Magnesium in PDB 7o4g: Human Phosphomannomutase 2 (PMM2) Wild-Type Soaked with the Activator Glucose 1,6-Bisphosphate
Enzymatic activity of Human Phosphomannomutase 2 (PMM2) Wild-Type Soaked with the Activator Glucose 1,6-Bisphosphate
All present enzymatic activity of Human Phosphomannomutase 2 (PMM2) Wild-Type Soaked with the Activator Glucose 1,6-Bisphosphate:
5.4.2.8;
Protein crystallography data
The structure of Human Phosphomannomutase 2 (PMM2) Wild-Type Soaked with the Activator Glucose 1,6-Bisphosphate, PDB code: 7o4g
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)
|
60.21 /
2.66
|
Space group
|
P 65 2 2
|
Cell size a, b, c (Å), α, β, γ (°)
|
71.144,
71.144,
361.266,
90,
90,
120
|
R / Rfree (%)
|
22.4 /
27.3
|
Other elements in 7o4g:
The structure of Human Phosphomannomutase 2 (PMM2) Wild-Type Soaked with the Activator Glucose 1,6-Bisphosphate also contains other interesting chemical elements:
Magnesium Binding Sites:
The binding sites of Magnesium atom in the Human Phosphomannomutase 2 (PMM2) Wild-Type Soaked with the Activator Glucose 1,6-Bisphosphate
(pdb code 7o4g). 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 Soaked with the Activator Glucose 1,6-Bisphosphate, PDB code: 7o4g:
Jump to Magnesium binding site number:
1;
2;
3;
4;
Magnesium binding site 1 out
of 4 in 7o4g
Go back to
Magnesium Binding Sites List in 7o4g
Magnesium binding site 1 out
of 4 in the Human Phosphomannomutase 2 (PMM2) Wild-Type Soaked with the Activator Glucose 1,6-Bisphosphate
![](/pictures/MG/pdb/o4/7o4g-MG-sphere_01.jpg) Mono view
![](/pictures/MG/pdb/o4/7o4g-MG-sphere_01_stereo.jpg) 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 Soaked with the Activator Glucose 1,6-Bisphosphate within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg302
b:57.9
occ:1.00
|
O
|
A:HOH417
|
1.8
|
58.3
|
1.0
|
O
|
A:HOH411
|
1.8
|
56.4
|
1.0
|
O
|
A:ASP14
|
2.1
|
57.0
|
1.0
|
OD2
|
A:ASP12
|
2.1
|
48.5
|
1.0
|
OD1
|
A:ASP209
|
2.3
|
58.9
|
1.0
|
O
|
A:HOH409
|
2.6
|
55.6
|
1.0
|
CG
|
A:ASP209
|
3.0
|
62.9
|
1.0
|
CG
|
A:ASP12
|
3.0
|
50.7
|
1.0
|
OD2
|
A:ASP209
|
3.1
|
63.1
|
1.0
|
OD1
|
A:ASP12
|
3.3
|
59.1
|
1.0
|
C
|
A:ASP14
|
3.3
|
52.5
|
1.0
|
HG1
|
A:THR16
|
3.5
|
56.9
|
1.0
|
HB3
|
A:ASP14
|
3.7
|
71.5
|
1.0
|
HG2
|
A:LYS210
|
3.7
|
71.0
|
1.0
|
HA3
|
A:GLY15
|
3.7
|
65.2
|
1.0
|
OD2
|
A:ASP217
|
3.7
|
42.3
|
1.0
|
H
|
A:ASP209
|
3.8
|
53.5
|
1.0
|
HD22
|
A:ASN216
|
3.9
|
59.6
|
1.0
|
HG3
|
A:LYS210
|
4.1
|
71.0
|
1.0
|
CA
|
A:ASP14
|
4.2
|
57.0
|
1.0
|
N
|
A:GLY15
|
4.2
|
53.6
|
1.0
|
OG1
|
A:THR16
|
4.2
|
46.4
|
1.0
|
CB
|
A:ASP14
|
4.3
|
58.6
|
1.0
|
CB
|
A:ASP12
|
4.3
|
47.5
|
1.0
|
CG
|
A:LYS210
|
4.3
|
58.2
|
1.0
|
CB
|
A:ASP209
|
4.3
|
52.0
|
1.0
|
CA
|
A:GLY15
|
4.4
|
53.3
|
1.0
|
OD1
|
A:ASP14
|
4.4
|
75.0
|
1.0
|
HB3
|
A:ASP12
|
4.4
|
58.2
|
1.0
|
N
|
A:ASP14
|
4.4
|
62.1
|
1.0
|
OD1
|
A:ASN216
|
4.4
|
58.2
|
1.0
|
H
|
A:ASP14
|
4.4
|
75.7
|
1.0
|
HB2
|
A:LYS210
|
4.5
|
63.7
|
1.0
|
H
|
A:THR16
|
4.5
|
63.6
|
1.0
|
N
|
A:ASP209
|
4.6
|
43.6
|
1.0
|
HB3
|
A:ASP209
|
4.6
|
63.5
|
1.0
|
HB2
|
A:ASP12
|
4.6
|
58.2
|
1.0
|
ND2
|
A:ASN216
|
4.6
|
48.7
|
1.0
|
CG
|
A:ASP14
|
4.6
|
74.1
|
1.0
|
CG
|
A:ASP217
|
4.6
|
50.7
|
1.0
|
HZ3
|
A:LYS210
|
4.7
|
100.0
|
1.0
|
H
|
A:LYS210
|
4.7
|
73.0
|
1.0
|
OD1
|
A:ASP217
|
4.7
|
54.9
|
1.0
|
C
|
A:GLY15
|
4.7
|
48.5
|
1.0
|
N
|
A:THR16
|
4.7
|
52.0
|
1.0
|
CA
|
A:ASP209
|
4.9
|
44.4
|
1.0
|
CG
|
A:ASN216
|
4.9
|
54.7
|
1.0
|
CB
|
A:LYS210
|
4.9
|
52.2
|
1.0
|
N
|
A:LYS210
|
5.0
|
59.9
|
1.0
|
H
|
A:VAL13
|
5.0
|
53.0
|
1.0
|
HB2
|
A:ASP209
|
5.0
|
63.5
|
1.0
|
|
Magnesium binding site 2 out
of 4 in 7o4g
Go back to
Magnesium Binding Sites List in 7o4g
Magnesium binding site 2 out
of 4 in the Human Phosphomannomutase 2 (PMM2) Wild-Type Soaked with the Activator Glucose 1,6-Bisphosphate
![](/pictures/MG/pdb/o4/7o4g-MG-sphere_02.jpg) Mono view
![](/pictures/MG/pdb/o4/7o4g-MG-sphere_02_stereo.jpg) 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 Soaked with the Activator Glucose 1,6-Bisphosphate within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg303
b:42.0
occ:1.00
|
O
|
A:PHE221
|
2.5
|
53.3
|
1.0
|
OG1
|
A:THR226
|
2.5
|
40.5
|
1.0
|
O
|
A:ASP223
|
2.5
|
39.1
|
1.0
|
HG1
|
A:THR226
|
2.8
|
49.7
|
1.0
|
O
|
A:THR226
|
2.9
|
53.4
|
1.0
|
O
|
A:HOH438
|
3.1
|
37.9
|
1.0
|
H
|
A:GLY228
|
3.1
|
61.5
|
1.0
|
C
|
A:THR226
|
3.4
|
39.6
|
1.0
|
C
|
A:PHE221
|
3.4
|
47.4
|
1.0
|
H
|
A:THR226
|
3.5
|
49.4
|
1.0
|
HA
|
A:THR222
|
3.6
|
51.9
|
1.0
|
C
|
A:ASP223
|
3.6
|
41.9
|
1.0
|
CB
|
A:THR226
|
3.7
|
48.9
|
1.0
|
C
|
A:THR222
|
3.8
|
43.6
|
1.0
|
N
|
A:GLY228
|
3.8
|
50.3
|
1.0
|
N
|
A:ASP223
|
3.8
|
50.9
|
1.0
|
CA
|
A:THR226
|
3.9
|
44.0
|
1.0
|
H
|
A:ASP223
|
4.0
|
62.2
|
1.0
|
CA
|
A:THR222
|
4.0
|
42.3
|
1.0
|
HA
|
A:PRO224
|
4.0
|
57.6
|
1.0
|
N
|
A:THR222
|
4.0
|
51.0
|
1.0
|
HA3
|
A:GLY228
|
4.1
|
47.2
|
1.0
|
N
|
A:THR226
|
4.1
|
40.2
|
1.0
|
N
|
A:MET227
|
4.2
|
50.0
|
1.0
|
HA
|
A:PHE221
|
4.2
|
56.2
|
1.0
|
HA
|
A:MET227
|
4.2
|
58.5
|
1.0
|
O
|
A:THR222
|
4.2
|
55.3
|
1.0
|
HB
|
A:THR226
|
4.3
|
59.9
|
1.0
|
CA
|
A:ASP223
|
4.4
|
37.4
|
1.0
|
O
|
A:ILE220
|
4.4
|
54.7
|
1.0
|
CA
|
A:PHE221
|
4.4
|
45.9
|
1.0
|
HG23
|
A:THR226
|
4.5
|
76.6
|
1.0
|
CA
|
A:GLY228
|
4.5
|
38.4
|
1.0
|
N
|
A:PRO224
|
4.5
|
53.1
|
1.0
|
CA
|
A:MET227
|
4.6
|
47.8
|
1.0
|
CA
|
A:PRO224
|
4.6
|
47.0
|
1.0
|
HB3
|
A:ASP223
|
4.7
|
57.0
|
1.0
|
C
|
A:MET227
|
4.7
|
44.7
|
1.0
|
CG2
|
A:THR226
|
4.7
|
62.9
|
1.0
|
C
|
A:PRO224
|
4.8
|
52.9
|
1.0
|
H
|
A:MET227
|
4.8
|
61.1
|
1.0
|
H
|
A:THR222
|
4.8
|
62.4
|
1.0
|
HA2
|
A:GLY228
|
4.8
|
47.2
|
1.0
|
HA
|
A:THR226
|
4.9
|
53.9
|
1.0
|
O
|
A:PRO224
|
4.9
|
54.3
|
1.0
|
|
Magnesium binding site 3 out
of 4 in 7o4g
Go back to
Magnesium Binding Sites List in 7o4g
Magnesium binding site 3 out
of 4 in the Human Phosphomannomutase 2 (PMM2) Wild-Type Soaked with the Activator Glucose 1,6-Bisphosphate
![](/pictures/MG/pdb/o4/7o4g-MG-sphere_03.jpg) Mono view
![](/pictures/MG/pdb/o4/7o4g-MG-sphere_03_stereo.jpg) 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 Soaked with the Activator Glucose 1,6-Bisphosphate within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg301
b:57.3
occ:1.00
|
O
|
B:HOH402
|
2.0
|
54.3
|
1.0
|
O
|
B:ASP14
|
2.0
|
56.8
|
1.0
|
OD2
|
B:ASP12
|
2.0
|
65.0
|
1.0
|
O
|
B:HOH421
|
2.4
|
57.6
|
1.0
|
OD1
|
B:ASP209
|
2.5
|
74.8
|
1.0
|
O
|
B:HOH403
|
2.6
|
54.9
|
1.0
|
OD2
|
B:ASP209
|
3.1
|
74.1
|
1.0
|
CG
|
B:ASP209
|
3.1
|
70.4
|
1.0
|
C
|
B:ASP14
|
3.2
|
54.1
|
1.0
|
HA3
|
B:GLY15
|
3.2
|
79.2
|
1.0
|
CG
|
B:ASP12
|
3.2
|
60.4
|
1.0
|
HB3
|
B:ASP14
|
3.5
|
85.5
|
1.0
|
HG2
|
B:LYS210
|
3.7
|
80.4
|
1.0
|
H
|
B:ASP209
|
3.8
|
74.1
|
1.0
|
OD2
|
B:ASP217
|
3.9
|
62.2
|
1.0
|
OD1
|
B:ASP12
|
3.9
|
59.5
|
1.0
|
N
|
B:GLY15
|
4.0
|
68.3
|
1.0
|
CA
|
B:GLY15
|
4.0
|
65.1
|
1.0
|
HD22
|
B:ASN216
|
4.0
|
67.6
|
1.0
|
HG1
|
B:THR16
|
4.0
|
72.9
|
1.0
|
CA
|
B:ASP14
|
4.2
|
58.2
|
1.0
|
HB3
|
B:ASP12
|
4.2
|
73.1
|
1.0
|
CB
|
B:ASP14
|
4.2
|
70.2
|
1.0
|
H
|
B:LYS210
|
4.3
|
78.3
|
1.0
|
H
|
B:THR16
|
4.3
|
79.6
|
1.0
|
CB
|
B:ASP12
|
4.4
|
60.0
|
1.0
|
N
|
B:ASP14
|
4.4
|
70.1
|
1.0
|
H
|
B:ASP14
|
4.5
|
85.3
|
1.0
|
HG3
|
B:LYS210
|
4.5
|
80.4
|
1.0
|
CG
|
B:LYS210
|
4.5
|
66.0
|
1.0
|
C
|
B:GLY15
|
4.6
|
71.0
|
1.0
|
CB
|
B:ASP209
|
4.6
|
65.5
|
1.0
|
N
|
B:THR16
|
4.6
|
65.4
|
1.0
|
N
|
B:ASP209
|
4.6
|
60.8
|
1.0
|
HE3
|
B:LYS210
|
4.7
|
78.9
|
1.0
|
OD1
|
B:ASN216
|
4.7
|
58.0
|
1.0
|
HA2
|
B:GLY15
|
4.7
|
79.2
|
1.0
|
CG
|
B:ASP217
|
4.8
|
58.7
|
1.0
|
OD1
|
B:ASP217
|
4.8
|
56.4
|
1.0
|
H
|
B:GLY15
|
4.8
|
83.1
|
1.0
|
OG1
|
B:THR16
|
4.8
|
59.8
|
1.0
|
ND2
|
B:ASN216
|
4.8
|
55.4
|
1.0
|
HB2
|
B:ASP12
|
4.8
|
73.1
|
1.0
|
OD2
|
B:ASP14
|
4.9
|
67.0
|
1.0
|
HB2
|
B:ASP14
|
4.9
|
85.5
|
1.0
|
N
|
B:LYS210
|
4.9
|
64.3
|
1.0
|
HB
|
B:THR16
|
4.9
|
68.8
|
1.0
|
HZ2
|
B:LYS189
|
4.9
|
61.0
|
1.0
|
|
Magnesium binding site 4 out
of 4 in 7o4g
Go back to
Magnesium Binding Sites List in 7o4g
Magnesium binding site 4 out
of 4 in the Human Phosphomannomutase 2 (PMM2) Wild-Type Soaked with the Activator Glucose 1,6-Bisphosphate
![](/pictures/MG/pdb/o4/7o4g-MG-sphere_04.jpg) Mono view
![](/pictures/MG/pdb/o4/7o4g-MG-sphere_04_stereo.jpg) 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 Soaked with the Activator Glucose 1,6-Bisphosphate within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg302
b:64.4
occ:1.00
|
O
|
B:HOH431
|
2.1
|
60.5
|
1.0
|
O
|
B:THR226
|
2.4
|
46.8
|
1.0
|
OG1
|
B:THR226
|
2.6
|
50.5
|
1.0
|
O
|
B:ASP223
|
2.6
|
54.3
|
1.0
|
O
|
B:PHE221
|
2.8
|
60.1
|
1.0
|
HG1
|
B:THR226
|
3.0
|
61.7
|
1.0
|
H
|
B:GLY228
|
3.1
|
50.1
|
1.0
|
C
|
B:THR226
|
3.2
|
51.6
|
1.0
|
H
|
B:THR226
|
3.4
|
62.4
|
1.0
|
CB
|
B:THR226
|
3.7
|
45.6
|
1.0
|
N
|
B:GLY228
|
3.8
|
40.8
|
1.0
|
CA
|
B:THR226
|
3.8
|
49.6
|
1.0
|
C
|
B:ASP223
|
3.8
|
60.2
|
1.0
|
HA
|
B:MET227
|
3.9
|
66.7
|
1.0
|
C
|
B:PHE221
|
3.9
|
56.6
|
1.0
|
N
|
B:THR226
|
4.0
|
51.0
|
1.0
|
HA
|
B:PRO224
|
4.1
|
69.8
|
1.0
|
N
|
B:MET227
|
4.1
|
50.7
|
1.0
|
HB
|
B:THR226
|
4.1
|
55.9
|
1.0
|
HA3
|
B:GLY228
|
4.1
|
61.0
|
1.0
|
N
|
B:ASP223
|
4.3
|
57.5
|
1.0
|
CA
|
B:MET227
|
4.3
|
54.6
|
1.0
|
H
|
B:ASP223
|
4.4
|
70.2
|
1.0
|
C
|
B:THR222
|
4.4
|
56.2
|
1.0
|
HA
|
B:PHE221
|
4.4
|
68.6
|
1.0
|
HA
|
B:THR222
|
4.4
|
60.9
|
1.0
|
C
|
B:MET227
|
4.5
|
55.9
|
1.0
|
CA
|
B:GLY228
|
4.5
|
49.9
|
1.0
|
CA
|
B:PRO224
|
4.6
|
57.2
|
1.0
|
CA
|
B:ASP223
|
4.7
|
52.0
|
1.0
|
N
|
B:PRO224
|
4.7
|
59.3
|
1.0
|
O
|
B:THR222
|
4.7
|
56.3
|
1.0
|
C
|
B:PRO224
|
4.7
|
53.8
|
1.0
|
CA
|
B:THR222
|
4.7
|
49.8
|
1.0
|
N
|
B:THR222
|
4.7
|
51.2
|
1.0
|
HA
|
B:THR226
|
4.8
|
60.6
|
1.0
|
O
|
B:ILE220
|
4.8
|
55.3
|
1.0
|
CA
|
B:PHE221
|
4.8
|
56.2
|
1.0
|
H
|
B:MET227
|
4.8
|
62.0
|
1.0
|
O
|
B:PRO224
|
4.9
|
49.8
|
1.0
|
CG2
|
B:THR226
|
4.9
|
54.9
|
1.0
|
HG23
|
B:THR226
|
4.9
|
67.0
|
1.0
|
HB3
|
B:ASP223
|
4.9
|
69.5
|
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 Apr 6 18:00:24 2023
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