Magnesium in PDB 7o4g: Human Phosphomannomutase 2 (PMM2) Wild-Type Soaked with the Activator Glucose 1,6-Bisphosphate

Enzymatic activity of Human Phosphomannomutase 2 (PMM2) Wild-Type Soaked with the Activator Glucose 1,6-Bisphosphate

All present enzymatic activity of Human Phosphomannomutase 2 (PMM2) Wild-Type Soaked with the Activator Glucose 1,6-Bisphosphate:
5.4.2.8;

Protein crystallography data

The structure of Human Phosphomannomutase 2 (PMM2) Wild-Type Soaked with the Activator Glucose 1,6-Bisphosphate, PDB code: 7o4g 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) 60.21 / 2.66
Space group P 65 2 2
Cell size a, b, c (Å), α, β, γ (°) 71.144, 71.144, 361.266, 90, 90, 120
R / Rfree (%) 22.4 / 27.3

Other elements in 7o4g:

The structure of Human Phosphomannomutase 2 (PMM2) Wild-Type Soaked with the Activator Glucose 1,6-Bisphosphate also contains other interesting chemical elements:

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

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Human Phosphomannomutase 2 (PMM2) Wild-Type Soaked with the Activator Glucose 1,6-Bisphosphate (pdb code 7o4g). 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) Wild-Type Soaked with the Activator Glucose 1,6-Bisphosphate, PDB code: 7o4g:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 7o4g

Go back to Magnesium Binding Sites List in 7o4g
Magnesium binding site 1 out of 4 in the Human Phosphomannomutase 2 (PMM2) Wild-Type Soaked 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) Wild-Type Soaked with the Activator Glucose 1,6-Bisphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg302

b:57.9
occ:1.00
 O A:HOH417 1.8 58.3 1.0
O A:HOH411 1.8 56.4 1.0
O A:ASP14 2.1 57.0 1.0
OD2 A:ASP12 2.1 48.5 1.0
OD1 A:ASP209 2.3 58.9 1.0
O A:HOH409 2.6 55.6 1.0
CG A:ASP209 3.0 62.9 1.0
CG A:ASP12 3.0 50.7 1.0
OD2 A:ASP209 3.1 63.1 1.0
OD1 A:ASP12 3.3 59.1 1.0
C A:ASP14 3.3 52.5 1.0
HG1 A:THR16 3.5 56.9 1.0
HB3 A:ASP14 3.7 71.5 1.0
HG2 A:LYS210 3.7 71.0 1.0
HA3 A:GLY15 3.7 65.2 1.0
OD2 A:ASP217 3.7 42.3 1.0
H A:ASP209 3.8 53.5 1.0
HD22 A:ASN216 3.9 59.6 1.0
HG3 A:LYS210 4.1 71.0 1.0
CA A:ASP14 4.2 57.0 1.0
N A:GLY15 4.2 53.6 1.0
OG1 A:THR16 4.2 46.4 1.0
CB A:ASP14 4.3 58.6 1.0
CB A:ASP12 4.3 47.5 1.0
CG A:LYS210 4.3 58.2 1.0
CB A:ASP209 4.3 52.0 1.0
CA A:GLY15 4.4 53.3 1.0
OD1 A:ASP14 4.4 75.0 1.0
HB3 A:ASP12 4.4 58.2 1.0
N A:ASP14 4.4 62.1 1.0
OD1 A:ASN216 4.4 58.2 1.0
H A:ASP14 4.4 75.7 1.0
HB2 A:LYS210 4.5 63.7 1.0
H A:THR16 4.5 63.6 1.0
N A:ASP209 4.6 43.6 1.0
HB3 A:ASP209 4.6 63.5 1.0
HB2 A:ASP12 4.6 58.2 1.0
ND2 A:ASN216 4.6 48.7 1.0
CG A:ASP14 4.6 74.1 1.0
CG A:ASP217 4.6 50.7 1.0
HZ3 A:LYS210 4.7 100.0 1.0
H A:LYS210 4.7 73.0 1.0
OD1 A:ASP217 4.7 54.9 1.0
C A:GLY15 4.7 48.5 1.0
N A:THR16 4.7 52.0 1.0
CA A:ASP209 4.9 44.4 1.0
CG A:ASN216 4.9 54.7 1.0
CB A:LYS210 4.9 52.2 1.0
N A:LYS210 5.0 59.9 1.0
H A:VAL13 5.0 53.0 1.0
HB2 A:ASP209 5.0 63.5 1.0

Magnesium binding site 2 out of 4 in 7o4g

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Magnesium binding site 2 out of 4 in the Human Phosphomannomutase 2 (PMM2) Wild-Type Soaked 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) Wild-Type Soaked with the Activator Glucose 1,6-Bisphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg303

b:42.0
occ:1.00
 O A:PHE221 2.5 53.3 1.0
OG1 A:THR226 2.5 40.5 1.0
O A:ASP223 2.5 39.1 1.0
HG1 A:THR226 2.8 49.7 1.0
O A:THR226 2.9 53.4 1.0
O A:HOH438 3.1 37.9 1.0
H A:GLY228 3.1 61.5 1.0
C A:THR226 3.4 39.6 1.0
C A:PHE221 3.4 47.4 1.0
H A:THR226 3.5 49.4 1.0
HA A:THR222 3.6 51.9 1.0
C A:ASP223 3.6 41.9 1.0
CB A:THR226 3.7 48.9 1.0
C A:THR222 3.8 43.6 1.0
N A:GLY228 3.8 50.3 1.0
N A:ASP223 3.8 50.9 1.0
CA A:THR226 3.9 44.0 1.0
H A:ASP223 4.0 62.2 1.0
CA A:THR222 4.0 42.3 1.0
HA A:PRO224 4.0 57.6 1.0
N A:THR222 4.0 51.0 1.0
HA3 A:GLY228 4.1 47.2 1.0
N A:THR226 4.1 40.2 1.0
N A:MET227 4.2 50.0 1.0
HA A:PHE221 4.2 56.2 1.0
HA A:MET227 4.2 58.5 1.0
O A:THR222 4.2 55.3 1.0
HB A:THR226 4.3 59.9 1.0
CA A:ASP223 4.4 37.4 1.0
O A:ILE220 4.4 54.7 1.0
CA A:PHE221 4.4 45.9 1.0
HG23 A:THR226 4.5 76.6 1.0
CA A:GLY228 4.5 38.4 1.0
N A:PRO224 4.5 53.1 1.0
CA A:MET227 4.6 47.8 1.0
CA A:PRO224 4.6 47.0 1.0
HB3 A:ASP223 4.7 57.0 1.0
C A:MET227 4.7 44.7 1.0
CG2 A:THR226 4.7 62.9 1.0
C A:PRO224 4.8 52.9 1.0
H A:MET227 4.8 61.1 1.0
H A:THR222 4.8 62.4 1.0
HA2 A:GLY228 4.8 47.2 1.0
HA A:THR226 4.9 53.9 1.0
O A:PRO224 4.9 54.3 1.0

Magnesium binding site 3 out of 4 in 7o4g

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Magnesium binding site 3 out of 4 in the Human Phosphomannomutase 2 (PMM2) Wild-Type Soaked 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) Wild-Type Soaked with the Activator Glucose 1,6-Bisphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg301

b:57.3
occ:1.00
 O B:HOH402 2.0 54.3 1.0
O B:ASP14 2.0 56.8 1.0
OD2 B:ASP12 2.0 65.0 1.0
O B:HOH421 2.4 57.6 1.0
OD1 B:ASP209 2.5 74.8 1.0
O B:HOH403 2.6 54.9 1.0
OD2 B:ASP209 3.1 74.1 1.0
CG B:ASP209 3.1 70.4 1.0
C B:ASP14 3.2 54.1 1.0
HA3 B:GLY15 3.2 79.2 1.0
CG B:ASP12 3.2 60.4 1.0
HB3 B:ASP14 3.5 85.5 1.0
HG2 B:LYS210 3.7 80.4 1.0
H B:ASP209 3.8 74.1 1.0
OD2 B:ASP217 3.9 62.2 1.0
OD1 B:ASP12 3.9 59.5 1.0
N B:GLY15 4.0 68.3 1.0
CA B:GLY15 4.0 65.1 1.0
HD22 B:ASN216 4.0 67.6 1.0
HG1 B:THR16 4.0 72.9 1.0
CA B:ASP14 4.2 58.2 1.0
HB3 B:ASP12 4.2 73.1 1.0
CB B:ASP14 4.2 70.2 1.0
H B:LYS210 4.3 78.3 1.0
H B:THR16 4.3 79.6 1.0
CB B:ASP12 4.4 60.0 1.0
N B:ASP14 4.4 70.1 1.0
H B:ASP14 4.5 85.3 1.0
HG3 B:LYS210 4.5 80.4 1.0
CG B:LYS210 4.5 66.0 1.0
C B:GLY15 4.6 71.0 1.0
CB B:ASP209 4.6 65.5 1.0
N B:THR16 4.6 65.4 1.0
N B:ASP209 4.6 60.8 1.0
HE3 B:LYS210 4.7 78.9 1.0
OD1 B:ASN216 4.7 58.0 1.0
HA2 B:GLY15 4.7 79.2 1.0
CG B:ASP217 4.8 58.7 1.0
OD1 B:ASP217 4.8 56.4 1.0
H B:GLY15 4.8 83.1 1.0
OG1 B:THR16 4.8 59.8 1.0
ND2 B:ASN216 4.8 55.4 1.0
HB2 B:ASP12 4.8 73.1 1.0
OD2 B:ASP14 4.9 67.0 1.0
HB2 B:ASP14 4.9 85.5 1.0
N B:LYS210 4.9 64.3 1.0
HB B:THR16 4.9 68.8 1.0
HZ2 B:LYS189 4.9 61.0 1.0

Magnesium binding site 4 out of 4 in 7o4g

Go back to Magnesium Binding Sites List in 7o4g
Magnesium binding site 4 out of 4 in the Human Phosphomannomutase 2 (PMM2) Wild-Type Soaked 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) Wild-Type Soaked with the Activator Glucose 1,6-Bisphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg302

b:64.4
occ:1.00
 O B:HOH431 2.1 60.5 1.0
O B:THR226 2.4 46.8 1.0
OG1 B:THR226 2.6 50.5 1.0
O B:ASP223 2.6 54.3 1.0
O B:PHE221 2.8 60.1 1.0
HG1 B:THR226 3.0 61.7 1.0
H B:GLY228 3.1 50.1 1.0
C B:THR226 3.2 51.6 1.0
H B:THR226 3.4 62.4 1.0
CB B:THR226 3.7 45.6 1.0
N B:GLY228 3.8 40.8 1.0
CA B:THR226 3.8 49.6 1.0
C B:ASP223 3.8 60.2 1.0
HA B:MET227 3.9 66.7 1.0
C B:PHE221 3.9 56.6 1.0
N B:THR226 4.0 51.0 1.0
HA B:PRO224 4.1 69.8 1.0
N B:MET227 4.1 50.7 1.0
HB B:THR226 4.1 55.9 1.0
HA3 B:GLY228 4.1 61.0 1.0
N B:ASP223 4.3 57.5 1.0
CA B:MET227 4.3 54.6 1.0
H B:ASP223 4.4 70.2 1.0
C B:THR222 4.4 56.2 1.0
HA B:PHE221 4.4 68.6 1.0
HA B:THR222 4.4 60.9 1.0
C B:MET227 4.5 55.9 1.0
CA B:GLY228 4.5 49.9 1.0
CA B:PRO224 4.6 57.2 1.0
CA B:ASP223 4.7 52.0 1.0
N B:PRO224 4.7 59.3 1.0
O B:THR222 4.7 56.3 1.0
C B:PRO224 4.7 53.8 1.0
CA B:THR222 4.7 49.8 1.0
N B:THR222 4.7 51.2 1.0
HA B:THR226 4.8 60.6 1.0
O B:ILE220 4.8 55.3 1.0
CA B:PHE221 4.8 56.2 1.0
H B:MET227 4.8 62.0 1.0
O B:PRO224 4.9 49.8 1.0
CG2 B:THR226 4.9 54.9 1.0
HG23 B:THR226 4.9 67.0 1.0
HB3 B:ASP223 4.9 69.5 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 Apr 6 18:00:24 2023

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