Magnesium in PDB 8q1f: D10N,P146A Variant of Beta-Phosphoglucomutase From Lactococcus Lactis in Complex with Native Beta-Glucose 1,6-Bisphosphate Intermediate

The structure of D10N,P146A Variant of Beta-Phosphoglucomutase From Lactococcus Lactis in Complex with Native Beta-Glucose 1,6-Bisphosphate Intermediate, PDB code: 8q1f was solved by F.A.Cruz-Navarrete, N.J.Baxter, A.J.Flinders, A.Buzoianu, M.J.Cliff, P.J.Baker, J.P.Waltho, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.83 / 1.01
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	32.023, 79.663, 79.848, 90, 97.61, 90
R / Rfree (%)	11.5 / 13.5

The structure of D10N,P146A Variant of Beta-Phosphoglucomutase From Lactococcus Lactis in Complex with Native Beta-Glucose 1,6-Bisphosphate Intermediate also contains other interesting chemical elements:

Sodium

(Na)

1 atom

The binding sites of Magnesium atom in the D10N,P146A Variant of Beta-Phosphoglucomutase From Lactococcus Lactis in Complex with Native Beta-Glucose 1,6-Bisphosphate Intermediate (pdb code 8q1f). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the D10N,P146A Variant of Beta-Phosphoglucomutase From Lactococcus Lactis in Complex with Native Beta-Glucose 1,6-Bisphosphate Intermediate, PDB code: 8q1f:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in the D10N,P146A Variant of Beta-Phosphoglucomutase From Lactococcus Lactis in Complex with Native Beta-Glucose 1,6-Bisphosphate Intermediate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of D10N,P146A Variant of Beta-Phosphoglucomutase From Lactococcus Lactis in Complex with Native Beta-Glucose 1,6-Bisphosphate Intermediate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg302 b:7.8 occ:1.00 OD1 A:ASP8 2.0 7.7 1.0 O A:HOH499 2.0 9.2 1.0 O A:HOH500 2.1 8.2 1.0 O3X A:B16301 2.1 7.9 1.0 OE1 A:GLU169 2.2 8.1 1.0 O A:HOH404 2.2 7.4 1.0 CG A:ASP8 3.0 7.4 1.0 CD A:GLU169 3.1 7.5 1.0 P' A:B16301 3.2 7.2 1.0 O2X A:B16301 3.5 7.0 1.0 OE2 A:GLU169 3.5 9.4 1.0 OD2 A:ASP8 3.6 8.5 1.0 MG A:MG303 3.7 7.6 1.0 O A:HOH613 3.9 11.1 1.0 O1X A:B16301 3.9 6.7 1.0 CB A:ASP8 4.2 6.5 1.0 N A:ALA115 4.3 7.5 1.0 O A:GLY46 4.4 14.8 1.0 O A:ALA113 4.4 8.2 1.0 CG A:GLU169 4.5 7.6 1.0 O A:HOH543 4.5 12.5 1.0 CA A:GLY46 4.5 12.7 1.0 O1 A:B16301 4.6 7.1 1.0 OG A:SER171 4.7 11.5 1.0 CA A:SER114 4.7 6.9 1.0 CB A:ALA115 4.8 8.5 1.0 CA A:ASP8 4.8 6.5 1.0 OD1 A:ASP170 4.9 7.7 1.0 C A:SER114 4.9 7.0 1.0 C A:GLY46 5.0 14.3 1.0

Magnesium binding site 2 out of 6 in the D10N,P146A Variant of Beta-Phosphoglucomutase From Lactococcus Lactis in Complex with Native Beta-Glucose 1,6-Bisphosphate Intermediate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of D10N,P146A Variant of Beta-Phosphoglucomutase From Lactococcus Lactis in Complex with Native Beta-Glucose 1,6-Bisphosphate Intermediate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg303 b:7.6 occ:1.00 OD2 A:ASP8 2.0 8.5 1.0 O A:ASN10 2.0 8.4 1.0 O2X A:B16301 2.0 7.0 1.0 O A:HOH433 2.1 8.3 1.0 OD1 A:ASP170 2.1 7.7 1.0 O A:HOH404 2.1 7.4 1.0 CG A:ASP8 3.0 7.4 1.0 CG A:ASP170 3.1 6.9 1.0 C A:ASN10 3.2 6.8 1.0 P' A:B16301 3.3 7.2 1.0 OD1 A:ASP8 3.4 7.7 1.0 OD2 A:ASP170 3.5 10.1 1.0 MG A:MG302 3.7 7.8 1.0 OE2 A:GLU169 3.7 9.4 1.0 O3X A:B16301 3.9 7.9 1.0 O1X A:B16301 3.9 6.7 1.0 CA A:ASN10 3.9 6.6 1.0 OG A:SER171 4.0 11.5 1.0 N A:ASN10 4.0 6.9 1.0 O2 A:B16301 4.1 10.3 1.0 CB A:ASN10 4.1 7.5 1.0 N A:GLY11 4.3 7.7 1.0 CB A:ASP8 4.3 6.5 1.0 O A:HOH539 4.4 10.6 1.0 CB A:ASP170 4.4 8.0 1.0 CD A:GLU169 4.5 7.5 1.0 O1 A:B16301 4.5 7.1 1.0 CA A:GLY11 4.5 7.8 1.0 OE1 A:GLU169 4.6 8.1 1.0 CA A:GLY46 4.7 12.7 1.0 N A:ASP170 4.7 6.7 1.0 C A:LEU9 4.8 6.4 1.0 O A:HOH499 4.9 9.2 1.0 N A:GLY46 4.9 13.9 1.0 N A:SER171 4.9 8.5 1.0

Magnesium binding site 3 out of 6 in the D10N,P146A Variant of Beta-Phosphoglucomutase From Lactococcus Lactis in Complex with Native Beta-Glucose 1,6-Bisphosphate Intermediate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of D10N,P146A Variant of Beta-Phosphoglucomutase From Lactococcus Lactis in Complex with Native Beta-Glucose 1,6-Bisphosphate Intermediate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg304 b:26.1 occ:1.00 O A:HOH609 1.9 37.1 1.0 O A:HOH607 1.9 30.6 1.0 O A:HOH602 2.1 34.6 1.0 O A:HOH460 2.1 21.4 1.0 O A:HOH497 2.2 28.3 1.0 O A:HOH643 2.3 51.1 1.0 O A:HOH549 4.2 34.9 1.0 O A:ASP86 4.2 14.2 1.0 O A:HOH419 4.3 27.8 1.0 OD2 A:ASP91 4.3 12.8 1.0 OD1 A:ASP91 4.4 17.5 1.0 CG A:ASP91 4.8 12.3 1.0

Magnesium binding site 4 out of 6 in the D10N,P146A Variant of Beta-Phosphoglucomutase From Lactococcus Lactis in Complex with Native Beta-Glucose 1,6-Bisphosphate Intermediate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of D10N,P146A Variant of Beta-Phosphoglucomutase From Lactococcus Lactis in Complex with Native Beta-Glucose 1,6-Bisphosphate Intermediate within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg302 b:6.5 occ:1.00 OD2 B:ASP8 2.0 7.1 1.0 O2X B:B16301 2.0 6.5 1.0 O B:ASN10 2.1 7.3 1.0 O B:HOH429 2.1 7.3 1.0 OD1 B:ASP170 2.1 7.1 1.0 O B:HOH403 2.1 7.0 1.0 CG B:ASP8 3.0 6.3 1.0 CG B:ASP170 3.1 6.6 1.0 C B:ASN10 3.2 6.1 1.0 P' B:B16301 3.3 6.5 1.0 OD1 B:ASP8 3.4 6.8 1.0 OD2 B:ASP170 3.4 8.7 1.0 MG B:MG303 3.7 6.9 1.0 OE2 B:GLU169 3.8 8.2 1.0 O3X B:B16301 3.9 7.1 1.0 O1X B:B16301 3.9 6.2 1.0 CA B:ASN10 3.9 6.3 1.0 OG B:SER171 4.0 10.6 1.0 N B:ASN10 4.0 6.2 1.0 O2 B:B16301 4.0 7.9 1.0 CB B:ASN10 4.1 6.7 1.0 N B:GLY11 4.3 6.7 1.0 CB B:ASP8 4.3 6.2 1.0 O B:HOH561 4.4 9.8 1.0 CB B:ASP170 4.4 6.8 1.0 O1 B:B16301 4.5 6.4 1.0 CD B:GLU169 4.5 6.6 1.0 OE1 B:GLU169 4.6 7.6 1.0 CA B:GLY11 4.6 6.7 1.0 N B:ASP170 4.7 6.7 1.0 C B:LEU9 4.8 6.1 1.0 N B:GLY46 4.9 10.1 1.0 N B:SER171 4.9 7.7 1.0 CA B:ASP170 5.0 6.7 1.0

Magnesium binding site 5 out of 6 in the D10N,P146A Variant of Beta-Phosphoglucomutase From Lactococcus Lactis in Complex with Native Beta-Glucose 1,6-Bisphosphate Intermediate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of D10N,P146A Variant of Beta-Phosphoglucomutase From Lactococcus Lactis in Complex with Native Beta-Glucose 1,6-Bisphosphate Intermediate within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg303 b:6.9 occ:1.00 OD1 B:ASP8 2.0 6.8 1.0 O B:HOH565 2.0 8.2 1.0 O3X B:B16301 2.1 7.1 1.0 O B:HOH489 2.1 7.3 1.0 OE1 B:GLU169 2.1 7.6 1.0 O B:HOH403 2.3 7.0 1.0 CG B:ASP8 3.0 6.3 1.0 CD B:GLU169 3.1 6.6 1.0 P' B:B16301 3.2 6.5 1.0 OE2 B:GLU169 3.5 8.2 1.0 O2X B:B16301 3.5 6.5 1.0 OD2 B:ASP8 3.6 7.1 1.0 MG B:MG302 3.7 6.5 1.0 O B:HOH423 3.9 9.4 1.0 O1X B:B16301 3.9 6.2 1.0 CB B:ASP8 4.1 6.2 1.0 N B:ALA115 4.2 6.5 1.0 O B:ALA113 4.4 7.7 1.0 CA B:GLY46 4.4 11.2 1.0 CG B:GLU169 4.5 6.8 1.0 O B:HOH532 4.5 10.2 1.0 O1 B:B16301 4.5 6.4 1.0 CA B:SER114 4.6 6.6 1.0 CA B:ASP8 4.8 6.5 1.0 CB B:ALA115 4.8 7.5 1.0 OG B:SER171 4.8 10.6 1.0 C B:SER114 4.9 6.8 1.0 OD1 B:ASP170 4.9 7.1 1.0 CZ B:PHE151 5.0 8.2 1.0

Magnesium binding site 6 out of 6 in the D10N,P146A Variant of Beta-Phosphoglucomutase From Lactococcus Lactis in Complex with Native Beta-Glucose 1,6-Bisphosphate Intermediate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of D10N,P146A Variant of Beta-Phosphoglucomutase From Lactococcus Lactis in Complex with Native Beta-Glucose 1,6-Bisphosphate Intermediate within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg304 b:33.5 occ:1.00 O B:HOH631 1.7 39.2 1.0 O B:HOH598 1.9 48.1 1.0 O B:HOH609 2.1 55.9 1.0 O B:HOH437 2.1 21.8 1.0 O B:HOH443 2.3 28.6 1.0 O B:HOH582 2.4 40.4 1.0 O B:ASP86 4.3 13.1 1.0 OD1 B:ASP91 4.4 17.1 1.0 OD2 B:ASP91 4.4 11.5 1.0 OG B:SER88 4.7 17.2 1.0 CG B:ASP91 4.8 12.0 1.0

F.A.Cruz-Navarrete, N.J.Baxter, A.J.Flinders, A.Buzoianu, M.J.Cliff, P.J.Baker, J.P.Waltho. Peri Active Site Catalysis of Proline Isomerisation Is the Molecular Basis of Allomorphy in Beta-Phosphoglucomutase. Commun Biol V. 7 909 2024.
ISSN: ESSN 2399-3642
PubMed: 39068257
DOI: 10.1038/S42003-024-06577-9