Chlorine 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:

Magnesium

(Mg)

4 atoms

The binding sites of Chlorine 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 Chlorine atom.
In total 3 binding sites of Chlorine where determined in the E. Coli Dhfr Complex with A Reaction Intermediate, PDB code: 6mr9:
Jump to Chlorine binding site number: 1; 2; 3;

Chlorine binding site 1 out of 3 in the E. Coli Dhfr Complex with A Reaction Intermediate


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl 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:Cl201 b:15.7 occ:1.00 H A:GLY96 2.3 15.0 1.0 H A:THR46 2.5 15.4 1.0 HG1 A:THR46 2.6 18.8 1.0 HB3 A:HIS45 2.7 30.4 0.5 HA3 A:GLY43 2.7 11.9 1.0 HB3 A:HIS45 2.7 30.2 0.5 O A:HOH431 3.0 21.9 1.0 N A:GLY96 3.2 12.5 1.0 H A:HIS45 3.2 18.6 1.0 N A:THR46 3.3 12.8 1.0 OG1 A:THR46 3.3 15.6 1.0 O A:HOH420 3.4 30.7 1.0 H A:GLY43 3.4 13.4 1.0 CA A:GLY43 3.4 10.0 1.0 HA3 A:GLY96 3.4 12.4 1.0 C A:GLY43 3.5 13.0 1.0 CB A:HIS45 3.5 25.3 0.5 HB A:THR46 3.6 15.3 1.0 CB A:HIS45 3.6 25.1 0.5 N A:HIS45 3.7 15.5 1.0 O A:GLY43 3.8 12.3 1.0 HB2 A:HIS45 3.8 30.4 0.5 N A:GLY43 3.8 11.1 1.0 CA A:GLY96 3.8 10.3 1.0 O A:HOH447 3.9 28.9 1.0 CB A:THR46 3.9 12.8 1.0 HB2 A:HIS45 3.9 30.2 0.5 CA A:HIS45 3.9 16.9 0.5 CA A:HIS45 3.9 17.0 0.5 N A:ARG44 4.0 13.9 1.0 C A:HIS45 4.1 16.9 1.0 C A:GLY95 4.1 11.2 1.0 O A:HOH421 4.1 27.3 1.0 O A:GLY95 4.1 12.4 1.0 CA A:THR46 4.2 12.6 1.0 H A:ARG44 4.2 16.7 1.0 O A:HOH450 4.2 28.7 1.0 HG23 A:VAL99 4.2 19.1 1.0 HA2 A:GLY43 4.2 11.9 1.0 HG21 A:VAL99 4.3 19.1 1.0 HD1 A:HIS45 4.4 38.9 0.5 C A:ARG44 4.6 15.2 1.0 HA2 A:GLY96 4.6 12.4 1.0 HA A:THR46 4.6 15.2 1.0 CG A:HIS45 4.6 27.0 0.5 HE1 A:MET16 4.7 72.1 1.0 C A:GLY96 4.7 10.5 1.0 CG2 A:VAL99 4.7 15.9 1.0 CG A:HIS45 4.7 26.8 0.5 HB A:VAL99 4.7 15.7 1.0 ND1 A:HIS45 4.9 32.4 0.5 HA A:HIS45 4.9 20.2 0.5 H A:TRP47 4.9 14.6 1.0 CA A:ARG44 4.9 13.5 1.0 O A:HOH392 4.9 29.6 1.0 H A:GLY97 5.0 16.1 1.0 H A:VAL99 5.0 12.9 1.0

Chlorine binding site 2 out of 3 in the E. Coli Dhfr Complex with A Reaction Intermediate


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl 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:Cl202 b:27.0 occ:1.00 H A:ALA145 2.3 18.1 1.0 HB2 A:ASP144 2.6 23.3 1.0 HB1 A:ALA145 3.1 24.8 1.0 O A:HOH367 3.1 19.2 1.0 N A:ALA145 3.2 15.1 1.0 HB2 A:ALA145 3.3 24.8 1.0 CB A:ASP144 3.5 19.4 1.0 CB A:ALA145 3.6 20.7 1.0 HA A:ASP144 3.9 19.4 1.0 HB3 A:ASP144 4.0 23.3 1.0 CA A:ALA145 4.0 19.9 1.0 CA A:ASP144 4.0 16.1 1.0 C A:ASP144 4.1 16.4 1.0 HB3 A:ALA145 4.5 24.8 1.0 HA A:ALA145 4.5 23.9 1.0 CG A:ASP144 4.5 23.9 1.0 H A:GLN146 4.8 19.9 1.0 OE1 A:GLN146 4.8 25.6 1.0 OD1 A:ASP144 5.0 19.4 1.0

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


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl 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:Cl203 b:32.2 occ:1.00 HE A:ARG33 2.3 43.2 1.0 HA A:TRP30 2.9 14.4 1.0 HH21 A:ARG33 3.0 48.0 1.0 O A:HOH366 3.1 20.9 1.0 O A:HOH452 3.1 47.3 1.0 NE A:ARG33 3.2 36.0 1.0 HE3 A:TRP30 3.2 16.4 1.0 HB2 A:TRP30 3.3 14.9 1.0 CA A:TRP30 3.7 12.0 1.0 NH2 A:ARG33 3.7 40.0 1.0 HD3 A:ARG33 3.8 28.1 1.0 CZ A:ARG33 3.9 49.2 1.0 CB A:TRP30 4.0 12.4 1.0 N A:TRP30 4.0 12.3 1.0 CE3 A:TRP30 4.1 13.6 1.0 CD A:ARG33 4.1 23.4 1.0 HB3 A:ARG33 4.2 20.6 1.0 H A:TRP30 4.3 14.8 1.0 O A:HOH474 4.4 31.4 1.0 C A:ALA29 4.4 12.5 1.0 HB2 A:ARG33 4.4 20.6 1.0 O A:ALA29 4.4 13.6 1.0 HH22 A:ARG33 4.5 48.0 1.0 HB1 A:ALA29 4.6 19.0 1.0 O A:HOH479 4.6 44.7 1.0 HB3 A:TRP30 4.7 14.9 1.0 CB A:ARG33 4.7 17.1 1.0 HB2 A:ALA29 4.7 19.0 1.0 O A:HOH494 4.8 35.3 1.0 HD2 A:ARG33 4.8 28.1 1.0 CD2 A:TRP30 4.8 12.2 1.0 HE2 A:PHE153 4.8 16.8 1.0 CG A:TRP30 4.8 12.2 1.0 O A:ALA26 5.0 13.1 1.0 C A:TRP30 5.0 11.2 1.0 HZ3 A:TRP30 5.0 16.3 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