Magnesium in PDB 7zqs: Cryo-Em Structure of Human Transferrin Receptor 1 Bound to Dna Aptamer

The binding sites of Magnesium atom in the Cryo-Em Structure of Human Transferrin Receptor 1 Bound to Dna Aptamer (pdb code 7zqs). 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 Human Transferrin Receptor 1 Bound to Dna Aptamer, PDB code: 7zqs:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Cryo-Em Structure of Human Transferrin Receptor 1 Bound to Dna Aptamer


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 Human Transferrin Receptor 1 Bound to Dna Aptamer within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg101 b:81.9 occ:1.00 OP2 A:DG34 2.3 84.1 1.0 OP2 A:DA35 2.3 79.5 1.0 P A:DA35 3.5 79.5 1.0 P A:DG34 3.7 84.1 1.0 OP1 A:DA35 3.9 79.5 1.0 OP2 A:DG36 4.0 85.0 1.0 C2' A:DG33 4.3 98.6 1.0 C3' A:DG34 4.4 84.1 1.0 OP1 A:DG34 4.5 84.1 1.0 C3' A:DG33 4.5 98.6 1.0 O3' A:DG34 4.5 84.1 1.0 O3' A:DG33 4.5 98.6 1.0 C3' A:DA35 4.5 79.5 1.0 O5' A:DA35 4.6 79.5 1.0 O5' A:DG34 4.6 84.1 1.0 N3 A:DT37 4.6 90.5 1.0 C2' A:DG36 4.7 85.0 1.0 C2' A:DA35 4.7 79.5 1.0 C8 A:DG36 4.7 85.0 1.0 O2 A:DT37 4.8 90.5 1.0 C5' A:DG34 5.0 84.1 1.0

Magnesium binding site 2 out of 4 in the Cryo-Em Structure of Human Transferrin Receptor 1 Bound to Dna Aptamer


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 Human Transferrin Receptor 1 Bound to Dna Aptamer within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg102 b:65.9 occ:1.00 OP2 A:DG28 3.9 99.3 1.0 O6 A:DG17 4.0 87.6 1.0 O6 A:DG18 4.2 79.2 1.0 N7 A:DG17 4.3 87.6 1.0 OP1 A:DG28 4.4 99.3 1.0 OP2 A:DG26 4.7 74.9 1.0 P A:DG28 4.7 99.3 1.0 NH2 B:ARG629 4.7 66.5 1.0 C6 A:DG17 4.8 87.6 1.0 C5 A:DG17 5.0 87.6 1.0

Magnesium binding site 3 out of 4 in the Cryo-Em Structure of Human Transferrin Receptor 1 Bound to Dna Aptamer


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 Human Transferrin Receptor 1 Bound to Dna Aptamer within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg101 b:82.4 occ:1.00 OP2 C:DG34 2.3 84.1 1.0 OP2 C:DA35 2.3 79.3 1.0 P C:DA35 3.5 79.3 1.0 P C:DG34 3.7 84.1 1.0 OP1 C:DA35 3.9 79.3 1.0 OP2 C:DG36 4.0 85.0 1.0 C2' C:DG33 4.3 99.0 1.0 C3' C:DG34 4.4 84.1 1.0 OP1 C:DG34 4.5 84.1 1.0 C3' C:DG33 4.5 99.0 1.0 O3' C:DG34 4.5 84.1 1.0 C3' C:DA35 4.5 79.3 1.0 O3' C:DG33 4.5 99.0 1.0 O5' C:DA35 4.6 79.3 1.0 O5' C:DG34 4.6 84.1 1.0 N3 C:DT37 4.6 90.7 1.0 C2' C:DG36 4.7 85.0 1.0 C2' C:DA35 4.7 79.3 1.0 C8 C:DG36 4.7 85.0 1.0 O2 C:DT37 4.8 90.7 1.0 C5' C:DG34 5.0 84.1 1.0

Magnesium binding site 4 out of 4 in the Cryo-Em Structure of Human Transferrin Receptor 1 Bound to Dna Aptamer


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 Human Transferrin Receptor 1 Bound to Dna Aptamer within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg102 b:66.2 occ:1.00 OP2 C:DG28 3.9 99.9 1.0 O6 C:DG17 4.0 88.2 1.0 O6 C:DG18 4.2 79.5 1.0 N7 C:DG17 4.3 88.2 1.0 OP1 C:DG28 4.4 99.9 1.0 OP2 C:DG26 4.7 74.7 1.0 P C:DG28 4.7 99.9 1.0 NH2 D:ARG629 4.7 67.0 1.0 C6 C:DG17 4.8 88.2 1.0 C5 C:DG17 5.0 88.2 1.0

E.L.Cheng, I.I.Cardle, N.Kacherovsky, H.Bansia, T.Wang, Y.Zhou, J.Raman, A.Yen, D.Gutierrez, S.J.Salipante, A.Des Georges, M.C.Jensen, S.H.Pun. Discovery of A Transferrin Receptor 1-Binding Aptamer and Its Application in Cancer Cell Depletion For Adoptive T-Cell Therapy Manufacturing. J.Am.Chem.Soc. V. 144 13851 2022.
ISSN: ESSN 1520-5126
PubMed: 35875870
DOI: 10.1021/JACS.2C05349