Atomistry » Magnesium » PDB 7o2d-7o9g » 7o5z
Atomistry »
  Magnesium »
    PDB 7o2d-7o9g »
      7o5z »

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

Go back to Magnesium Binding Sites List in 7o5z
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

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy