Magnesium in PDB 4qr8: Crystal Structure of E Coli Pepq

All present enzymatic activity of Crystal Structure of E Coli Pepq:
3.4.13.9;

The structure of Crystal Structure of E Coli Pepq, PDB code: 4qr8 was solved by L.Pingwei, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.45 / 2.00
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	72.569, 97.440, 126.936, 90.00, 90.00, 90.00
R / Rfree (%)	17.3 / 21.1

The binding sites of Magnesium atom in the Crystal Structure of E Coli Pepq (pdb code 4qr8). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of E Coli Pepq, PDB code: 4qr8:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Crystal Structure of E Coli Pepq


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 E Coli Pepq within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg501 b:11.1 occ:1.00 OD2 A:ASP257 2.2 21.3 1.0 OE2 A:GLU384 2.3 20.8 1.0 OE2 A:GLU423 2.3 14.7 1.0 NE2 A:HIS339 2.4 19.5 1.0 CD A:GLU384 3.0 20.1 1.0 MG A:MG502 3.0 27.6 1.0 CE1 A:HIS339 3.1 17.8 1.0 OE1 A:GLU384 3.2 25.1 1.0 CG A:ASP257 3.3 20.1 1.0 CD A:GLU423 3.3 15.5 1.0 CD2 A:HIS339 3.5 16.5 1.0 OE1 A:GLU423 3.6 18.4 1.0 OG1 A:THR382 3.8 10.0 1.0 O A:HOH994 3.8 35.9 1.0 CG2 A:THR382 3.9 7.8 1.0 OD1 A:ASP257 3.9 21.1 1.0 O A:HOH1174 4.0 51.1 1.0 CB A:THR382 4.1 9.4 1.0 ND1 A:HIS339 4.3 18.1 1.0 CG A:GLU384 4.3 18.0 1.0 CB A:ASP257 4.4 14.9 1.0 CG A:HIS339 4.5 17.6 1.0 CG A:GLU423 4.6 7.9 1.0 CB A:GLU384 5.0 13.2 1.0

Magnesium binding site 2 out of 4 in the Crystal Structure of E Coli Pepq


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 E Coli Pepq within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:27.6 occ:1.00 OE1 A:GLU423 2.3 18.4 1.0 O A:HOH1174 2.3 51.1 1.0 OD1 A:ASP257 2.4 21.1 1.0 OD2 A:ASP246 2.4 16.7 1.0 OD1 A:ASP246 2.5 14.5 1.0 CG A:ASP246 2.8 16.9 1.0 OD2 A:ASP257 2.8 21.3 1.0 CG A:ASP257 2.9 20.1 1.0 MG A:MG501 3.0 11.1 1.0 CD A:GLU423 3.2 15.5 1.0 OE2 A:GLU423 3.3 14.7 1.0 OG1 A:THR259 3.6 9.4 1.0 OE1 A:GLU384 3.8 25.1 1.0 OH A:TYR214 4.0 23.9 1.0 CB A:ASP246 4.3 11.8 1.0 CB A:ASP257 4.4 14.9 1.0 CD A:GLU384 4.4 20.1 1.0 CZ A:TYR214 4.5 30.1 1.0 OE2 A:GLU384 4.5 20.8 1.0 CG A:GLU423 4.6 7.9 1.0 CE1 A:TYR214 4.6 31.4 1.0 O A:ASP257 4.6 15.1 1.0 C A:ASP257 4.7 14.8 1.0 O A:HOH994 4.7 35.9 1.0 NE A:ARG421 4.8 10.2 1.0 O A:LEU258 4.9 14.6 1.0 CB A:THR259 5.0 9.9 1.0 CB A:GLU423 5.0 8.5 1.0

Magnesium binding site 3 out of 4 in the Crystal Structure of E Coli Pepq


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of E Coli Pepq within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg501 b:14.4 occ:1.00 OD2 B:ASP257 2.1 19.7 1.0 OE2 B:GLU384 2.3 24.6 1.0 OE2 B:GLU423 2.4 17.7 1.0 NE2 B:HIS339 2.5 15.5 1.0 MG B:MG502 2.8 25.3 1.0 CD B:GLU384 3.0 25.9 1.0 OE1 B:GLU384 3.2 30.4 1.0 CG B:ASP257 3.3 17.9 1.0 CE1 B:HIS339 3.4 15.5 1.0 CD B:GLU423 3.4 18.9 1.0 CD2 B:HIS339 3.5 13.6 1.0 OE1 B:GLU423 3.6 19.6 1.0 O B:HOH1124 3.7 43.9 1.0 OD1 B:ASP257 3.9 17.5 1.0 OG1 B:THR382 3.9 13.6 1.0 CG2 B:THR382 4.0 11.4 1.0 CB B:THR382 4.2 12.8 1.0 CG B:GLU384 4.3 22.4 1.0 CB B:ASP257 4.4 12.5 1.0 ND1 B:HIS339 4.5 14.3 1.0 CG B:HIS339 4.6 13.5 1.0 CG B:GLU423 4.7 12.9 1.0 CB B:GLU384 4.9 16.9 1.0

Magnesium binding site 4 out of 4 in the Crystal Structure of E Coli Pepq


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of E Coli Pepq within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg502 b:25.3 occ:1.00 OD2 B:ASP246 2.4 13.3 1.0 OD1 B:ASP257 2.5 17.5 1.0 OE1 B:GLU423 2.5 19.6 1.0 OD1 B:ASP246 2.7 13.5 1.0 OD2 B:ASP257 2.8 19.7 1.0 MG B:MG501 2.8 14.4 1.0 CG B:ASP246 2.9 13.8 1.0 CG B:ASP257 3.0 17.9 1.0 CD B:GLU423 3.3 18.9 1.0 OE2 B:GLU423 3.4 17.7 1.0 O B:HOH1106 3.6 40.5 1.0 OG1 B:THR259 3.8 11.4 1.0 OE1 B:GLU384 3.8 30.4 1.0 OH B:TYR214 4.1 29.7 1.0 O B:HOH1124 4.3 43.9 1.0 CB B:ASP246 4.4 9.1 1.0 CD B:GLU384 4.4 25.9 1.0 CB B:ASP257 4.5 12.5 1.0 CZ B:TYR214 4.5 35.1 1.0 OE2 B:GLU384 4.5 24.6 1.0 CE1 B:TYR214 4.5 36.9 1.0 NE B:ARG421 4.8 13.9 1.0 CG B:GLU423 4.8 12.9 1.0 O B:ASP257 4.8 13.1 1.0 C B:ASP257 4.9 11.3 1.0 NH2 B:ARG421 5.0 14.8 1.0

J.Weaver, T.Watts, P.Li, H.S.Rye. Structural Basis of Substrate Selectivity of E. Coli Prolidase. Plos One V. 9 11531 2014.
ISSN: ESSN 1932-6203
PubMed: 25354344
DOI: 10.1371/JOURNAL.PONE.0111531