 3.5 41.7 1.0 HE1 C:HIS204 3.9 38.6 1.0 HG D:SER147 3.9 36.6 1.0 HE21 C:GLN94 3.9 31.5 1.0 H D:GLY149 4.0 35.2 1.0 HA3 D:GLY148 4.0 34.7 1.0 HA C:SER44 4.0 38.9 1.0 H D:GLY148 4.0 34.7 1.0 MG C:MG302 4.1 35.9 1.0 H C:GLY45 4.2 40.3 1.0 OG D:SER147 4.2 36.6 1.0 OE1 C:GLN94 4.2 31.5 1.0 OE2 C:GLU171 4.2 34.2 1.0 CD C:GLN94 4.3 31.5 1.0 O2B C:AOV301 4.4 41.7 1.0 N D:GLY149 4.4 35.2 1.0 CA D:GLY148 4.6 34.7 1.0 CE1 C:HIS204 4.6 38.6 1.0 N D:GLY148 4.6 34.7 1.0 HB2 C:SER44 4.7 38.9 1.0 HZ2 C:LYS48 4.7 40.8 1.0 O D:ASN175 4.7 34.3 1.0 HD2 C:LYS48 4.8 40.8 1.0 HA3 D:GLY149 4.8 35.2 1.0 CA C:SER44 4.9 38.9 1.0 OD1 D:ASN175 4.9 34.3 1.0 C D:GLY148 4.9 34.7 1.0 HB3 C:SER44 4.9 38.9 1.0 PA C:AOV301 5.0 41.7 1.0 HB3 C:SER49 5.0 37.5 1.0 CD C:GLU171 5.0 34.2 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