Magnesium in PDB 5zlp: Crystal Structure of Glutamine Synthetase From Helicobacter Pylori

All present enzymatic activity of Crystal Structure of Glutamine Synthetase From Helicobacter Pylori:
6.3.1.2;

The structure of Crystal Structure of Glutamine Synthetase From Helicobacter Pylori, PDB code: 5zlp was solved by H.K.Joo, J.Y.Lee, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.26 / 2.93
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	234.409, 135.167, 203.080, 90.00, 91.61, 90.00
R / Rfree (%)	16.8 / 24.6

The binding sites of Magnesium atom in the Crystal Structure of Glutamine Synthetase From Helicobacter Pylori (pdb code 5zlp). 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 Glutamine Synthetase From Helicobacter Pylori, PDB code: 5zlp:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Crystal Structure of Glutamine Synthetase From Helicobacter Pylori


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 Glutamine Synthetase From Helicobacter Pylori within 5.0Å range: probe atom residue distance (Å) B Occ J:Mg503 b:41.9 occ:1.00 OE2 J:GLU230 2.0 36.3 1.0 OE2 J:GLU141 2.5 26.8 1.0 OE2 J:GLU223 2.5 30.8 1.0 OEA J:PPQ502 2.6 36.0 0.8 CD J:GLU230 2.9 37.6 1.0 OE1 J:GLU230 3.2 45.3 1.0 CD J:GLU223 3.3 29.8 1.0 PDP J:PPQ502 3.6 45.5 0.8 CD J:GLU141 3.7 28.3 1.0 CEP J:PPQ502 3.9 28.7 0.8 OE1 J:GLU223 3.9 33.4 1.0 OE2 J:GLU139 3.9 35.0 1.0 CE1 J:HIS279 4.0 27.0 1.0 ND1 J:HIS279 4.2 20.6 1.0 NE2 J:HIS221 4.2 22.9 1.0 CG J:GLU223 4.2 19.6 1.0 CGP J:PPQ502 4.3 35.4 0.8 CG J:GLU230 4.3 21.2 1.0 CBP J:PPQ502 4.4 31.1 0.8 CD J:GLU139 4.4 42.1 1.0 CG J:GLU141 4.4 23.2 1.0 CE1 J:HIS221 4.5 24.4 1.0 OE1 J:GLU141 4.5 29.6 1.0 OE1 J:GLU139 4.5 51.8 1.0 O J:HOH601 4.6 39.6 1.0 CB J:GLU230 4.8 17.9 1.0 OEB J:PPQ502 4.9 37.2 0.8

Magnesium binding site 2 out of 4 in the Crystal Structure of Glutamine Synthetase From Helicobacter Pylori


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 Glutamine Synthetase From Helicobacter Pylori within 5.0Å range: probe atom residue distance (Å) B Occ L:Mg502 b:48.4 occ:1.00 OE1 L:GLU230 2.4 40.0 1.0 OE2 L:GLU223 2.5 31.6 1.0 OE1 L:GLU141 2.5 30.9 1.0 OEB L:P3P501 2.7 45.9 1.0 O15 L:P3P501 2.7 58.6 1.0 CD L:GLU230 3.0 48.8 1.0 OE2 L:GLU230 3.0 57.1 1.0 P12 L:P3P501 3.2 78.6 1.0 CD L:GLU223 3.4 31.9 1.0 CD L:GLU141 3.4 25.9 1.0 O14 L:P3P501 3.7 47.9 1.0 OE1 L:GLU139 3.7 43.0 1.0 PDP L:P3P501 3.8 51.8 1.0 CGP L:P3P501 3.9 41.5 1.0 OE1 L:GLU223 3.9 39.2 1.0 ND1 L:HIS279 4.0 30.5 1.0 CG L:GLU141 4.0 27.2 1.0 CE1 L:HIS279 4.0 36.4 1.0 CG L:GLU230 4.3 29.4 1.0 OE2 L:GLU141 4.3 26.5 1.0 CE1 L:HIS221 4.4 27.2 1.0 MG L:MG504 4.4 53.7 1.0 CG L:GLU223 4.4 26.5 1.0 CEP L:P3P501 4.5 43.2 1.0 O13 L:P3P501 4.6 68.5 1.0 CB L:GLU230 4.6 24.5 1.0 NE2 L:HIS221 4.9 24.6 1.0 CBP L:P3P501 4.9 34.9 1.0 CD L:GLU139 5.0 41.3 1.0

Magnesium binding site 3 out of 4 in the Crystal Structure of Glutamine Synthetase From Helicobacter Pylori


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 Glutamine Synthetase From Helicobacter Pylori within 5.0Å range: probe atom residue distance (Å) B Occ L:Mg504 b:53.7 occ:1.00 OE2 L:GLU230 2.5 57.1 1.0 O2B L:ADP503 3.0 80.2 1.0 O15 L:P3P501 3.0 58.6 1.0 NE2 L:HIS221 3.2 24.6 1.0 O2A L:ADP503 3.7 70.8 1.0 CD L:GLU230 3.8 48.8 1.0 CE1 L:HIS221 4.0 27.2 1.0 CG1 L:VAL219 4.1 25.1 1.0 CD2 L:HIS221 4.2 26.7 1.0 PB L:ADP503 4.2 85.1 1.0 OE1 L:GLU139 4.2 43.0 1.0 O1B L:ADP503 4.3 77.9 1.0 MG L:MG502 4.4 48.4 1.0 P12 L:P3P501 4.4 78.6 1.0 CD L:GLU139 4.6 41.3 1.0 OE1 L:GLU230 4.6 40.0 1.0 CG L:GLU230 4.6 29.4 1.0 OE2 L:GLU139 4.7 47.4 1.0 O14 L:P3P501 4.9 47.9 1.0 O3A L:ADP503 5.0 61.8 1.0 PA L:ADP503 5.0 70.8 1.0

Magnesium binding site 4 out of 4 in the Crystal Structure of Glutamine Synthetase From Helicobacter Pylori


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 Glutamine Synthetase From Helicobacter Pylori within 5.0Å range: probe atom residue distance (Å) B Occ I:Mg503 b:44.2 occ:1.00 OE2 I:GLU230 1.6 48.1 1.0 OEA I:PPQ502 1.8 51.2 1.0 OE2 I:GLU223 2.5 27.9 1.0 CD I:GLU230 2.6 50.0 1.0 OE2 I:GLU141 2.8 24.4 1.0 OE1 I:GLU230 3.0 50.8 1.0 PDP I:PPQ502 3.2 58.6 1.0 CD I:GLU223 3.4 31.8 1.0 OE1 I:GLU139 3.8 39.1 1.0 CD I:GLU141 3.8 28.2 1.0 CG I:GLU230 3.8 28.8 1.0 OEB I:PPQ502 3.9 47.6 1.0 CEP I:PPQ502 4.0 40.6 1.0 CG I:GLU141 4.0 28.9 1.0 OE1 I:GLU223 4.1 34.2 1.0 NE2 I:HIS221 4.3 25.6 1.0 CE1 I:HIS221 4.3 27.7 1.0 CG I:GLU223 4.4 27.8 1.0 CB I:GLU230 4.4 24.2 1.0 CE1 I:HIS279 4.5 26.5 1.0 CBP I:PPQ502 4.5 36.4 1.0 ND1 I:HIS279 4.5 22.1 1.0 CGP I:PPQ502 4.5 35.1 1.0 CD I:GLU139 4.7 47.1 1.0 OE1 I:GLU141 5.0 22.3 1.0

H.K.Joo, Y.W.Park, Y.Y.Jang, J.Y.Lee. Structural Analysis of Glutamine Synthetase From Helicobacter Pylori. Sci Rep V. 8 11657 2018.
ISSN: ESSN 2045-2322
PubMed: 30076387
DOI: 10.1038/S41598-018-30191-5