Magnesium 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:
Magnesium Binding Sites:
The binding sites of Magnesium 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 Magnesium atom.
In total 4 binding sites of Magnesium 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 Magnesium binding site number:
1;
2;
3;
4;
Magnesium binding site 1 out
of 4 in 7o58
Go back to
Magnesium Binding Sites List in 7o58
Magnesium binding site 1 out
of 4 in the Human Phosphomannomutase 2 (PMM2) with Mutation T237M in Complex with the Activator Glucose 1,6-Bisphosphate
![](/pictures/MG/pdb/o5/7o58-MG-sphere_01.jpg) Mono view
![](/pictures/MG/pdb/o5/7o58-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) with Mutation T237M in Complex with the Activator Glucose 1,6-Bisphosphate within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg407
b:36.1
occ:1.00
|
O
|
A:HOH509
|
1.9
|
35.5
|
1.0
|
OD2
|
A:ASP12
|
2.0
|
37.7
|
1.0
|
O
|
A:HOH604
|
2.0
|
36.5
|
1.0
|
OD1
|
A:ASP209
|
2.0
|
37.2
|
1.0
|
O
|
A:HOH551
|
2.1
|
37.0
|
1.0
|
O
|
A:ASP14
|
2.1
|
40.8
|
1.0
|
CG
|
A:ASP12
|
3.0
|
37.7
|
1.0
|
CG
|
A:ASP209
|
3.1
|
39.7
|
1.0
|
HG1
|
A:THR16
|
3.3
|
43.8
|
1.0
|
C
|
A:ASP14
|
3.3
|
39.7
|
1.0
|
OD1
|
A:ASP12
|
3.4
|
40.2
|
1.0
|
OD2
|
A:ASP209
|
3.5
|
43.4
|
1.0
|
H
|
A:ASP209
|
3.7
|
40.0
|
1.0
|
HA3
|
A:GLY15
|
3.7
|
45.0
|
1.0
|
HB3
|
A:ASP14
|
3.8
|
54.2
|
1.0
|
HG2
|
A:LYS210
|
3.9
|
47.4
|
1.0
|
OD2
|
A:ASP217
|
4.0
|
37.8
|
1.0
|
OG1
|
A:THR16
|
4.1
|
36.5
|
1.0
|
HD22
|
A:ASN216
|
4.1
|
54.4
|
1.0
|
O
|
A:HOH638
|
4.2
|
47.9
|
1.0
|
OD1
|
A:ASN216
|
4.2
|
45.2
|
1.0
|
CB
|
A:ASP12
|
4.3
|
33.7
|
1.0
|
CA
|
A:ASP14
|
4.3
|
41.7
|
1.0
|
N
|
A:GLY15
|
4.3
|
39.4
|
1.0
|
HB3
|
A:ASP12
|
4.3
|
40.4
|
1.0
|
HG3
|
A:LYS210
|
4.3
|
47.4
|
1.0
|
H
|
A:ASP14
|
4.3
|
50.8
|
1.0
|
CA
|
A:GLY15
|
4.4
|
37.5
|
1.0
|
N
|
A:ASP14
|
4.4
|
42.3
|
1.0
|
H
|
A:THR16
|
4.4
|
43.8
|
1.0
|
CB
|
A:ASP209
|
4.5
|
31.5
|
1.0
|
CB
|
A:ASP14
|
4.5
|
45.2
|
1.0
|
CG
|
A:LYS210
|
4.5
|
39.5
|
1.0
|
N
|
A:ASP209
|
4.5
|
33.3
|
1.0
|
HB2
|
A:LYS210
|
4.6
|
47.1
|
1.0
|
HZ1
|
A:LYS189
|
4.6
|
53.6
|
1.0
|
HB2
|
A:ASP12
|
4.6
|
40.4
|
1.0
|
HB3
|
A:ASP209
|
4.6
|
37.8
|
1.0
|
H
|
A:LYS210
|
4.6
|
46.3
|
1.0
|
N
|
A:THR16
|
4.7
|
36.5
|
1.0
|
C
|
A:GLY15
|
4.7
|
39.0
|
1.0
|
O
|
A:HOH629
|
4.8
|
44.4
|
1.0
|
ND2
|
A:ASN216
|
4.8
|
45.3
|
1.0
|
HZ3
|
A:LYS189
|
4.8
|
53.6
|
1.0
|
CG
|
A:ASP217
|
4.8
|
36.1
|
1.0
|
OD1
|
A:ASP217
|
4.8
|
43.0
|
1.0
|
H
|
A:VAL13
|
4.9
|
41.1
|
1.0
|
HB
|
A:THR16
|
4.9
|
47.3
|
1.0
|
CA
|
A:ASP209
|
4.9
|
33.4
|
1.0
|
N
|
A:LYS210
|
4.9
|
38.5
|
1.0
|
CG
|
A:ASN216
|
5.0
|
42.8
|
1.0
|
OD2
|
A:ASP14
|
5.0
|
59.6
|
1.0
|
C
|
A:VAL13
|
5.0
|
40.5
|
1.0
|
|
Magnesium binding site 2 out
of 4 in 7o58
Go back to
Magnesium Binding Sites List in 7o58
Magnesium binding site 2 out
of 4 in the Human Phosphomannomutase 2 (PMM2) with Mutation T237M in Complex with the Activator Glucose 1,6-Bisphosphate
![](/pictures/MG/pdb/o5/7o58-MG-sphere_02.jpg) Mono view
![](/pictures/MG/pdb/o5/7o58-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) with Mutation T237M in Complex with the Activator Glucose 1,6-Bisphosphate within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg408
b:37.5
occ:1.00
|
O
|
A:ASP223
|
2.3
|
36.0
|
1.0
|
O
|
A:THR226
|
2.3
|
35.4
|
1.0
|
O
|
A:PHE221
|
2.3
|
37.6
|
1.0
|
O
|
A:HOH640
|
2.3
|
47.9
|
1.0
|
OG1
|
A:THR226
|
2.6
|
37.0
|
1.0
|
O
|
A:HOH585
|
2.6
|
39.7
|
1.0
|
HG1
|
A:THR226
|
3.0
|
44.4
|
1.0
|
H
|
A:THR226
|
3.2
|
40.0
|
1.0
|
C
|
A:THR226
|
3.2
|
36.2
|
1.0
|
C
|
A:ASP223
|
3.3
|
38.6
|
1.0
|
H
|
A:GLY228
|
3.4
|
42.5
|
1.0
|
C
|
A:PHE221
|
3.5
|
36.1
|
1.0
|
N
|
A:ASP223
|
3.7
|
37.3
|
1.0
|
CB
|
A:THR226
|
3.8
|
37.0
|
1.0
|
CA
|
A:THR226
|
3.8
|
37.4
|
1.0
|
C
|
A:THR222
|
3.8
|
38.7
|
1.0
|
H
|
A:ASP223
|
3.8
|
44.7
|
1.0
|
O
|
A:HOH644
|
3.8
|
51.2
|
1.0
|
N
|
A:THR226
|
3.8
|
33.4
|
1.0
|
HA
|
A:PRO224
|
3.9
|
45.5
|
1.0
|
HA
|
A:THR222
|
3.9
|
40.9
|
1.0
|
N
|
A:GLY228
|
4.0
|
35.4
|
1.0
|
O
|
A:ILE220
|
4.1
|
38.5
|
1.0
|
HA3
|
A:GLY228
|
4.1
|
44.4
|
1.0
|
CA
|
A:ASP223
|
4.1
|
39.1
|
1.0
|
CA
|
A:THR222
|
4.2
|
34.1
|
1.0
|
O
|
A:THR222
|
4.2
|
43.3
|
1.0
|
HA
|
A:PHE221
|
4.2
|
40.1
|
1.0
|
N
|
A:THR222
|
4.2
|
37.6
|
1.0
|
N
|
A:PRO224
|
4.3
|
40.0
|
1.0
|
N
|
A:MET227
|
4.3
|
40.1
|
1.0
|
HB
|
A:THR226
|
4.3
|
44.4
|
1.0
|
HA
|
A:MET227
|
4.3
|
45.1
|
1.0
|
HB3
|
A:ASP223
|
4.4
|
45.5
|
1.0
|
CA
|
A:PRO224
|
4.4
|
37.9
|
1.0
|
CA
|
A:PHE221
|
4.5
|
33.4
|
1.0
|
C
|
A:PRO224
|
4.6
|
40.1
|
1.0
|
CA
|
A:GLY228
|
4.6
|
37.0
|
1.0
|
CA
|
A:MET227
|
4.7
|
37.5
|
1.0
|
HG23
|
A:THR226
|
4.7
|
40.4
|
1.0
|
HA
|
A:THR226
|
4.7
|
44.9
|
1.0
|
O
|
A:HOH610
|
4.8
|
48.7
|
1.0
|
C
|
A:MET227
|
4.8
|
41.5
|
1.0
|
CG2
|
A:THR226
|
4.8
|
33.7
|
1.0
|
CB
|
A:ASP223
|
4.8
|
37.9
|
1.0
|
N
|
A:ARG225
|
4.9
|
38.6
|
1.0
|
HA
|
A:ASP223
|
4.9
|
47.0
|
1.0
|
O
|
A:PRO224
|
4.9
|
39.7
|
1.0
|
H
|
A:THR222
|
5.0
|
45.1
|
1.0
|
HA2
|
A:GLY228
|
5.0
|
44.4
|
1.0
|
|
Magnesium binding site 3 out
of 4 in 7o58
Go back to
Magnesium Binding Sites List in 7o58
Magnesium binding site 3 out
of 4 in the Human Phosphomannomutase 2 (PMM2) with Mutation T237M in Complex with the Activator Glucose 1,6-Bisphosphate
![](/pictures/MG/pdb/o5/7o58-MG-sphere_03.jpg) Mono view
![](/pictures/MG/pdb/o5/7o58-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) with Mutation T237M in Complex with the Activator Glucose 1,6-Bisphosphate within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg505
b:42.9
occ:1.00
|
OD2
|
B:ASP12
|
1.9
|
40.0
|
1.0
|
O
|
B:ASP14
|
2.0
|
39.0
|
1.0
|
OD1
|
B:ASP209
|
2.0
|
38.5
|
1.0
|
O
|
B:HOH607
|
2.1
|
38.4
|
1.0
|
O
|
B:HOH617
|
2.1
|
41.4
|
1.0
|
O
|
B:HOH632
|
2.2
|
46.7
|
1.0
|
CG
|
B:ASP12
|
2.9
|
42.6
|
1.0
|
CG
|
B:ASP209
|
3.0
|
46.8
|
1.0
|
OD1
|
B:ASP12
|
3.2
|
38.8
|
1.0
|
C
|
B:ASP14
|
3.2
|
41.9
|
1.0
|
HG1
|
B:THR16
|
3.4
|
46.8
|
1.0
|
OD2
|
B:ASP209
|
3.4
|
44.8
|
1.0
|
HB3
|
B:ASP14
|
3.6
|
58.0
|
1.0
|
HA3
|
B:GLY15
|
3.7
|
49.7
|
1.0
|
H
|
B:ASP209
|
3.8
|
46.8
|
1.0
|
HG2
|
B:LYS210
|
3.9
|
61.6
|
1.0
|
OD2
|
B:ASP217
|
4.1
|
43.8
|
1.0
|
CA
|
B:ASP14
|
4.1
|
42.8
|
1.0
|
OG1
|
B:THR16
|
4.1
|
39.0
|
1.0
|
N
|
B:GLY15
|
4.1
|
45.3
|
1.0
|
N
|
B:ASP14
|
4.2
|
41.0
|
1.0
|
CB
|
B:ASP12
|
4.2
|
34.8
|
1.0
|
H
|
B:ASP14
|
4.2
|
49.2
|
1.0
|
O
|
B:HOH714
|
4.2
|
54.1
|
1.0
|
CA
|
B:GLY15
|
4.3
|
41.4
|
1.0
|
HB3
|
B:ASP12
|
4.3
|
41.8
|
1.0
|
CB
|
B:ASP14
|
4.3
|
48.3
|
1.0
|
O
|
B:HOH610
|
4.4
|
46.9
|
1.0
|
CB
|
B:ASP209
|
4.4
|
44.8
|
1.0
|
HD21
|
B:ASN216
|
4.4
|
57.6
|
1.0
|
OD1
|
B:ASN216
|
4.5
|
47.1
|
1.0
|
HG3
|
B:LYS210
|
4.5
|
61.6
|
1.0
|
H
|
B:THR16
|
4.5
|
44.8
|
1.0
|
N
|
B:ASP209
|
4.6
|
39.0
|
1.0
|
HZ1
|
B:LYS189
|
4.6
|
61.2
|
1.0
|
HB2
|
B:ASP12
|
4.6
|
41.8
|
1.0
|
CG
|
B:LYS210
|
4.6
|
51.4
|
1.0
|
C
|
B:GLY15
|
4.6
|
38.3
|
1.0
|
HB3
|
B:ASP209
|
4.7
|
53.7
|
1.0
|
N
|
B:THR16
|
4.7
|
37.3
|
1.0
|
H
|
B:VAL13
|
4.8
|
38.5
|
1.0
|
H
|
B:LYS210
|
4.8
|
51.4
|
1.0
|
C
|
B:VAL13
|
4.8
|
44.1
|
1.0
|
HB
|
B:THR16
|
4.8
|
39.5
|
1.0
|
HZ3
|
B:LYS189
|
4.8
|
61.2
|
1.0
|
OD1
|
B:ASP217
|
4.9
|
41.4
|
1.0
|
HB2
|
B:LYS210
|
4.9
|
46.8
|
1.0
|
CG
|
B:ASP217
|
4.9
|
41.7
|
1.0
|
O
|
B:HOH715
|
4.9
|
47.2
|
1.0
|
CA
|
B:ASP209
|
5.0
|
39.5
|
1.0
|
H
|
B:GLY15
|
5.0
|
54.4
|
1.0
|
HA
|
B:ASP14
|
5.0
|
51.4
|
1.0
|
HB2
|
B:ASP14
|
5.0
|
58.0
|
1.0
|
|
Magnesium binding site 4 out
of 4 in 7o58
Go back to
Magnesium Binding Sites List in 7o58
Magnesium binding site 4 out
of 4 in the Human Phosphomannomutase 2 (PMM2) with Mutation T237M in Complex with the Activator Glucose 1,6-Bisphosphate
![](/pictures/MG/pdb/o5/7o58-MG-sphere_04.jpg) Mono view
![](/pictures/MG/pdb/o5/7o58-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) with Mutation T237M in Complex with the Activator Glucose 1,6-Bisphosphate within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg506
b:41.0
occ:1.00
|
O
|
B:HOH732
|
2.2
|
44.8
|
1.0
|
O
|
B:ASP223
|
2.3
|
39.9
|
1.0
|
O
|
B:PHE221
|
2.4
|
38.0
|
1.0
|
OG1
|
B:THR226
|
2.5
|
34.6
|
1.0
|
O
|
B:THR226
|
2.5
|
35.7
|
1.0
|
O
|
B:HOH683
|
2.6
|
52.9
|
1.0
|
HG1
|
B:THR226
|
2.9
|
41.5
|
1.0
|
H
|
B:THR226
|
3.2
|
47.1
|
1.0
|
C
|
B:THR226
|
3.4
|
35.1
|
1.0
|
C
|
B:ASP223
|
3.4
|
40.1
|
1.0
|
C
|
B:PHE221
|
3.5
|
39.9
|
1.0
|
C
|
B:THR222
|
3.6
|
39.3
|
1.0
|
N
|
B:ASP223
|
3.7
|
43.2
|
1.0
|
CB
|
B:THR226
|
3.7
|
37.5
|
1.0
|
H
|
B:GLY228
|
3.8
|
46.3
|
1.0
|
CA
|
B:THR226
|
3.8
|
36.8
|
1.0
|
HA
|
B:THR222
|
3.8
|
47.7
|
1.0
|
H
|
B:ASP223
|
3.8
|
51.9
|
1.0
|
N
|
B:THR226
|
3.8
|
39.2
|
1.0
|
O
|
B:THR222
|
3.9
|
39.7
|
1.0
|
HA
|
B:PRO224
|
3.9
|
48.2
|
1.0
|
O
|
B:ILE220
|
4.1
|
39.3
|
1.0
|
CA
|
B:THR222
|
4.1
|
39.7
|
1.0
|
CA
|
B:ASP223
|
4.1
|
43.2
|
1.0
|
N
|
B:THR222
|
4.2
|
36.1
|
1.0
|
HB
|
B:THR226
|
4.2
|
45.0
|
1.0
|
HA
|
B:PHE221
|
4.2
|
42.2
|
1.0
|
N
|
B:PRO224
|
4.3
|
38.8
|
1.0
|
O
|
B:HOH663
|
4.3
|
55.8
|
1.0
|
N
|
B:GLY228
|
4.3
|
38.6
|
1.0
|
HA3
|
B:GLY228
|
4.3
|
46.0
|
1.0
|
N
|
B:MET227
|
4.4
|
34.9
|
1.0
|
CA
|
B:PRO224
|
4.4
|
40.2
|
1.0
|
HB3
|
B:ASP223
|
4.4
|
43.3
|
1.0
|
HA
|
B:MET227
|
4.5
|
53.6
|
1.0
|
CA
|
B:PHE221
|
4.5
|
35.2
|
1.0
|
C
|
B:PRO224
|
4.6
|
42.8
|
1.0
|
HG23
|
B:THR226
|
4.7
|
48.9
|
1.0
|
HA
|
B:THR226
|
4.8
|
44.1
|
1.0
|
CG2
|
B:THR226
|
4.8
|
40.7
|
1.0
|
CA
|
B:MET227
|
4.8
|
44.6
|
1.0
|
N
|
B:ARG225
|
4.9
|
37.1
|
1.0
|
CA
|
B:GLY228
|
4.9
|
38.4
|
1.0
|
CB
|
B:ASP223
|
4.9
|
36.1
|
1.0
|
H
|
B:ARG225
|
4.9
|
44.6
|
1.0
|
HA
|
B:ASP223
|
4.9
|
51.9
|
1.0
|
H
|
B:THR222
|
5.0
|
43.4
|
1.0
|
O
|
B:PRO224
|
5.0
|
38.8
|
1.0
|
C
|
B:MET227
|
5.0
|
39.4
|
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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