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Vanadium in PDB 7mdy: Lolcde Nucleotide-Free

Other elements in 7mdy:

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

Magnesium (Mg) 2 atoms

Vanadium Binding Sites:

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 7mdy

Go back to Vanadium Binding Sites List in 7mdy
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 7mdy

Go back to Vanadium Binding Sites List in 7mdy
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

Reference:

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
Page generated: Sat Aug 21 17:35:24 2021

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