Magnesium in PDB 6mr9: E. Coli Dhfr Complex with A Reaction Intermediate

All present enzymatic activity of E. Coli Dhfr Complex with A Reaction Intermediate:
1.5.1.3;

The structure of E. Coli Dhfr Complex with A Reaction Intermediate, PDB code: 6mr9 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 (%)	16.8 / 19.1

The structure of E. Coli Dhfr Complex with A Reaction Intermediate also contains other interesting chemical elements:

Chlorine

(Cl)

3 atoms

The binding sites of Magnesium atom in the E. Coli Dhfr Complex with A Reaction Intermediate (pdb code 6mr9). 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 with A Reaction Intermediate, PDB code: 6mr9:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the E. Coli Dhfr Complex with A Reaction Intermediate


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 with A Reaction Intermediate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg204 b:17.3 occ:1.00 O A:HOH386 2.1 17.7 1.0 OE1 A:GLU101 2.1 12.5 1.0 O A:HOH334 2.2 17.5 1.0 CD A:GLU101 3.1 12.3 1.0 OE2 A:GLU101 3.4 12.6 1.0 HB2 A:ASP127 3.6 27.8 1.0 O A:HOH371 3.9 18.1 1.0 H A:ASP127 3.9 21.5 1.0 HB3 A:PRO126 4.1 16.8 1.0 O A:HOH313 4.1 35.8 1.0 O A:ASP127 4.4 20.4 1.0 CG A:GLU101 4.5 13.1 1.0 HG3 A:GLU101 4.5 15.7 1.0 CB A:ASP127 4.5 23.2 1.0 O A:HOH445 4.6 44.0 1.0 N A:ASP127 4.6 17.9 1.0 HG2 A:GLU101 4.8 15.7 1.0 HA A:PRO126 4.9 15.2 1.0 O A:HOH427 4.9 41.6 1.0 CB A:PRO126 5.0 14.0 1.0

Magnesium binding site 2 out of 4 in the E. Coli Dhfr Complex with A Reaction Intermediate


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 with A Reaction Intermediate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg205 b:15.9 occ:1.00 O A:HOH368 2.3 12.9 1.0 OE2 A:GLU101 2.4 12.6 1.0 O A:HOH456 2.5 30.3 1.0 HB2 A:GLU101 3.1 14.5 1.0 CD A:GLU101 3.3 12.3 1.0 HA A:PRO126 3.4 15.2 1.0 HG2 A:GLU101 3.7 15.7 1.0 CG A:GLU101 3.8 13.1 1.0 CB A:GLU101 3.9 12.1 1.0 O A:HOH334 3.9 17.5 1.0 HG3 A:PRO126 4.0 22.2 1.0 CA A:PRO126 4.3 12.6 1.0 HB3 A:PRO126 4.3 16.8 1.0 OE1 A:GLU101 4.3 12.5 1.0 HB3 A:GLU101 4.4 14.5 1.0 O A:GLY97 4.4 11.4 1.0 O A:HIS124 4.5 18.0 1.0 CB A:PRO126 4.6 14.0 1.0 N A:PRO126 4.6 12.0 1.0 CG A:PRO126 4.7 18.5 1.0 O A:HOH426 4.7 23.5 1.0 HG3 A:GLU101 4.8 15.7 1.0 HA A:GLU101 4.8 11.6 1.0 H A:ASP127 4.8 21.5 1.0 HA A:ARG98 4.9 15.5 1.0 HD3 A:PRO126 4.9 15.0 1.0 HB2 A:HIS124 4.9 20.9 1.0 CA A:GLU101 4.9 9.7 1.0

Magnesium binding site 3 out of 4 in the E. Coli Dhfr Complex with A Reaction Intermediate


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 with A Reaction Intermediate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg206 b:30.5 occ:1.00 O A:HOH414 2.0 26.3 1.0 O A:HOH378 2.0 33.1 1.0 O A:HOH442 2.1 33.4 1.0 O A:HOH486 2.1 40.2 1.0 NE2 A:HIS160 2.2 24.4 1.0 O A:HOH323 2.3 34.7 1.0 CD2 A:HIS160 3.1 25.9 1.0 HD2 A:HIS160 3.2 31.1 1.0 CE1 A:HIS160 3.2 22.9 1.0 HE1 A:HIS160 3.4 27.5 1.0 CG A:HIS160 4.2 21.8 1.0 ND1 A:HIS160 4.3 29.0 1.0 O A:ASP131 4.3 22.6 1.0 HB3 A:ARG159 4.7 20.6 1.0 O A:HOH317 4.7 38.7 1.0 OD2 A:ASP131 4.7 47.6 1.0 HB2 A:ARG159 4.8 20.6 1.0

Magnesium binding site 4 out of 4 in the E. Coli Dhfr Complex with A Reaction Intermediate


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 with A Reaction Intermediate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg207 b:36.5 occ:1.00 O A:HOH339 2.1 39.9 1.0 OD2 A:ASP70 2.1 28.4 1.0 O A:HOH390 2.1 38.5 1.0 O A:HOH383 2.3 37.3 1.0 CG A:ASP70 3.1 22.6 1.0 OD1 A:ASP70 3.5 33.3 1.0 O A:THR68 4.0 31.9 1.0 HA A:ASP70 4.1 16.6 1.0 CB A:ASP70 4.4 18.5 1.0 HB3 A:ASP70 4.6 22.2 1.0 CA A:ASP70 4.7 13.8 1.0 O A:HOH493 4.9 26.5 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