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Sodium 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
Magnesium (Mg) 4 atoms

Sodium Binding Sites:

The binding sites of Sodium 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 Sodium atom.
In total 3 binding sites of Sodium 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 Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in 7o58

Go back to Sodium Binding Sites List in 7o58
Sodium binding site 1 out of 3 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 Sodium with other atoms in the Na 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:Na410

b:51.5
occ:0.50
 O A:HOH552 2.2 48.2 1.0
O A:HOH600 2.2 49.3 1.0
O A:HOH587 2.4 47.7 1.0
O A:LEU170 4.3 33.6 1.0
O A:HOH654 4.3 57.8 1.0
O A:HOH550 4.3 36.2 1.0
O A:HOH602 4.4 35.3 1.0
OD1 A:ASP185 4.5 42.1 1.0
CG A:ASP185 4.6 41.2 1.0
OG1 A:THR171 4.6 39.2 1.0
HB2 A:ASP185 4.7 41.7 1.0
OD2 A:ASP185 4.7 41.3 1.0
HG1 A:THR171 4.9 47.0 1.0
HA A:THR171 5.0 37.8 1.0

Sodium binding site 2 out of 3 in 7o58

Go back to Sodium Binding Sites List in 7o58
Sodium binding site 2 out of 3 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 Sodium with other atoms in the Na 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:Na411

b:64.6
occ:1.00
 O A:HOH553 2.2 60.1 1.0
O A:HOH503 2.3 52.8 1.0
O A:HOH656 2.3 65.9 1.0
O A:HOH621 2.3 66.9 1.0
OD2 A:ASP48 2.3 51.4 1.0
O A:HOH548 2.4 50.7 1.0
CG A:ASP48 3.3 46.6 1.0
OD1 A:ASP48 3.5 44.4 1.0
HB2 A:GLU50 3.7 49.9 1.0
O A:HOH525 4.0 51.3 1.0
OE1 A:GLU50 4.3 59.5 1.0
CB A:GLU50 4.6 41.6 1.0
CB A:ASP48 4.6 41.2 1.0
HB3 A:ASP48 4.7 49.4 1.0
HB3 A:GLU50 4.8 49.9 1.0
HG2 A:GLU50 4.8 77.3 1.0
HB2 A:ASP48 4.8 49.4 1.0
O A:HOH613 4.9 44.3 1.0

Sodium binding site 3 out of 3 in 7o58

Go back to Sodium Binding Sites List in 7o58
Sodium binding site 3 out of 3 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 Sodium with other atoms in the Na 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:Na507

b:60.1
occ:1.00
 O B:HOH601 2.2 54.5 1.0
O B:HOH604 2.2 46.3 1.0
O B:HOH717 2.2 45.6 1.0
OE2 B:GLU197 2.2 44.1 1.0
O B:HOH615 2.2 56.3 1.0
CD B:GLU197 3.3 48.9 1.0
HB2 B:ARG194 3.5 49.5 1.0
HA B:ARG194 3.5 47.7 1.0
HD21 B:ASN198 3.6 64.7 1.0
HG3 B:GLU197 3.6 50.6 1.0
HG2 B:GLU197 3.7 50.6 1.0
CG B:GLU197 3.8 42.2 1.0
O B:ARG194 4.1 35.9 1.0
OD1 B:ASN198 4.2 48.7 1.0
ND2 B:ASN198 4.2 53.9 1.0
CB B:ARG194 4.2 41.2 1.0
CA B:ARG194 4.3 39.7 1.0
OE1 B:GLU197 4.3 42.0 1.0
HB3 B:ARG194 4.5 49.5 1.0
CG B:ASN198 4.6 54.9 1.0
C B:ARG194 4.7 38.4 1.0
O B:HOH712 4.8 48.0 1.0
HD22 B:ASN198 4.8 64.7 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: Tue Oct 8 18:17:49 2024

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