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Magnesium in PDB 7o58: Human Phosphomannomutase 2 (PMM2) with Mutation T237M in Complex with the Activator Glucose 1,6-Bisphosphate

Enzymatic activity of Human Phosphomannomutase 2 (PMM2) with Mutation T237M in Complex with the Activator Glucose 1,6-Bisphosphate

All present enzymatic activity of Human Phosphomannomutase 2 (PMM2) with Mutation T237M in Complex with the Activator Glucose 1,6-Bisphosphate:
5.4.2.8;

Protein crystallography data

The structure of Human Phosphomannomutase 2 (PMM2) with Mutation T237M in Complex with the Activator Glucose 1,6-Bisphosphate, PDB code: 7o58 was solved by S.Ramon-Maiques, A.Briso-Montiano, F.Del Cano-Ochoa, A.Vilas, B.Perez, V.Rubio, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 59.95 / 1.97
Space group P 65 2 2
Cell size a, b, c (Å), α, β, γ (°) 70.52, 70.52, 359.72, 90, 90, 120
R / Rfree (%) 18.3 / 23

Other elements in 7o58:

The structure of Human Phosphomannomutase 2 (PMM2) with Mutation T237M in Complex with the Activator Glucose 1,6-Bisphosphate also contains other interesting chemical elements:

Chlorine (Cl) 1 atom
Sodium (Na) 3 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Human Phosphomannomutase 2 (PMM2) with Mutation T237M in Complex with the Activator Glucose 1,6-Bisphosphate (pdb code 7o58). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Human Phosphomannomutase 2 (PMM2) with Mutation T237M in Complex with the Activator Glucose 1,6-Bisphosphate, PDB code: 7o58:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 7o58

Go back to Magnesium Binding Sites List in 7o58
Magnesium binding site 1 out of 4 in the Human Phosphomannomutase 2 (PMM2) with Mutation T237M in Complex with the Activator Glucose 1,6-Bisphosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Human Phosphomannomutase 2 (PMM2) with Mutation T237M in Complex with the Activator Glucose 1,6-Bisphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg407

b:36.1
occ:1.00
 O A:HOH509 1.9 35.5 1.0
OD2 A:ASP12 2.0 37.7 1.0
O A:HOH604 2.0 36.5 1.0
OD1 A:ASP209 2.0 37.2 1.0
O A:HOH551 2.1 37.0 1.0
O A:ASP14 2.1 40.8 1.0
CG A:ASP12 3.0 37.7 1.0
CG A:ASP209 3.1 39.7 1.0
HG1 A:THR16 3.3 43.8 1.0
C A:ASP14 3.3 39.7 1.0
OD1 A:ASP12 3.4 40.2 1.0
OD2 A:ASP209 3.5 43.4 1.0
H A:ASP209 3.7 40.0 1.0
HA3 A:GLY15 3.7 45.0 1.0
HB3 A:ASP14 3.8 54.2 1.0
HG2 A:LYS210 3.9 47.4 1.0
OD2 A:ASP217 4.0 37.8 1.0
OG1 A:THR16 4.1 36.5 1.0
HD22 A:ASN216 4.1 54.4 1.0
O A:HOH638 4.2 47.9 1.0
OD1 A:ASN216 4.2 45.2 1.0
CB A:ASP12 4.3 33.7 1.0
CA A:ASP14 4.3 41.7 1.0
N A:GLY15 4.3 39.4 1.0
HB3 A:ASP12 4.3 40.4 1.0
HG3 A:LYS210 4.3 47.4 1.0
H A:ASP14 4.3 50.8 1.0
CA A:GLY15 4.4 37.5 1.0
N A:ASP14 4.4 42.3 1.0
H A:THR16 4.4 43.8 1.0
CB A:ASP209 4.5 31.5 1.0
CB A:ASP14 4.5 45.2 1.0
CG A:LYS210 4.5 39.5 1.0
N A:ASP209 4.5 33.3 1.0
HB2 A:LYS210 4.6 47.1 1.0
HZ1 A:LYS189 4.6 53.6 1.0
HB2 A:ASP12 4.6 40.4 1.0
HB3 A:ASP209 4.6 37.8 1.0
H A:LYS210 4.6 46.3 1.0
N A:THR16 4.7 36.5 1.0
C A:GLY15 4.7 39.0 1.0
O A:HOH629 4.8 44.4 1.0
ND2 A:ASN216 4.8 45.3 1.0
HZ3 A:LYS189 4.8 53.6 1.0
CG A:ASP217 4.8 36.1 1.0
OD1 A:ASP217 4.8 43.0 1.0
H A:VAL13 4.9 41.1 1.0
HB A:THR16 4.9 47.3 1.0
CA A:ASP209 4.9 33.4 1.0
N A:LYS210 4.9 38.5 1.0
CG A:ASN216 5.0 42.8 1.0
OD2 A:ASP14 5.0 59.6 1.0
C A:VAL13 5.0 40.5 1.0

Magnesium binding site 2 out of 4 in 7o58

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Magnesium binding site 2 out of 4 in the Human Phosphomannomutase 2 (PMM2) with Mutation T237M in Complex with the Activator Glucose 1,6-Bisphosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Human Phosphomannomutase 2 (PMM2) with Mutation T237M in Complex with the Activator Glucose 1,6-Bisphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg408

b:37.5
occ:1.00
 O A:ASP223 2.3 36.0 1.0
O A:THR226 2.3 35.4 1.0
O A:PHE221 2.3 37.6 1.0
O A:HOH640 2.3 47.9 1.0
OG1 A:THR226 2.6 37.0 1.0
O A:HOH585 2.6 39.7 1.0
HG1 A:THR226 3.0 44.4 1.0
H A:THR226 3.2 40.0 1.0
C A:THR226 3.2 36.2 1.0
C A:ASP223 3.3 38.6 1.0
H A:GLY228 3.4 42.5 1.0
C A:PHE221 3.5 36.1 1.0
N A:ASP223 3.7 37.3 1.0
CB A:THR226 3.8 37.0 1.0
CA A:THR226 3.8 37.4 1.0
C A:THR222 3.8 38.7 1.0
H A:ASP223 3.8 44.7 1.0
O A:HOH644 3.8 51.2 1.0
N A:THR226 3.8 33.4 1.0
HA A:PRO224 3.9 45.5 1.0
HA A:THR222 3.9 40.9 1.0
N A:GLY228 4.0 35.4 1.0
O A:ILE220 4.1 38.5 1.0
HA3 A:GLY228 4.1 44.4 1.0
CA A:ASP223 4.1 39.1 1.0
CA A:THR222 4.2 34.1 1.0
O A:THR222 4.2 43.3 1.0
HA A:PHE221 4.2 40.1 1.0
N A:THR222 4.2 37.6 1.0
N A:PRO224 4.3 40.0 1.0
N A:MET227 4.3 40.1 1.0
HB A:THR226 4.3 44.4 1.0
HA A:MET227 4.3 45.1 1.0
HB3 A:ASP223 4.4 45.5 1.0
CA A:PRO224 4.4 37.9 1.0
CA A:PHE221 4.5 33.4 1.0
C A:PRO224 4.6 40.1 1.0
CA A:GLY228 4.6 37.0 1.0
CA A:MET227 4.7 37.5 1.0
HG23 A:THR226 4.7 40.4 1.0
HA A:THR226 4.7 44.9 1.0
O A:HOH610 4.8 48.7 1.0
C A:MET227 4.8 41.5 1.0
CG2 A:THR226 4.8 33.7 1.0
CB A:ASP223 4.8 37.9 1.0
N A:ARG225 4.9 38.6 1.0
HA A:ASP223 4.9 47.0 1.0
O A:PRO224 4.9 39.7 1.0
H A:THR222 5.0 45.1 1.0
HA2 A:GLY228 5.0 44.4 1.0

Magnesium binding site 3 out of 4 in 7o58

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Magnesium binding site 3 out of 4 in the Human Phosphomannomutase 2 (PMM2) with Mutation T237M in Complex with the Activator Glucose 1,6-Bisphosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Human Phosphomannomutase 2 (PMM2) with Mutation T237M in Complex with the Activator Glucose 1,6-Bisphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg505

b:42.9
occ:1.00
 OD2 B:ASP12 1.9 40.0 1.0
O B:ASP14 2.0 39.0 1.0
OD1 B:ASP209 2.0 38.5 1.0
O B:HOH607 2.1 38.4 1.0
O B:HOH617 2.1 41.4 1.0
O B:HOH632 2.2 46.7 1.0
CG B:ASP12 2.9 42.6 1.0
CG B:ASP209 3.0 46.8 1.0
OD1 B:ASP12 3.2 38.8 1.0
C B:ASP14 3.2 41.9 1.0
HG1 B:THR16 3.4 46.8 1.0
OD2 B:ASP209 3.4 44.8 1.0
HB3 B:ASP14 3.6 58.0 1.0
HA3 B:GLY15 3.7 49.7 1.0
H B:ASP209 3.8 46.8 1.0
HG2 B:LYS210 3.9 61.6 1.0
OD2 B:ASP217 4.1 43.8 1.0
CA B:ASP14 4.1 42.8 1.0
OG1 B:THR16 4.1 39.0 1.0
N B:GLY15 4.1 45.3 1.0
N B:ASP14 4.2 41.0 1.0
CB B:ASP12 4.2 34.8 1.0
H B:ASP14 4.2 49.2 1.0
O B:HOH714 4.2 54.1 1.0
CA B:GLY15 4.3 41.4 1.0
HB3 B:ASP12 4.3 41.8 1.0
CB B:ASP14 4.3 48.3 1.0
O B:HOH610 4.4 46.9 1.0
CB B:ASP209 4.4 44.8 1.0
HD21 B:ASN216 4.4 57.6 1.0
OD1 B:ASN216 4.5 47.1 1.0
HG3 B:LYS210 4.5 61.6 1.0
H B:THR16 4.5 44.8 1.0
N B:ASP209 4.6 39.0 1.0
HZ1 B:LYS189 4.6 61.2 1.0
HB2 B:ASP12 4.6 41.8 1.0
CG B:LYS210 4.6 51.4 1.0
C B:GLY15 4.6 38.3 1.0
HB3 B:ASP209 4.7 53.7 1.0
N B:THR16 4.7 37.3 1.0
H B:VAL13 4.8 38.5 1.0
H B:LYS210 4.8 51.4 1.0
C B:VAL13 4.8 44.1 1.0
HB B:THR16 4.8 39.5 1.0
HZ3 B:LYS189 4.8 61.2 1.0
OD1 B:ASP217 4.9 41.4 1.0
HB2 B:LYS210 4.9 46.8 1.0
CG B:ASP217 4.9 41.7 1.0
O B:HOH715 4.9 47.2 1.0
CA B:ASP209 5.0 39.5 1.0
H B:GLY15 5.0 54.4 1.0
HA B:ASP14 5.0 51.4 1.0
HB2 B:ASP14 5.0 58.0 1.0

Magnesium binding site 4 out of 4 in 7o58

Go back to Magnesium Binding Sites List in 7o58
Magnesium binding site 4 out of 4 in the Human Phosphomannomutase 2 (PMM2) with Mutation T237M in Complex with the Activator Glucose 1,6-Bisphosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Human Phosphomannomutase 2 (PMM2) with Mutation T237M in Complex with the Activator Glucose 1,6-Bisphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg506

b:41.0
occ:1.00
 O B:HOH732 2.2 44.8 1.0
O B:ASP223 2.3 39.9 1.0
O B:PHE221 2.4 38.0 1.0
OG1 B:THR226 2.5 34.6 1.0
O B:THR226 2.5 35.7 1.0
O B:HOH683 2.6 52.9 1.0
HG1 B:THR226 2.9 41.5 1.0
H B:THR226 3.2 47.1 1.0
C B:THR226 3.4 35.1 1.0
C B:ASP223 3.4 40.1 1.0
C B:PHE221 3.5 39.9 1.0
C B:THR222 3.6 39.3 1.0
N B:ASP223 3.7 43.2 1.0
CB B:THR226 3.7 37.5 1.0
H B:GLY228 3.8 46.3 1.0
CA B:THR226 3.8 36.8 1.0
HA B:THR222 3.8 47.7 1.0
H B:ASP223 3.8 51.9 1.0
N B:THR226 3.8 39.2 1.0
O B:THR222 3.9 39.7 1.0
HA B:PRO224 3.9 48.2 1.0
O B:ILE220 4.1 39.3 1.0
CA B:THR222 4.1 39.7 1.0
CA B:ASP223 4.1 43.2 1.0
N B:THR222 4.2 36.1 1.0
HB B:THR226 4.2 45.0 1.0
HA B:PHE221 4.2 42.2 1.0
N B:PRO224 4.3 38.8 1.0
O B:HOH663 4.3 55.8 1.0
N B:GLY228 4.3 38.6 1.0
HA3 B:GLY228 4.3 46.0 1.0
N B:MET227 4.4 34.9 1.0
CA B:PRO224 4.4 40.2 1.0
HB3 B:ASP223 4.4 43.3 1.0
HA B:MET227 4.5 53.6 1.0
CA B:PHE221 4.5 35.2 1.0
C B:PRO224 4.6 42.8 1.0
HG23 B:THR226 4.7 48.9 1.0
HA B:THR226 4.8 44.1 1.0
CG2 B:THR226 4.8 40.7 1.0
CA B:MET227 4.8 44.6 1.0
N B:ARG225 4.9 37.1 1.0
CA B:GLY228 4.9 38.4 1.0
CB B:ASP223 4.9 36.1 1.0
H B:ARG225 4.9 44.6 1.0
HA B:ASP223 4.9 51.9 1.0
H B:THR222 5.0 43.4 1.0
O B:PRO224 5.0 38.8 1.0
C B:MET227 5.0 39.4 1.0

Reference:

A.Briso-Montiano, F.Del Cano-Ochoa, A.Vilas, A.Velazquez-Campoy, V.Rubio, B.Perez, S.Ramon-Maiques. Insight on Molecular Pathogenesis and Pharmacochaperoning Potential in Phosphomannomutase 2 Deficiency, Provided By Novel Human Phosphomannomutase 2 Structures. J Inherit Metab Dis V. 45 318 2022.
ISSN: ISSN 1573-2665
PubMed: 34859900
DOI: 10.1002/JIMD.12461
Page generated: Thu Oct 3 02:32:45 2024

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