Atomistry » Sodium » PDB 7o1y-7opy » 7o58
Atomistry »
  Sodium »
    PDB 7o1y-7opy »
      7o58 »

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

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy