Magnesium in PDB 6zy9: Cryo-Em Structure of Mlafedb in Complex with Amp-Pnp

The binding sites of Magnesium atom in the Cryo-Em Structure of Mlafedb in Complex with Amp-Pnp (pdb code 6zy9). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Cryo-Em Structure of Mlafedb in Complex with Amp-Pnp, PDB code: 6zy9:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Cryo-Em Structure of Mlafedb in Complex with Amp-Pnp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Cryo-Em Structure of Mlafedb in Complex with Amp-Pnp within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg402 b:50.6 occ:1.00 OG1 F:THR48 2.3 50.3 1.0 N3B F:ANP401 2.5 58.2 1.0 O2G F:ANP401 2.7 58.2 1.0 PG F:ANP401 3.2 58.2 1.0 CB F:THR48 3.5 50.3 1.0 CG2 F:THR48 3.9 50.3 1.0 O1A F:ANP401 4.0 58.2 1.0 PB F:ANP401 4.1 58.2 1.0 O1G F:ANP401 4.1 58.2 1.0 OD1 F:ASP169 4.4 40.7 1.0 OE1 F:GLN92 4.4 37.1 1.0 O3G F:ANP401 4.4 58.2 1.0 O3A F:ANP401 4.6 58.2 1.0 O2B F:ANP401 4.7 58.2 1.0 CA F:THR48 4.7 50.3 1.0 N F:THR48 4.9 50.3 1.0 OD2 F:ASP169 4.9 40.7 1.0 PA F:ANP401 4.9 58.2 1.0 OE2 F:GLU170 5.0 40.2 1.0 CG F:ASP169 5.0 40.7 1.0

Magnesium binding site 2 out of 2 in the Cryo-Em Structure of Mlafedb in Complex with Amp-Pnp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Cryo-Em Structure of Mlafedb in Complex with Amp-Pnp within 5.0Å range: probe atom residue distance (Å) B Occ G:Mg402 b:59.1 occ:1.00 OG1 G:THR48 2.2 47.7 1.0 N3B G:ANP401 2.4 59.0 1.0 O2G G:ANP401 3.4 59.0 1.0 CB G:THR48 3.4 47.7 1.0 PG G:ANP401 3.5 59.0 1.0 PB G:ANP401 3.7 59.0 1.0 CG2 G:THR48 3.8 47.7 1.0 O1A G:ANP401 4.0 59.0 1.0 O2B G:ANP401 4.1 59.0 1.0 O3A G:ANP401 4.1 59.0 1.0 OE1 G:GLN92 4.3 35.0 1.0 O1G G:ANP401 4.5 59.0 1.0 OE2 G:GLU170 4.6 36.3 1.0 CA G:THR48 4.6 47.7 1.0 O3G G:ANP401 4.6 59.0 1.0 PA G:ANP401 4.7 59.0 1.0 OD2 G:ASP169 4.7 37.0 1.0 N G:THR48 4.8 47.7 1.0 O1B G:ANP401 5.0 59.0 1.0

X.Tang, S.Chang, W.Qiao, Q.Luo, Y.Chen, Z.Jia, J.Coleman, K.Zhang, T.Wang, Z.Zhang, C.Zhang, X.Zhu, X.Wei, C.Dong, X.Zhang, H.Dong. Structural Insights Into Outer Membrane Asymmetry Maintenance in Gram-Negative Bacteria By Mlafedb. Nat.Struct.Mol.Biol. 2020.
ISSN: ESSN 1545-9985
PubMed: 33199922
DOI: 10.1038/S41594-020-00532-Y