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Magnesium in PDB 8ooo: Glutamine Synthetase From Methanothermococcus Thermolithotrophicus in Complex with 2-Oxoglutarate and Mgatp at 2.15 A Resolution

Enzymatic activity of Glutamine Synthetase From Methanothermococcus Thermolithotrophicus in Complex with 2-Oxoglutarate and Mgatp at 2.15 A Resolution

All present enzymatic activity of Glutamine Synthetase From Methanothermococcus Thermolithotrophicus in Complex with 2-Oxoglutarate and Mgatp at 2.15 A Resolution:
6.3.1.2;

Protein crystallography data

The structure of Glutamine Synthetase From Methanothermococcus Thermolithotrophicus in Complex with 2-Oxoglutarate and Mgatp at 2.15 A Resolution, PDB code: 8ooo was solved by M.-C.Mueller, T.Wagner, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 42.88 / 2.15
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 112.337, 131.773, 131.507, 60.04, 87.72, 67.34
R / Rfree (%) 18.2 / 21.4

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Glutamine Synthetase From Methanothermococcus Thermolithotrophicus in Complex with 2-Oxoglutarate and Mgatp at 2.15 A Resolution (pdb code 8ooo). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Glutamine Synthetase From Methanothermococcus Thermolithotrophicus in Complex with 2-Oxoglutarate and Mgatp at 2.15 A Resolution, PDB code: 8ooo:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 8ooo

Go back to Magnesium Binding Sites List in 8ooo
Magnesium binding site 1 out of 3 in the Glutamine Synthetase From Methanothermococcus Thermolithotrophicus in Complex with 2-Oxoglutarate and Mgatp at 2.15 A Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Glutamine Synthetase From Methanothermococcus Thermolithotrophicus in Complex with 2-Oxoglutarate and Mgatp at 2.15 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg505

b:50.0
occ:0.50
 O H:HOH921 2.8 57.3 1.0
OD2 B:ASP203 3.0 38.5 1.0
NE2 B:HIS192 3.0 24.7 1.0
O B:HOH651 3.0 36.8 1.0
O2G B:ATP506 3.1 64.2 1.0
OE2 B:GLU201 3.6 46.0 1.0
CD2 B:HIS192 3.7 23.5 1.0
CD B:GLU201 3.9 44.3 1.0
CE1 B:HIS192 4.0 25.1 1.0
CG B:ASP203 4.0 32.2 1.0
O1A B:ATP506 4.1 55.4 1.0
OE1 B:GLU201 4.2 48.4 1.0
PG B:ATP506 4.4 63.8 1.0
OD1 B:ASP203 4.4 33.4 1.0
OE2 B:GLU137 4.6 47.5 1.0
O1G B:ATP506 4.7 63.6 1.0
O2B B:ATP506 4.8 59.7 1.0
CG B:GLU201 4.8 37.7 1.0
CG B:HIS192 4.9 24.4 1.0

Magnesium binding site 2 out of 3 in 8ooo

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Magnesium binding site 2 out of 3 in the Glutamine Synthetase From Methanothermococcus Thermolithotrophicus in Complex with 2-Oxoglutarate and Mgatp at 2.15 A Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Glutamine Synthetase From Methanothermococcus Thermolithotrophicus in Complex with 2-Oxoglutarate and Mgatp at 2.15 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg602

b:50.4
occ:0.50
 O2G E:ATP604 2.6 66.9 1.0
OD2 E:ASP203 2.8 39.1 1.0
O D:HOH822 2.9 60.5 1.0
O E:HOH743 3.0 46.2 1.0
OE2 E:GLU201 3.4 44.2 1.0
O1A E:ATP604 3.6 58.2 1.0
NE2 E:HIS192 3.6 29.8 1.0
CG E:ASP203 3.9 33.6 1.0
CD E:GLU201 4.0 41.6 1.0
PG E:ATP604 4.0 66.3 1.0
OE2 E:GLU137 4.0 51.5 1.0
O2B E:ATP604 4.2 62.5 1.0
OE1 E:GLU201 4.3 45.4 1.0
OD1 E:ASP203 4.3 34.1 1.0
CD2 E:HIS192 4.4 27.9 1.0
O1G E:ATP604 4.4 66.3 1.0
CE1 E:HIS192 4.6 29.9 1.0
O3B E:ATP604 4.8 64.3 1.0
O3G E:ATP604 4.9 66.5 1.0
CD E:GLU137 5.0 46.7 1.0
CG E:GLU201 5.0 33.2 1.0

Magnesium binding site 3 out of 3 in 8ooo

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Magnesium binding site 3 out of 3 in the Glutamine Synthetase From Methanothermococcus Thermolithotrophicus in Complex with 2-Oxoglutarate and Mgatp at 2.15 A Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Glutamine Synthetase From Methanothermococcus Thermolithotrophicus in Complex with 2-Oxoglutarate and Mgatp at 2.15 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Mg502

b:31.7
occ:0.50
 O2G K:ATP504 2.2 67.0 1.0
OD2 K:ASP203 2.4 46.9 1.0
O1A K:ATP504 2.8 59.0 1.0
O I:HOH831 3.0 44.2 1.0
OE2 K:GLU137 3.0 52.5 1.0
OE2 K:GLU201 3.1 38.1 1.0
CG K:ASP203 3.4 42.6 1.0
PG K:ATP504 3.6 66.0 1.0
O K:HOH688 3.7 43.4 1.0
OD1 K:ASP203 3.8 44.9 1.0
O K:HOH670 3.8 43.6 1.0
O2B K:ATP504 3.9 63.5 1.0
CD K:GLU201 4.0 37.5 1.0
O1G K:ATP504 4.0 65.8 1.0
CD K:GLU137 4.1 46.2 1.0
PA K:ATP504 4.3 59.1 1.0
O3B K:ATP504 4.3 64.3 1.0
NE2 K:HIS192 4.4 30.4 1.0
OE1 K:GLU201 4.4 36.9 1.0
PB K:ATP504 4.6 62.6 1.0
O3G K:ATP504 4.6 66.0 1.0
OE1 K:GLU137 4.7 47.0 1.0
CB K:ASP203 4.7 33.5 1.0
O K:HOH757 4.8 52.6 1.0
O3A K:ATP504 4.9 61.0 1.0

Reference:

M.C.Muller, O.N.Lemaire, J.M.Kurth, C.U.Welte, T.Wagner. Differences in Regulation Mechanisms of Glutamine Synthetases From Methanogenic Archaea Unveiled By Structural Investigations. Commun Biol V. 7 111 2024.
ISSN: ESSN 2399-3642
PubMed: 38243071
DOI: 10.1038/S42003-023-05726-W
Page generated: Fri Oct 4 15:00:19 2024

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