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Magnesium in PDB 7o5z: Human Phosphomannomutase 2 (PMM2) with Mutation T237M in Apo State

Enzymatic activity of Human Phosphomannomutase 2 (PMM2) with Mutation T237M in Apo State

All present enzymatic activity of Human Phosphomannomutase 2 (PMM2) with Mutation T237M in Apo State:
5.4.2.8;

Protein crystallography data

The structure of Human Phosphomannomutase 2 (PMM2) with Mutation T237M in Apo State, PDB code: 7o5z 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) 61.43 / 2.07
Space group P 65 2 2
Cell size a, b, c (Å), α, β, γ (°) 70.934, 70.934, 363.616, 90, 90, 120
R / Rfree (%) 20.4 / 22.4

Other elements in 7o5z:

The structure of Human Phosphomannomutase 2 (PMM2) with Mutation T237M in Apo State also contains other interesting chemical elements:

Chlorine (Cl) 1 atom
Sodium (Na) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Human Phosphomannomutase 2 (PMM2) with Mutation T237M in Apo State (pdb code 7o5z). 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 Apo State, PDB code: 7o5z:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 7o5z

Go back to Magnesium Binding Sites List in 7o5z
Magnesium binding site 1 out of 4 in the Human Phosphomannomutase 2 (PMM2) with Mutation T237M in Apo State


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 Apo State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg305

b:37.1
occ:1.00
 O A:HOH426 1.9 35.3 1.0
O A:HOH404 1.9 32.7 1.0
OD2 A:ASP12 2.0 36.9 1.0
O A:ASP14 2.1 40.9 1.0
O A:HOH450 2.1 35.3 1.0
OD1 A:ASP209 2.2 36.0 1.0
CG A:ASP12 3.0 36.4 1.0
CG A:ASP209 3.1 38.1 1.0
C A:ASP14 3.3 37.2 1.0
HG1 A:THR16 3.3 42.0 1.0
OD1 A:ASP12 3.4 38.1 1.0
OD2 A:ASP209 3.4 40.4 1.0
HB3 A:ASP14 3.6 58.2 1.0
HG2 A:LYS210 3.8 47.9 1.0
HA3 A:GLY15 3.8 49.6 1.0
H A:ASP209 3.8 40.0 1.0
OD2 A:ASP217 4.0 36.7 1.0
HD22 A:ASN216 4.1 49.4 1.0
OG1 A:THR16 4.1 35.0 1.0
CA A:ASP14 4.1 42.9 1.0
N A:GLY15 4.2 41.0 1.0
H A:ASP14 4.3 47.3 1.0
N A:ASP14 4.3 39.4 1.0
CB A:ASP14 4.3 48.5 1.0
CB A:ASP12 4.3 34.9 1.0
HB3 A:ASP12 4.3 41.9 1.0
CA A:GLY15 4.4 41.4 1.0
H A:THR16 4.4 42.7 1.0
OD1 A:ASN216 4.4 41.1 1.0
HG3 A:LYS210 4.4 47.9 1.0
CB A:ASP209 4.5 37.1 1.0
CG A:LYS210 4.5 40.0 1.0
N A:THR16 4.6 35.6 1.0
N A:ASP209 4.7 33.3 1.0
HB A:THR16 4.7 42.8 1.0
HB3 A:ASP209 4.7 44.5 1.0
C A:GLY15 4.7 36.0 1.0
HB2 A:ASP12 4.7 41.9 1.0
H A:LYS210 4.7 45.4 1.0
HZ3 A:LYS189 4.8 44.5 1.0
HB2 A:LYS210 4.8 45.3 1.0
H A:VAL13 4.8 40.7 1.0
ND2 A:ASN216 4.9 41.2 1.0
C A:VAL13 4.9 39.1 1.0
HZ2 A:LYS189 4.9 44.5 1.0
HB2 A:ASP14 4.9 58.2 1.0
CG A:ASP217 4.9 36.5 1.0
CB A:THR16 5.0 35.6 1.0

Magnesium binding site 2 out of 4 in 7o5z

Go back to Magnesium Binding Sites List in 7o5z
Magnesium binding site 2 out of 4 in the Human Phosphomannomutase 2 (PMM2) with Mutation T237M in Apo State


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 Apo State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg306

b:37.0
occ:1.00
 O A:ASP223 2.3 39.4 1.0
O A:PHE221 2.4 37.5 1.0
O A:THR226 2.4 36.4 1.0
OG1 A:THR226 2.6 34.8 1.0
O A:HOH515 2.6 43.3 1.0
O A:HOH468 2.8 38.4 1.0
HG1 A:THR226 3.0 41.8 1.0
H A:THR226 3.2 39.4 1.0
C A:THR226 3.3 35.7 1.0
C A:ASP223 3.4 39.4 1.0
C A:PHE221 3.4 36.8 1.0
H A:GLY228 3.4 41.8 1.0
N A:ASP223 3.7 37.5 1.0
C A:THR222 3.7 35.3 1.0
CB A:THR226 3.7 34.5 1.0
HA A:THR222 3.8 44.0 1.0
CA A:THR226 3.8 35.1 1.0
H A:ASP223 3.8 45.0 1.0
N A:THR226 3.8 32.9 1.0
N A:GLY228 4.0 34.9 1.0
O A:THR222 4.0 39.4 1.0
O A:ILE220 4.0 33.8 1.0
CA A:THR222 4.1 36.6 1.0
HA A:PRO224 4.1 49.7 1.0
CA A:ASP223 4.1 37.4 1.0
N A:THR222 4.1 38.4 1.0
HA3 A:GLY228 4.1 42.0 1.0
HA A:PHE221 4.2 43.4 1.0
HB A:THR226 4.2 41.4 1.0
HB3 A:ASP223 4.3 47.8 1.0
N A:MET227 4.3 34.0 1.0
HA A:MET227 4.4 44.1 1.0
N A:PRO224 4.4 40.6 1.0
CA A:PHE221 4.4 36.1 1.0
CA A:PRO224 4.5 41.4 1.0
C A:PRO224 4.6 39.5 1.0
CA A:GLY228 4.6 35.0 1.0
HG23 A:THR226 4.6 44.9 1.0
CA A:MET227 4.7 36.8 1.0
HA A:THR226 4.7 42.1 1.0
C A:MET227 4.8 35.7 1.0
CB A:ASP223 4.8 39.8 1.0
O A:PRO224 4.8 36.2 1.0
CG2 A:THR226 4.8 37.5 1.0
HA A:ASP223 4.9 44.9 1.0
H A:THR222 4.9 46.0 1.0
N A:ARG225 4.9 41.4 1.0
HA2 A:GLY228 4.9 42.0 1.0
C A:ILE220 5.0 35.4 1.0

Magnesium binding site 3 out of 4 in 7o5z

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Magnesium binding site 3 out of 4 in the Human Phosphomannomutase 2 (PMM2) with Mutation T237M in Apo State


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 Apo State within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1005

b:38.9
occ:1.00
 OD2 B:ASP12 1.9 37.0 1.0
O B:HOH1117 1.9 44.7 1.0
O B:ASP14 2.0 37.8 1.0
O B:HOH1101 2.2 33.5 1.0
OD1 B:ASP209 2.2 42.0 1.0
O B:HOH1119 2.3 39.7 1.0
CG B:ASP12 2.9 37.0 1.0
C B:ASP14 3.2 39.6 1.0
CG B:ASP209 3.2 46.8 1.0
HG1 B:THR16 3.3 40.6 1.0
OD1 B:ASP12 3.3 36.7 1.0
OD2 B:ASP209 3.6 48.7 1.0
HA3 B:GLY15 3.6 49.0 1.0
HB3 B:ASP14 3.7 49.9 1.0
H B:ASP209 3.7 46.9 1.0
HG2 B:LYS210 3.9 56.9 1.0
OD2 B:ASP217 4.0 38.7 1.0
OG1 B:THR16 4.1 33.8 1.0
N B:GLY15 4.1 40.5 1.0
CA B:ASP14 4.1 40.8 1.0
CA B:GLY15 4.2 40.9 1.0
CB B:ASP12 4.2 34.1 1.0
HD21 B:ASN216 4.2 50.8 1.0
HB3 B:ASP12 4.2 40.9 1.0
N B:ASP14 4.3 39.2 1.0
H B:ASP14 4.3 47.0 1.0
H B:THR16 4.3 44.6 1.0
CB B:ASP14 4.4 41.6 1.0
HG3 B:LYS210 4.5 56.9 1.0
CB B:ASP209 4.5 43.7 1.0
C B:GLY15 4.5 40.2 1.0
N B:ASP209 4.5 39.1 1.0
N B:THR16 4.5 37.1 1.0
CG B:LYS210 4.6 47.4 1.0
HB2 B:ASP12 4.6 40.9 1.0
OD1 B:ASN216 4.6 41.4 1.0
HB3 B:ASP209 4.7 52.5 1.0
H B:LYS210 4.7 51.7 1.0
HB2 B:LYS210 4.7 49.8 1.0
HZ3 B:LYS189 4.7 50.0 1.0
HZ2 B:LYS189 4.8 50.0 1.0
HB B:THR16 4.8 43.0 1.0
C B:VAL13 4.8 37.0 1.0
CG B:ASP217 4.9 36.8 1.0
H B:VAL13 4.9 42.2 1.0
OD1 B:ASP217 4.9 35.9 1.0
CA B:ASP209 5.0 42.1 1.0
H B:GLY15 5.0 48.6 1.0
ND2 B:ASN216 5.0 42.3 1.0
N B:LYS210 5.0 43.1 1.0
CB B:THR16 5.0 35.9 1.0

Magnesium binding site 4 out of 4 in 7o5z

Go back to Magnesium Binding Sites List in 7o5z
Magnesium binding site 4 out of 4 in the Human Phosphomannomutase 2 (PMM2) with Mutation T237M in Apo State


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 Apo State within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1006

b:39.0
occ:1.00
 O B:THR226 2.3 33.7 1.0
O B:ASP223 2.4 39.0 1.0
OG1 B:THR226 2.5 31.9 1.0
O B:PHE221 2.6 36.7 1.0
O B:HOH1207 2.7 45.4 1.0
HG1 B:THR226 2.9 38.3 1.0
O B:HOH1160 2.9 48.1 1.0
H B:THR226 3.1 40.0 1.0
C B:THR226 3.2 36.0 1.0
H B:GLY228 3.4 45.5 1.0
C B:ASP223 3.5 38.6 1.0
CB B:THR226 3.6 34.2 1.0
C B:PHE221 3.6 38.4 1.0
CA B:THR226 3.7 34.9 1.0
N B:THR226 3.8 33.3 1.0
C B:THR222 3.9 38.3 1.0
N B:ASP223 3.9 39.1 1.0
N B:GLY228 4.0 37.9 1.0
HA B:PRO224 4.0 48.3 1.0
HA B:THR222 4.1 47.6 1.0
O B:THR222 4.1 42.2 1.0
H B:ASP223 4.1 46.9 1.0
HA3 B:GLY228 4.1 47.6 1.0
HB B:THR226 4.2 41.0 1.0
O B:ILE220 4.2 32.1 1.0
HA B:MET227 4.2 46.1 1.0
O B:HOH1211 4.2 48.8 0.5
N B:MET227 4.2 36.3 1.0
HA B:PHE221 4.3 44.3 1.0
CA B:THR222 4.3 39.7 1.0
CA B:ASP223 4.3 40.5 1.0
N B:THR222 4.3 34.9 1.0
HG23 B:THR226 4.4 41.3 1.0
N B:PRO224 4.5 38.3 1.0
HB3 B:ASP223 4.5 43.4 1.0
CA B:PRO224 4.5 40.3 1.0
CA B:PHE221 4.6 36.9 1.0
CA B:GLY228 4.6 39.6 1.0
CA B:MET227 4.6 38.4 1.0
HA B:THR226 4.6 41.9 1.0
CG2 B:THR226 4.6 34.5 1.0
C B:PRO224 4.7 36.3 1.0
C B:MET227 4.7 37.9 1.0
N B:ARG225 4.9 36.6 1.0
H B:ARG225 4.9 43.9 1.0
H B:MET227 5.0 43.6 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 02:33:38 2024

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