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

Enzymatic activity of Crystal Structure of E Coli Pepq

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

Protein crystallography data

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

Magnesium Binding Sites:

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 4qr8

Go back to Magnesium Binding Sites List in 4qr8
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 4qr8

Go back to Magnesium Binding Sites List in 4qr8
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 4qr8

Go back to Magnesium Binding Sites List in 4qr8
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 4qr8

Go back to Magnesium Binding Sites List in 4qr8
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

Reference:

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
Page generated: Mon Dec 14 19:24:19 2020

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