Magnesium in PDB 6zy4: Cryo-Em Structure of Mlafedb in Complex with Adp

The binding sites of Magnesium atom in the Cryo-Em Structure of Mlafedb in Complex with Adp (pdb code 6zy4). 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 Adp, PDB code: 6zy4:
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 Adp


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 Adp within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg302 b:0.7 occ:1.00 O1B F:ADP301 2.7 0.8 1.0 PB F:ADP301 2.8 0.8 1.0 O2B F:ADP301 2.9 0.8 1.0 O3B F:ADP301 2.9 0.8 1.0 CG2 F:THR48 3.4 0.2 1.0 OG1 F:THR48 3.4 0.2 1.0 CB F:THR48 4.0 0.2 1.0 OE1 F:GLN92 4.1 0.8 1.0 O3A F:ADP301 4.4 0.8 1.0

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


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 Adp within 5.0Å range: probe atom residue distance (Å) B Occ G:Mg302 b:0.1 occ:1.00 OG1 G:THR48 2.5 0.7 1.0 O3B G:ADP301 2.6 0.9 1.0 PB G:ADP301 2.8 0.9 1.0 O2B G:ADP301 2.8 0.9 1.0 O1B G:ADP301 3.0 0.9 1.0 CB G:THR48 3.5 0.7 1.0 CG2 G:THR48 4.0 0.7 1.0 OE1 G:GLN92 4.0 0.7 1.0 O3A G:ADP301 4.4 0.9 1.0 CA G:THR48 4.8 0.7 1.0 N G:THR48 5.0 0.7 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