Magnesium in PDB 7rg7: Crystal Structure of NANOCLAMP8:Vhh in Complex with Mtx

The structure of Crystal Structure of NANOCLAMP8:Vhh in Complex with Mtx, PDB code: 7rg7 was solved by Z.Guo, T.Peat, J.Newman, K.Alexandrov, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	59.05 / 1.83
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	54.121, 95.882, 118.096, 90, 90, 90
R / Rfree (%)	14.9 / 20.2

The binding sites of Magnesium atom in the Crystal Structure of NANOCLAMP8:Vhh in Complex with Mtx (pdb code 7rg7). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of NANOCLAMP8:Vhh in Complex with Mtx, PDB code: 7rg7:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of NANOCLAMP8:Vhh in Complex with Mtx


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of NANOCLAMP8:Vhh in Complex with Mtx within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg302 b:7.4 occ:1.00 O A:ASN19 2.2 14.8 1.0 O A:ASP24 2.3 17.6 1.0 OE1 A:GLU134 2.3 16.5 1.0 O A:SER133 2.4 14.0 1.0 OD1 A:ASP22 2.5 19.8 1.0 O A:THR27 2.5 14.5 1.0 OG1 A:THR27 2.5 14.5 1.0 C A:ASP24 3.4 18.8 1.0 C A:THR27 3.4 16.3 1.0 C A:ASN19 3.5 13.7 1.0 CG A:ASP22 3.5 19.9 1.0 CD A:GLU134 3.6 17.7 1.0 C A:SER133 3.6 12.4 1.0 CB A:THR27 3.7 15.6 1.0 OD2 A:ASP22 3.8 18.5 1.0 N A:ASP24 3.9 19.6 1.0 CA A:THR27 4.0 16.6 1.0 N A:THR27 4.0 19.1 1.0 CA A:ASP24 4.0 20.1 1.0 CB A:ASP24 4.3 21.4 1.0 CA A:LEU20 4.3 11.8 1.0 OE2 A:GLU134 4.3 19.3 1.0 CB A:GLU134 4.4 13.6 1.0 CA A:ASN19 4.4 14.0 1.0 CA A:SER133 4.4 12.4 1.0 N A:LEU20 4.4 12.4 1.0 N A:GLY28 4.5 15.7 1.0 CG A:GLU134 4.5 15.3 1.0 N A:ASP25 4.5 18.0 1.0 CA A:GLU134 4.5 12.2 1.0 N A:GLU134 4.5 11.8 1.0 C A:LEU20 4.6 13.2 1.0 N A:ASP22 4.6 16.6 1.0 CB A:ASN19 4.6 14.4 1.0 CA A:ASP25 4.8 18.4 1.0 CB A:SER133 4.8 13.3 1.0 C A:ASP25 4.8 19.4 1.0 CA A:GLY28 4.8 15.4 1.0 CB A:ASP22 4.8 18.4 1.0 CG2 A:THR27 4.9 16.0 1.0 N A:GLY23 4.9 18.2 1.0 N A:LEU21 4.9 14.4 1.0 N A:ASN26 5.0 19.2 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of NANOCLAMP8:Vhh in Complex with Mtx


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of NANOCLAMP8:Vhh in Complex with Mtx within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg303 b:29.6 occ:1.00 O A:HOH427 2.1 11.4 1.0 O A:HOH428 2.1 20.8 1.0 OD2 A:ASP286 2.1 24.2 1.0 OD1 A:ASP274 2.3 23.2 1.0 O A:HOH623 2.3 21.9 1.0 O A:HOH649 2.3 22.8 1.0 CG A:ASP286 3.0 22.9 1.0 CG A:ASP274 3.2 23.6 1.0 OD1 A:ASP286 3.2 28.2 1.0 OD2 A:ASP274 3.5 34.0 1.0 O A:HOH512 4.0 17.9 1.0 O A:HOH557 4.0 35.6 1.0 OD1 A:ASP273 4.0 11.9 1.0 O A:GLY284 4.2 13.1 1.0 N A:ASP274 4.3 12.2 1.0 CB A:ASP286 4.4 16.1 1.0 CB A:ASP274 4.5 16.1 1.0 CA A:ASP274 4.9 14.3 1.0 O A:HOH717 4.9 42.0 1.0

Z.Guo, O.Smutok, W.A.Johnston, P.Walden, J.P.J.Ungerer, T.S.Peat, J.Newman, J.Parker, T.Nebl, C.Hepburn, A.Melman, R.J.Suderman, E.Katz, K.Alexandrov. Design of A Methotrexate-Controlled Chemical Dimerization System and Its Use in Bio-Electronic Devices. Nat Commun V. 12 7137 2021.
ISSN: ESSN 2041-1723
PubMed: 34880210
DOI: 10.1038/S41467-021-27184-W