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:
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
![](/pictures/MG/pdb/o5/7o5z-MG-sphere_01.jpg) Mono view
![](/pictures/MG/pdb/o5/7o5z-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 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
![](/pictures/MG/pdb/o5/7o5z-MG-sphere_02.jpg) Mono view
![](/pictures/MG/pdb/o5/7o5z-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 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
![](/pictures/MG/pdb/o5/7o5z-MG-sphere_03.jpg) Mono view
![](/pictures/MG/pdb/o5/7o5z-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 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
![](/pictures/MG/pdb/o5/7o5z-MG-sphere_04.jpg) Mono view
![](/pictures/MG/pdb/o5/7o5z-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 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 Apr 6 18:00:24 2023
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