Magnesium in PDB 8y5i: Cryo-Em Structure of E.Coli Spermidine Transporter Potd-Potabc in Translocation Intermidiate State

All present enzymatic activity of Cryo-Em Structure of E.Coli Spermidine Transporter Potd-Potabc in Translocation Intermidiate State:
7.6.2.11;

The binding sites of Magnesium atom in the Cryo-Em Structure of E.Coli Spermidine Transporter Potd-Potabc in Translocation Intermidiate State (pdb code 8y5i). 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 E.Coli Spermidine Transporter Potd-Potabc in Translocation Intermidiate State, PDB code: 8y5i:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Cryo-Em Structure of E.Coli Spermidine Transporter Potd-Potabc in Translocation Intermidiate State


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 E.Coli Spermidine Transporter Potd-Potabc in Translocation Intermidiate State within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg402 b:58.1 occ:1.00 OE1 A:GLN96 2.4 54.7 1.0 OG1 A:THR57 3.0 51.0 1.0 O1G A:ATP401 3.2 62.9 1.0 CD A:GLN96 3.3 54.7 1.0 O3B A:ATP401 3.4 61.8 1.0 OD2 A:ASP172 3.7 58.0 1.0 PG A:ATP401 3.7 62.3 1.0 NE2 A:GLN96 3.7 54.3 1.0 O2B A:ATP401 4.0 63.0 1.0 O3G A:ATP401 4.1 61.9 1.0 OD1 A:ASP172 4.1 58.3 1.0 CG A:ASP172 4.3 57.9 1.0 CB A:THR57 4.3 50.5 1.0 PB A:ATP401 4.3 62.5 1.0 CG A:GLN96 4.6 54.6 1.0 CB A:GLN96 4.8 53.9 1.0 N D:GLY150 5.0 44.2 1.0

Magnesium binding site 2 out of 2 in the Cryo-Em Structure of E.Coli Spermidine Transporter Potd-Potabc in Translocation Intermidiate State


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 E.Coli Spermidine Transporter Potd-Potabc in Translocation Intermidiate State within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg402 b:47.2 occ:1.00 O1G D:ATP401 2.1 47.7 1.0 OE1 D:GLN96 2.2 47.9 1.0 CD D:GLN96 3.1 47.5 1.0 NE2 D:GLN96 3.5 47.0 1.0 PG D:ATP401 3.6 48.0 1.0 O1B D:ATP401 3.6 47.8 1.0 OD2 D:ASP172 3.9 49.0 1.0 O3B D:ATP401 4.1 46.4 1.0 OD1 D:ASP172 4.2 48.4 1.0 O3G D:ATP401 4.2 48.6 1.0 CG D:GLN96 4.3 46.9 1.0 CG D:ASP172 4.4 48.1 1.0 CB D:THR57 4.4 42.3 1.0 CG2 D:THR57 4.5 42.9 1.0 PB D:ATP401 4.6 46.0 1.0 CB D:GLN96 4.6 46.6 1.0 O2G D:ATP401 4.6 46.0 1.0 OG1 D:THR57 5.0 43.2 1.0

Z.Qiao, P.H.Do, J.Y.Yeo, R.Ero, Z.Li, L.Zhan, S.Basak, Y.G.Gao. Structural Insights Into Polyamine Spermidine Uptake By the Abc Transporter Potd-Potabc. Sci Adv V. 10 O8107 2024.
ISSN: ESSN 2375-2548
PubMed: 39303029
DOI: 10.1126/SCIADV.ADO8107