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Magnesium in PDB 7o1b: Human Phosphomannomutase 2 (PMM2) Wild-Type Co-Crystallized with the Activator Glucose 1,6-Bisphosphate

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

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

Protein crystallography data

The structure of Human Phosphomannomutase 2 (PMM2) Wild-Type Co-Crystallized with the Activator Glucose 1,6-Bisphosphate, PDB code: 7o1b 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) 61.45 / 3.08
Space group P 65 2 2
Cell size a, b, c (Å), α, β, γ (°) 70.96, 70.96, 364.28, 90, 90, 120
R / Rfree (%) 23.6 / 25.7

Other elements in 7o1b:

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

Chlorine (Cl) 1 atom

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Human Phosphomannomutase 2 (PMM2) Wild-Type Co-Crystallized with the Activator Glucose 1,6-Bisphosphate (pdb code 7o1b). 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 Co-Crystallized with the Activator Glucose 1,6-Bisphosphate, PDB code: 7o1b:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 7o1b

Go back to Magnesium Binding Sites List in 7o1b
Magnesium binding site 1 out of 4 in the Human Phosphomannomutase 2 (PMM2) Wild-Type Co-Crystallized 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 Co-Crystallized with the Activator Glucose 1,6-Bisphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg301

b:43.5
occ:1.00
 O A:HOH401 1.8 42.9 1.0
OD2 A:ASP12 1.8 40.3 1.0
O A:HOH403 2.0 41.3 1.0
O A:ASP14 2.0 41.3 1.0
O A:HOH407 2.2 43.9 1.0
OD1 A:ASP209 2.5 44.0 1.0
CG A:ASP12 2.8 42.9 1.0
CG A:ASP209 3.1 44.3 1.0
OD2 A:ASP209 3.2 41.9 1.0
OD1 A:ASP12 3.2 43.6 1.0
C A:ASP14 3.2 41.7 1.0
HG1 A:THR16 3.4 52.1 1.0
HB3 A:ASP14 3.5 59.8 1.0
HA3 A:GLY15 3.8 52.1 1.0
H A:ASP209 3.8 57.9 1.0
HG3 A:LYS210 3.9 61.6 1.0
OD2 A:ASP217 3.9 45.5 1.0
CA A:ASP14 4.1 45.3 1.0
CB A:ASP12 4.1 44.8 1.0
H A:ASP14 4.2 55.1 1.0
N A:ASP14 4.2 45.9 1.0
H A:THR16 4.2 51.6 1.0
HB3 A:ASP12 4.2 53.7 1.0
N A:GLY15 4.2 42.7 1.0
OG1 A:THR16 4.2 43.4 1.0
CB A:ASP14 4.3 49.8 1.0
HD22 A:ASN216 4.3 54.5 1.0
CA A:GLY15 4.4 43.4 1.0
CB A:ASP209 4.4 50.5 1.0
HD2 A:LYS210 4.5 62.2 1.0
HB3 A:ASP209 4.5 60.6 1.0
HB2 A:ASP12 4.5 53.7 1.0
OD1 A:ASN216 4.6 61.1 1.0
N A:THR16 4.6 43.0 1.0
HZ2 A:LYS210 4.6 79.0 1.0
N A:ASP209 4.7 48.3 1.0
H A:VAL13 4.7 49.3 1.0
C A:VAL13 4.8 42.3 1.0
C A:GLY15 4.8 40.8 1.0
CG A:LYS210 4.8 51.3 1.0
CG A:ASP217 4.8 44.5 1.0
H A:LYS210 4.9 59.6 1.0
HB2 A:LYS210 4.9 58.0 1.0
OD1 A:ASP217 4.9 45.2 1.0
OD2 A:ASP14 4.9 57.2 1.0
HZ1 A:LYS189 5.0 55.7 1.0
HA A:ASP14 5.0 54.3 1.0
HZ3 A:LYS210 5.0 79.0 1.0
N A:VAL13 5.0 41.1 1.0
HB2 A:ASP14 5.0 59.8 1.0

Magnesium binding site 2 out of 4 in 7o1b

Go back to Magnesium Binding Sites List in 7o1b
Magnesium binding site 2 out of 4 in the Human Phosphomannomutase 2 (PMM2) Wild-Type Co-Crystallized 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 Co-Crystallized with the Activator Glucose 1,6-Bisphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg302

b:45.5
occ:1.00
 O A:PHE221 2.2 46.2 1.0
O A:ASP223 2.2 47.2 1.0
OG1 A:THR226 2.3 46.9 1.0
O A:HOH412 2.4 48.4 1.0
O A:THR226 2.4 45.8 1.0
HG1 A:THR226 2.6 56.2 1.0
O A:HOH417 3.1 38.5 1.0
C A:PHE221 3.2 47.6 1.0
C A:THR226 3.2 44.4 1.0
C A:ASP223 3.3 47.2 1.0
H A:THR226 3.3 51.0 1.0
H A:GLY228 3.4 53.0 1.0
C A:THR222 3.5 44.6 1.0
CB A:THR226 3.6 46.1 1.0
N A:ASP223 3.6 44.7 1.0
O A:THR222 3.7 45.4 1.0
HA A:THR222 3.7 59.7 1.0
CA A:THR226 3.8 41.5 1.0
HA A:PRO224 3.9 55.7 1.0
O A:ILE220 3.9 47.3 1.0
H A:ASP223 3.9 53.7 1.0
N A:GLY228 3.9 44.2 1.0
HA3 A:GLY228 3.9 52.0 1.0
CA A:THR222 3.9 49.8 1.0
N A:THR226 3.9 42.5 1.0
N A:THR222 4.0 50.2 1.0
CA A:ASP223 4.0 44.2 1.0
HA A:PHE221 4.1 57.6 1.0
HB A:THR226 4.1 55.4 1.0
HG23 A:THR226 4.2 57.1 1.0
HB3 A:ASP223 4.2 55.6 1.0
N A:MET227 4.3 43.6 1.0
CA A:PHE221 4.3 48.0 1.0
N A:PRO224 4.3 47.6 1.0
HA A:MET227 4.4 49.9 1.0
CA A:GLY228 4.4 43.3 1.0
CA A:PRO224 4.4 46.4 1.0
CG2 A:THR226 4.5 47.6 1.0
C A:MET227 4.7 44.2 1.0
CA A:MET227 4.7 41.6 1.0
HA2 A:GLY228 4.7 52.0 1.0
C A:PRO224 4.7 45.0 1.0
HA A:THR226 4.7 49.8 1.0
CB A:ASP223 4.7 46.3 1.0
H A:THR222 4.8 60.3 1.0
C A:ILE220 4.8 47.8 1.0
HG21 A:THR226 4.8 57.1 1.0
HA A:ASP223 4.8 53.0 1.0
H A:MET227 5.0 52.3 1.0

Magnesium binding site 3 out of 4 in 7o1b

Go back to Magnesium Binding Sites List in 7o1b
Magnesium binding site 3 out of 4 in the Human Phosphomannomutase 2 (PMM2) Wild-Type Co-Crystallized 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 Co-Crystallized with the Activator Glucose 1,6-Bisphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg301

b:46.7
occ:1.00
 O B:ASP14 1.7 51.6 1.0
O B:HOH403 1.8 49.2 1.0
OD2 B:ASP12 1.8 49.4 1.0
O B:HOH401 2.1 46.0 1.0
O B:HOH402 2.4 47.6 1.0
OD1 B:ASP209 2.8 61.1 1.0
CG B:ASP12 2.9 47.8 1.0
C B:ASP14 3.0 53.6 1.0
OD2 B:ASP209 3.3 55.3 1.0
HA3 B:GLY15 3.3 65.0 1.0
CG B:ASP209 3.4 52.8 1.0
OD1 B:ASP12 3.4 48.0 1.0
HB3 B:ASP14 3.5 62.9 1.0
HG2 B:LYS210 3.8 64.5 1.0
HD21 B:ASN216 3.9 62.8 1.0
N B:GLY15 3.9 54.9 1.0
CA B:ASP14 3.9 51.5 1.0
CA B:GLY15 4.0 54.1 1.0
H B:ASP14 4.1 62.9 1.0
N B:ASP14 4.1 52.4 1.0
H B:ASP209 4.1 60.8 1.0
HB3 B:ASP12 4.2 54.7 1.0
CB B:ASP14 4.2 52.4 1.0
CB B:ASP12 4.2 45.6 1.0
HZ2 B:LYS189 4.4 59.2 1.0
OD2 B:ASP217 4.4 50.9 1.0
OG1 B:THR16 4.4 45.6 1.0
H B:THR16 4.4 63.8 1.0
C B:GLY15 4.5 53.3 1.0
ND2 B:ASN216 4.5 52.4 1.0
H B:LYS210 4.5 59.5 1.0
HD22 B:ASN216 4.6 62.8 1.0
HB2 B:ASP12 4.6 54.7 1.0
N B:THR16 4.6 53.2 1.0
OD1 B:ASP217 4.6 45.3 1.0
H B:GLY15 4.7 65.8 1.0
CG B:LYS210 4.7 53.8 1.0
CB B:ASP209 4.8 49.4 1.0
HA B:ASP14 4.8 61.8 1.0
HA2 B:GLY15 4.8 65.0 1.0
C B:VAL13 4.8 49.0 1.0
HG1 B:THR16 4.8 54.8 1.0
HB2 B:ASP14 4.8 62.9 1.0
HE2 B:LYS210 4.8 77.8 1.0
HG3 B:LYS210 4.9 64.5 1.0
OD2 B:ASP14 4.9 58.6 1.0
N B:ASP209 4.9 50.7 1.0
CG B:ASP217 4.9 44.8 1.0
HZ1 B:LYS189 4.9 59.2 1.0
H B:VAL13 5.0 51.9 1.0

Magnesium binding site 4 out of 4 in 7o1b

Go back to Magnesium Binding Sites List in 7o1b
Magnesium binding site 4 out of 4 in the Human Phosphomannomutase 2 (PMM2) Wild-Type Co-Crystallized 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 Co-Crystallized with the Activator Glucose 1,6-Bisphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg302

b:46.2
occ:1.00
 O B:HOH415 1.9 52.1 1.0
OG1 B:THR226 2.2 45.1 1.0
O B:PHE221 2.4 54.6 1.0
O B:ASP223 2.6 48.4 1.0
O B:THR226 2.7 45.4 1.0
H B:THR226 3.3 50.1 1.0
C B:THR226 3.3 41.6 1.0
H B:GLY228 3.4 49.6 1.0
CB B:THR226 3.5 42.4 1.0
C B:PHE221 3.6 49.2 1.0
C B:ASP223 3.7 47.6 1.0
CA B:THR226 3.7 41.6 1.0
N B:THR226 3.9 41.8 1.0
N B:GLY228 3.9 41.3 1.0
HA3 B:GLY228 3.9 56.3 1.0
HA B:THR222 4.0 53.1 1.0
C B:THR222 4.0 47.6 1.0
HB B:THR226 4.0 50.8 1.0
N B:ASP223 4.1 45.9 1.0
HA B:PRO224 4.1 56.0 1.0
HA B:PHE221 4.2 56.7 1.0
HA B:MET227 4.2 49.7 1.0
N B:MET227 4.3 40.1 1.0
H B:ASP223 4.3 55.1 1.0
O B:THR222 4.3 49.1 1.0
CA B:THR222 4.3 44.3 1.0
HG23 B:THR226 4.3 47.5 1.0
N B:THR222 4.4 47.6 1.0
CA B:GLY228 4.4 46.9 1.0
O B:ILE220 4.4 45.4 1.0
CA B:ASP223 4.5 43.2 1.0
CG2 B:THR226 4.5 39.6 1.0
CA B:PHE221 4.6 47.3 1.0
C B:MET227 4.6 39.8 1.0
CA B:MET227 4.6 41.4 1.0
N B:PRO224 4.6 47.5 1.0
CA B:PRO224 4.6 46.7 1.0
HB3 B:ASP223 4.7 53.6 1.0
HA B:THR226 4.7 49.9 1.0
HA2 B:GLY228 4.7 56.3 1.0
C B:PRO224 4.8 42.9 1.0
HG21 B:THR226 4.9 47.5 1.0
H B:MET227 5.0 48.1 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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