Magnesium in PDB 6mth: E. Coli Dhfr Complex Modeled with Three Ligand States

All present enzymatic activity of E. Coli Dhfr Complex Modeled with Three Ligand States:
1.5.1.3;

The structure of E. Coli Dhfr Complex Modeled with Three Ligand States, PDB code: 6mth was solved by H.Cao, J.Rodrigues, J.Benach, A.Frommelt, L.Morisco, J.Koss, E.Shakhnovich, J.Skolnick, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	31.27 / 1.35
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	34.050, 51.666, 79.014, 90.00, 90.00, 90.00
R / Rfree (%)	16.7 / 19

The structure of E. Coli Dhfr Complex Modeled with Three Ligand States also contains other interesting chemical elements:

Chlorine

(Cl)

3 atoms

The binding sites of Magnesium atom in the E. Coli Dhfr Complex Modeled with Three Ligand States (pdb code 6mth). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the E. Coli Dhfr Complex Modeled with Three Ligand States, PDB code: 6mth:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the E. Coli Dhfr Complex Modeled with Three Ligand States


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of E. Coli Dhfr Complex Modeled with Three Ligand States within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg204 b:17.4 occ:1.00 O A:HOH388 2.1 17.4 1.0 OE1 A:GLU101 2.1 12.6 1.0 O A:HOH336 2.2 17.5 1.0 CD A:GLU101 3.1 12.4 1.0 OE2 A:GLU101 3.4 12.5 1.0 HB2 A:ASP127 3.6 27.7 1.0 O A:HOH373 3.9 18.1 1.0 H A:ASP127 3.9 21.6 1.0 HB3 A:PRO126 4.1 16.9 1.0 O A:HOH316 4.1 36.4 1.0 O A:ASP127 4.4 20.0 1.0 CG A:GLU101 4.5 13.2 1.0 HG3 A:GLU101 4.5 15.9 1.0 CB A:ASP127 4.5 23.1 1.0 O A:HOH446 4.6 44.7 1.0 N A:ASP127 4.6 18.0 1.0 HG2 A:GLU101 4.8 15.9 1.0 HA A:PRO126 4.9 15.2 1.0 O A:HOH428 4.9 41.1 1.0 CB A:PRO126 5.0 14.1 1.0

Magnesium binding site 2 out of 4 in the E. Coli Dhfr Complex Modeled with Three Ligand States


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of E. Coli Dhfr Complex Modeled with Three Ligand States within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg205 b:16.0 occ:1.00 O A:HOH370 2.3 12.9 1.0 OE2 A:GLU101 2.4 12.5 1.0 O A:HOH457 2.5 29.8 1.0 HB2 A:GLU101 3.1 14.5 1.0 CD A:GLU101 3.3 12.4 1.0 HA A:PRO126 3.4 15.2 1.0 HG2 A:GLU101 3.7 15.9 1.0 CG A:GLU101 3.8 13.2 1.0 CB A:GLU101 3.9 12.1 1.0 O A:HOH336 3.9 17.5 1.0 HG3 A:PRO126 4.0 21.6 1.0 CA A:PRO126 4.3 12.7 1.0 HB3 A:PRO126 4.3 16.9 1.0 OE1 A:GLU101 4.3 12.6 1.0 HB3 A:GLU101 4.4 14.5 1.0 O A:GLY97 4.4 11.5 1.0 O A:HIS124 4.5 18.1 1.0 CB A:PRO126 4.6 14.1 1.0 N A:PRO126 4.6 12.2 1.0 CG A:PRO126 4.7 18.0 1.0 O A:HOH427 4.7 23.8 1.0 HG3 A:GLU101 4.8 15.9 1.0 HA A:GLU101 4.8 11.5 1.0 H A:ASP127 4.8 21.6 1.0 HA A:ARG98 4.9 15.5 1.0 HD3 A:PRO126 4.9 14.9 1.0 HB2 A:HIS124 4.9 20.7 1.0 CA A:GLU101 4.9 9.6 1.0

Magnesium binding site 3 out of 4 in the E. Coli Dhfr Complex Modeled with Three Ligand States


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of E. Coli Dhfr Complex Modeled with Three Ligand States within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg206 b:32.9 occ:1.00 O A:HOH415 2.0 26.4 1.0 O A:HOH380 2.0 32.6 1.0 O A:HOH443 2.1 34.0 1.0 O A:HOH486 2.1 40.8 1.0 NE2 A:HIS160 2.2 24.1 1.0 O A:HOH326 2.3 34.8 1.0 CD2 A:HIS160 3.1 26.2 1.0 HD2 A:HIS160 3.2 31.4 1.0 CE1 A:HIS160 3.2 23.3 1.0 HE1 A:HIS160 3.4 27.9 1.0 CG A:HIS160 4.2 21.4 1.0 ND1 A:HIS160 4.3 29.5 1.0 O A:ASP131 4.3 22.9 1.0 HB3 A:ARG159 4.7 20.4 1.0 O A:HOH320 4.7 38.8 1.0 OD2 A:ASP131 4.7 51.5 1.0 HB2 A:ARG159 4.8 20.4 1.0

Magnesium binding site 4 out of 4 in the E. Coli Dhfr Complex Modeled with Three Ligand States


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of E. Coli Dhfr Complex Modeled with Three Ligand States within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg207 b:40.5 occ:1.00 O A:HOH341 2.1 39.8 1.0 OD2 A:ASP70 2.1 28.3 1.0 O A:HOH392 2.1 37.5 1.0 O A:HOH385 2.3 37.1 1.0 CG A:ASP70 3.1 23.9 1.0 OD1 A:ASP70 3.5 32.9 1.0 O A:THR68 4.0 32.9 1.0 HA A:ASP70 4.1 16.9 1.0 CB A:ASP70 4.4 18.4 1.0 HB3 A:ASP70 4.6 22.1 1.0 CA A:ASP70 4.7 14.0 1.0 O A:HOH494 4.9 26.1 1.0

H.Cao, J.Skolnick. Time-Resolved X-Ray Crystallography Capture of A Slow Reaction Tetrahydrofolate Intermediate. Struct Dyn. V. 6 24701 2019.
ISSN: ESSN 2329-7778
PubMed: 30868089
DOI: 10.1063/1.5086436