Magnesium in PDB 8y5g: Cryo-Em Structure of E.Coli Spermidine Transporter Potabc with Spermidine

All present enzymatic activity of Cryo-Em Structure of E.Coli Spermidine Transporter Potabc with Spermidine:
7.6.2.11;

The binding sites of Magnesium atom in the Cryo-Em Structure of E.Coli Spermidine Transporter Potabc with Spermidine (pdb code 8y5g). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Cryo-Em Structure of E.Coli Spermidine Transporter Potabc with Spermidine, PDB code: 8y5g:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Cryo-Em Structure of E.Coli Spermidine Transporter Potabc with Spermidine


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 Potabc with Spermidine within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg401 b:43.3 occ:1.00 O A:PHE345 2.3 75.8 1.0 C A:PHE345 3.6 76.1 1.0 OD2 D:ASP298 3.9 69.5 1.0 ND2 A:ASN346 4.2 83.4 1.0 OD1 D:ASP298 4.2 68.8 1.0 OE2 D:GLU297 4.4 63.8 1.0 N A:ASN346 4.4 82.0 1.0 CA A:ASN346 4.5 82.7 1.0 CA A:PHE345 4.5 76.0 1.0 CG D:ASP298 4.5 68.5 1.0 CB A:PHE345 4.5 75.8 1.0 OE2 D:GLU237 4.6 63.1 1.0 OE1 D:GLU237 4.7 63.5 1.0 N A:PHE345 4.8 75.6 1.0 CE2 D:TYR236 4.8 59.8 1.0 CG D:GLU297 4.9 63.8 1.0 CD2 A:PHE345 4.9 76.5 1.0

Magnesium binding site 2 out of 4 in the Cryo-Em Structure of E.Coli Spermidine Transporter Potabc with Spermidine


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 Potabc with Spermidine within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg402 b:44.5 occ:1.00 OD1 A:ASP348 2.8 89.3 1.0 OD2 A:ASP348 3.1 89.2 1.0 CG A:ASP348 3.3 89.4 1.0 OE2 A:GLU347 3.8 91.4 1.0 CA D:TRP368 4.5 57.3 1.0 CD A:GLU347 4.7 91.5 1.0 CG A:GLU347 4.7 91.2 1.0 OE1 D:GLU237 4.7 63.5 1.0 CB A:ASP348 4.8 89.1 1.0 C D:TRP368 4.8 57.7 1.0 O D:GLU237 4.8 64.0 1.0

Magnesium binding site 3 out of 4 in the Cryo-Em Structure of E.Coli Spermidine Transporter Potabc with Spermidine


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Cryo-Em Structure of E.Coli Spermidine Transporter Potabc with Spermidine within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg401 b:35.6 occ:1.00 O D:PHE345 2.2 62.1 1.0 C D:PHE345 3.4 63.0 1.0 OE2 A:GLU237 4.1 64.2 1.0 N D:ASN346 4.3 70.1 1.0 CB D:PHE345 4.4 62.6 1.0 CA D:PHE345 4.4 63.5 1.0 CA D:ASN346 4.4 70.8 1.0 OE1 A:GLU237 4.5 64.4 1.0 OD1 A:ASP298 4.5 71.5 1.0 O D:MET325 4.6 66.2 1.0 CD2 D:PHE345 4.6 62.7 1.0 OD1 D:ASN346 4.6 71.4 1.0 CD A:GLU237 4.7 64.3 1.0 N D:PHE345 4.7 63.3 1.0 OD2 A:ASP298 4.8 71.2 1.0 OE2 A:GLU297 4.8 68.3 1.0 N D:GLU347 4.9 79.3 1.0 CG A:GLU297 4.9 68.5 1.0 CG D:PHE345 5.0 62.5 1.0 O D:GLY324 5.0 65.8 1.0

Magnesium binding site 4 out of 4 in the Cryo-Em Structure of E.Coli Spermidine Transporter Potabc with Spermidine


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Cryo-Em Structure of E.Coli Spermidine Transporter Potabc with Spermidine within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg402 b:46.0 occ:1.00 OD2 D:ASP348 2.1 75.8 1.0 CG D:ASP348 2.8 76.0 1.0 OD1 D:ASP348 2.8 76.6 1.0 CB D:ASP348 4.2 75.8 1.0 OE1 A:GLU237 4.4 64.4 1.0 O A:SER367 4.5 70.5 1.0 O A:GLU237 4.7 65.3 1.0 O A:TRP368 4.8 61.1 1.0 CA A:TRP368 4.8 60.2 1.0 C A:TRP368 4.9 60.5 1.0 O A:GLU369 4.9 72.3 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