Magnesium in PDB 7o0c: Human Phosphomannomutase 2 (PMM2) Wild-Type in Apo State

All present enzymatic activity of Human Phosphomannomutase 2 (PMM2) Wild-Type in Apo State:
5.4.2.8;

The structure of Human Phosphomannomutase 2 (PMM2) Wild-Type in Apo State, PDB code: 7o0c 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)	39.40 / 2.80
Space group	P 65 2 2
Cell size a, b, c (Å), α, β, γ (°)	70.582, 70.582, 360.801, 90, 90, 120
R / Rfree (%)	21.7 / 26.8

The structure of Human Phosphomannomutase 2 (PMM2) Wild-Type in Apo State also contains other interesting chemical elements:

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

The binding sites of Magnesium atom in the Human Phosphomannomutase 2 (PMM2) Wild-Type in Apo State (pdb code 7o0c). 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 in Apo State, PDB code: 7o0c:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Human Phosphomannomutase 2 (PMM2) Wild-Type 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) Wild-Type in Apo State within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg301 b:62.0 occ:1.00 OD1 A:ASP12 1.9 62.2 1.0 O A:ASP14 1.9 64.6 1.0 O A:HOH409 2.0 66.2 1.0 O A:HOH401 2.1 72.9 1.0 OD1 A:ASP209 2.6 62.2 1.0 O A:HOH405 2.6 69.5 1.0 CG A:ASP12 2.8 59.5 1.0 OD2 A:ASP12 3.0 60.6 1.0 C A:ASP14 3.0 62.4 1.0 CG A:ASP209 3.5 59.3 1.0 N A:ASP14 3.7 63.1 1.0 CA A:ASP14 3.7 60.3 1.0 OG1 A:THR16 3.7 56.6 1.0 OD2 A:ASP209 3.8 58.5 1.0 CB A:ASP14 3.9 66.4 1.0 ND2 A:ASN216 4.1 73.2 1.0 N A:GLY15 4.1 59.8 1.0 CB A:ASP12 4.2 52.6 1.0 OD2 A:ASP217 4.3 66.2 1.0 N A:THR16 4.4 56.4 1.0 C A:VAL13 4.4 62.7 1.0 CA A:GLY15 4.4 59.1 1.0 N A:VAL13 4.6 55.6 1.0 OD1 A:ASP217 4.7 63.6 1.0 N A:ASP209 4.7 64.3 1.0 NZ A:LYS189 4.7 64.2 1.0 CB A:ASP209 4.7 53.0 1.0 C A:GLY15 4.7 55.1 1.0 CB A:THR16 4.8 58.7 1.0 O A:VAL13 4.9 54.9 1.0 OD1 A:ASN216 4.9 88.3 1.0 O A:HOH412 4.9 40.1 1.0 CG A:ASP217 4.9 63.8 1.0 C A:ASP12 4.9 57.8 1.0 CG A:ASN216 4.9 67.7 1.0

Magnesium binding site 2 out of 4 in the Human Phosphomannomutase 2 (PMM2) Wild-Type 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) Wild-Type in Apo State within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg302 b:60.5 occ:1.00 O A:THR226 2.0 64.3 1.0 O A:ASP223 2.2 58.4 1.0 O A:PHE221 2.5 63.7 1.0 OG1 A:THR226 2.6 60.4 1.0 O A:HOH414 2.8 67.3 1.0 C A:THR226 3.1 57.0 1.0 C A:ASP223 3.3 65.2 1.0 N A:ASP223 3.6 61.5 1.0 C A:PHE221 3.6 60.8 1.0 CB A:THR226 3.7 59.7 1.0 CA A:THR226 3.7 58.3 1.0 C A:THR222 3.8 59.4 1.0 N A:THR226 3.8 59.2 1.0 N A:GLY228 3.9 61.0 1.0 CA A:ASP223 4.0 59.2 1.0 N A:MET227 4.1 56.2 1.0 CA A:THR222 4.2 58.0 1.0 O A:ILE220 4.3 61.9 1.0 N A:PRO224 4.3 70.0 1.0 N A:THR222 4.3 63.0 1.0 O A:THR222 4.4 63.7 1.0 CA A:MET227 4.4 60.3 1.0 CA A:PRO224 4.4 64.2 1.0 CA A:GLY228 4.5 52.8 1.0 C A:MET227 4.6 60.9 1.0 C A:PRO224 4.6 63.9 1.0 CA A:PHE221 4.6 58.8 1.0 CB A:ASP223 4.7 76.3 1.0 O A:PRO224 4.7 59.3 1.0 CG2 A:THR226 4.9 61.1 1.0

Magnesium binding site 3 out of 4 in the Human Phosphomannomutase 2 (PMM2) Wild-Type 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) Wild-Type in Apo State within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg301 b:67.7 occ:1.00 OD1 B:ASP12 1.9 67.7 1.0 O B:ASP14 2.1 64.7 1.0 O B:HOH409 2.2 80.4 1.0 O B:HOH401 2.2 66.2 1.0 O B:HOH414 2.2 73.9 1.0 OD1 B:ASP209 2.3 76.7 1.0 CG B:ASP12 2.9 66.3 1.0 CG B:ASP209 3.1 69.7 1.0 C B:ASP14 3.3 63.8 1.0 OD2 B:ASP209 3.3 67.0 1.0 OD2 B:ASP12 3.4 72.9 1.0 OD1 B:ASP217 4.0 64.5 1.0 CA B:ASP14 4.1 68.3 1.0 CB B:ASP14 4.1 67.2 1.0 ND2 B:ASN216 4.1 59.2 1.0 CB B:ASP12 4.2 56.9 1.0 N B:ASP14 4.2 68.4 1.0 N B:GLY15 4.3 61.9 1.0 CA B:GLY15 4.5 67.1 1.0 OD1 B:ASN216 4.5 77.7 1.0 CB B:ASP209 4.6 62.5 1.0 CG B:LYS210 4.6 56.6 1.0 OD2 B:ASP217 4.7 68.1 1.0 CG B:ASN216 4.8 61.0 1.0 N B:ASP209 4.8 64.2 1.0 CG B:ASP217 4.8 63.6 1.0 N B:THR16 4.8 56.9 1.0

Magnesium binding site 4 out of 4 in the Human Phosphomannomutase 2 (PMM2) Wild-Type 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) Wild-Type in Apo State within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg302 b:70.3 occ:1.00 O B:THR226 1.9 62.0 1.0 O B:ASP223 2.1 56.0 1.0 OG1 B:THR226 2.4 60.6 1.0 O B:HOH413 2.6 69.7 1.0 O B:HOH411 2.8 66.8 1.0 O B:PHE221 2.8 69.4 1.0 C B:THR226 2.8 56.8 1.0 C B:ASP223 3.2 63.0 1.0 CA B:THR226 3.3 54.2 1.0 CB B:THR226 3.4 57.9 1.0 N B:THR226 3.4 62.2 1.0 N B:ASP223 3.6 59.2 1.0 C B:PHE221 3.8 62.9 1.0 CA B:ASP223 3.9 58.7 1.0 C B:THR222 4.0 59.1 1.0 N B:MET227 4.0 62.3 1.0 O B:ILE220 4.0 60.5 1.0 N B:GLY228 4.2 52.7 1.0 N B:PRO224 4.3 61.4 1.0 O B:THR222 4.4 67.3 1.0 CG2 B:THR226 4.4 54.4 1.0 CA B:PRO224 4.5 60.0 1.0 CA B:MET227 4.5 63.1 1.0 C B:PRO224 4.5 59.6 1.0 CB B:ASP223 4.5 57.2 1.0 CA B:THR222 4.6 59.9 1.0 CA B:PHE221 4.6 62.4 1.0 N B:THR222 4.6 59.2 1.0 C B:ARG225 4.7 59.9 1.0 C B:MET227 4.8 62.8 1.0 N B:ARG225 4.8 54.3 1.0 O B:PRO224 4.8 65.3 1.0 CA B:GLY228 4.8 52.0 1.0

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