Magnesium in PDB 6oje: Dimeric Structure of LRRK2 Gtpase Domain
Enzymatic activity of Dimeric Structure of LRRK2 Gtpase Domain
All present enzymatic activity of Dimeric Structure of LRRK2 Gtpase Domain:
2.7.11.1;
Protein crystallography data
The structure of Dimeric Structure of LRRK2 Gtpase Domain, PDB code: 6oje
was solved by
Q.Q.Hoang,
C.X.Wu,
J.Liao,
Y.Park,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
43.80 /
1.95
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
44.647,
103.688,
44.593,
90.00,
101.20,
90.00
|
R / Rfree (%)
|
16 /
19.6
|
Magnesium Binding Sites:
The binding sites of Magnesium atom in the Dimeric Structure of LRRK2 Gtpase Domain
(pdb code 6oje). This binding sites where shown within
5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the
Dimeric Structure of LRRK2 Gtpase Domain, PDB code: 6oje:
Jump to Magnesium binding site number:
1;
2;
3;
4;
Magnesium binding site 1 out
of 4 in 6oje
Go back to
Magnesium Binding Sites List in 6oje
Magnesium binding site 1 out
of 4 in the Dimeric Structure of LRRK2 Gtpase Domain
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 1 of Dimeric Structure of LRRK2 Gtpase Domain within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg1601
b:28.4
occ:1.00
|
O
|
B:HOH1726
|
2.0
|
24.3
|
1.0
|
O1B
|
A:GDP1602
|
2.0
|
24.9
|
1.0
|
O
|
A:HOH1746
|
2.1
|
26.1
|
1.0
|
O
|
A:HOH1758
|
2.1
|
29.3
|
1.0
|
OG1
|
A:THR1348
|
2.1
|
28.6
|
1.0
|
O
|
A:HOH1717
|
2.1
|
29.7
|
1.0
|
CB
|
A:THR1348
|
3.2
|
30.0
|
1.0
|
PB
|
A:GDP1602
|
3.3
|
27.7
|
1.0
|
O3B
|
A:GDP1602
|
3.5
|
27.1
|
1.0
|
N
|
A:THR1348
|
3.9
|
30.0
|
1.0
|
O
|
B:HOH1729
|
4.0
|
33.2
|
1.0
|
O
|
B:HOH1779
|
4.1
|
43.1
|
1.0
|
OD2
|
B:ASP1394
|
4.1
|
30.7
|
1.0
|
CA
|
A:THR1348
|
4.1
|
29.7
|
1.0
|
CG2
|
A:THR1348
|
4.2
|
33.6
|
1.0
|
OD1
|
B:ASP1394
|
4.2
|
29.4
|
1.0
|
O2A
|
A:GDP1602
|
4.2
|
27.8
|
1.0
|
O3A
|
A:GDP1602
|
4.3
|
27.6
|
1.0
|
CB
|
B:THR1368
|
4.3
|
36.9
|
1.0
|
OG1
|
B:THR1368
|
4.3
|
36.7
|
1.0
|
O2B
|
A:GDP1602
|
4.4
|
25.2
|
1.0
|
O
|
A:HOH1805
|
4.4
|
52.6
|
1.0
|
NZ
|
A:LYS1347
|
4.5
|
26.0
|
1.0
|
CG
|
B:ASP1394
|
4.5
|
27.0
|
1.0
|
PA
|
A:GDP1602
|
4.5
|
28.3
|
1.0
|
O1A
|
A:GDP1602
|
4.6
|
27.0
|
1.0
|
CG2
|
B:THR1368
|
4.6
|
37.3
|
1.0
|
CA
|
B:ALA1396
|
4.8
|
28.9
|
1.0
|
CB
|
A:LYS1347
|
4.9
|
26.5
|
1.0
|
O
|
B:VAL1369
|
4.9
|
31.7
|
1.0
|
C
|
A:LYS1347
|
5.0
|
31.6
|
1.0
|
O
|
A:HOH1736
|
5.0
|
29.9
|
1.0
|
|
Magnesium binding site 2 out
of 4 in 6oje
Go back to
Magnesium Binding Sites List in 6oje
Magnesium binding site 2 out
of 4 in the Dimeric Structure of LRRK2 Gtpase Domain
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 2 of Dimeric Structure of LRRK2 Gtpase Domain within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg1603
b:62.5
occ:1.00
|
O
|
A:MET1409
|
2.5
|
67.1
|
1.0
|
O
|
A:HOH1702
|
3.1
|
56.1
|
1.0
|
NH1
|
A:ARG1441
|
3.3
|
41.2
|
1.0
|
C
|
A:MET1409
|
3.3
|
59.4
|
1.0
|
CG
|
A:ARG1441
|
3.5
|
41.6
|
1.0
|
CB
|
A:MET1409
|
3.7
|
52.9
|
1.0
|
CD
|
A:ARG1441
|
3.8
|
39.7
|
1.0
|
CE
|
A:MET1338
|
3.8
|
41.9
|
1.0
|
OH
|
A:TYR1415
|
3.8
|
35.3
|
1.0
|
CA
|
A:MET1409
|
3.9
|
51.2
|
1.0
|
N
|
A:THR1410
|
4.2
|
60.3
|
1.0
|
CZ
|
A:ARG1441
|
4.3
|
38.3
|
1.0
|
NE
|
A:ARG1441
|
4.4
|
34.8
|
1.0
|
CA
|
A:THR1410
|
4.5
|
57.8
|
1.0
|
CE1
|
B:PHE1401
|
4.7
|
32.5
|
1.0
|
CE
|
A:MET1409
|
4.7
|
49.6
|
1.0
|
CG2
|
A:THR1410
|
4.8
|
64.5
|
1.0
|
O
|
B:HOH1783
|
4.9
|
51.3
|
1.0
|
CG
|
A:MET1409
|
4.9
|
49.1
|
1.0
|
OG1
|
B:THR1404
|
4.9
|
35.3
|
1.0
|
CZ
|
B:PHE1401
|
4.9
|
32.4
|
1.0
|
CB
|
A:ARG1441
|
5.0
|
39.8
|
1.0
|
|
Magnesium binding site 3 out
of 4 in 6oje
Go back to
Magnesium Binding Sites List in 6oje
Magnesium binding site 3 out
of 4 in the Dimeric Structure of LRRK2 Gtpase Domain
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 3 of Dimeric Structure of LRRK2 Gtpase Domain within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg1601
b:28.9
occ:1.00
|
O3B
|
B:GDP1602
|
1.9
|
25.3
|
1.0
|
O
|
B:HOH1762
|
2.0
|
30.0
|
1.0
|
O
|
B:HOH1758
|
2.0
|
32.9
|
1.0
|
O
|
A:HOH1719
|
2.1
|
26.1
|
1.0
|
OG1
|
B:THR1348
|
2.1
|
29.9
|
1.0
|
O
|
A:HOH1709
|
2.2
|
26.5
|
1.0
|
CB
|
B:THR1348
|
3.2
|
30.5
|
1.0
|
PB
|
B:GDP1602
|
3.2
|
28.9
|
1.0
|
O2B
|
B:GDP1602
|
3.5
|
28.0
|
1.0
|
OG1
|
A:THR1368
|
3.6
|
56.7
|
1.0
|
N
|
B:THR1348
|
3.9
|
28.5
|
1.0
|
O
|
A:HOH1733
|
3.9
|
29.4
|
1.0
|
OD2
|
A:ASP1394
|
4.1
|
37.7
|
1.0
|
CA
|
B:THR1348
|
4.1
|
29.0
|
1.0
|
OD1
|
A:ASP1394
|
4.1
|
31.9
|
1.0
|
O2A
|
B:GDP1602
|
4.2
|
32.6
|
1.0
|
CG2
|
B:THR1348
|
4.2
|
34.2
|
1.0
|
O1B
|
B:GDP1602
|
4.2
|
26.6
|
1.0
|
CG2
|
A:THR1368
|
4.2
|
35.9
|
1.0
|
O3A
|
B:GDP1602
|
4.3
|
27.8
|
1.0
|
O
|
A:HOH1797
|
4.5
|
63.8
|
1.0
|
CG
|
A:ASP1394
|
4.5
|
31.2
|
1.0
|
NZ
|
B:LYS1347
|
4.5
|
32.2
|
1.0
|
PA
|
B:GDP1602
|
4.5
|
30.3
|
1.0
|
CB
|
A:THR1368
|
4.5
|
44.3
|
1.0
|
O
|
A:HOH1766
|
4.6
|
40.9
|
1.0
|
O1A
|
B:GDP1602
|
4.6
|
29.8
|
1.0
|
CB
|
B:LYS1347
|
4.8
|
27.9
|
1.0
|
CA
|
A:ALA1396
|
4.9
|
29.9
|
1.0
|
O
|
B:HOH1743
|
4.9
|
34.5
|
1.0
|
C
|
B:LYS1347
|
5.0
|
29.8
|
1.0
|
|
Magnesium binding site 4 out
of 4 in 6oje
Go back to
Magnesium Binding Sites List in 6oje
Magnesium binding site 4 out
of 4 in the Dimeric Structure of LRRK2 Gtpase Domain
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 4 of Dimeric Structure of LRRK2 Gtpase Domain within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg1603
b:64.0
occ:1.00
|
O
|
B:HOH1731
|
2.4
|
58.0
|
1.0
|
OH
|
B:TYR1415
|
2.6
|
39.0
|
1.0
|
O
|
B:MET1409
|
2.8
|
43.3
|
1.0
|
CE
|
B:MET1338
|
3.5
|
52.8
|
1.0
|
C
|
B:MET1409
|
3.6
|
43.8
|
1.0
|
CZ
|
B:TYR1415
|
3.8
|
35.9
|
1.0
|
NH1
|
B:ARG1441
|
4.0
|
37.6
|
1.0
|
O
|
B:HOH1770
|
4.0
|
48.2
|
1.0
|
CA
|
B:THR1410
|
4.1
|
42.0
|
1.0
|
N
|
B:THR1410
|
4.2
|
41.3
|
1.0
|
CB
|
B:ARG1441
|
4.2
|
45.2
|
1.0
|
CD
|
B:ARG1441
|
4.3
|
44.4
|
1.0
|
CG
|
B:ARG1441
|
4.4
|
45.1
|
1.0
|
CE1
|
A:PHE1401
|
4.5
|
32.1
|
1.0
|
CA
|
B:MET1409
|
4.6
|
38.3
|
1.0
|
CG2
|
B:THR1410
|
4.6
|
46.1
|
1.0
|
CB
|
B:MET1409
|
4.6
|
39.0
|
1.0
|
CZ
|
A:PHE1401
|
4.6
|
34.3
|
1.0
|
CE1
|
B:TYR1415
|
4.6
|
34.0
|
1.0
|
CE2
|
B:TYR1415
|
4.7
|
34.3
|
1.0
|
CB
|
B:ALA1413
|
4.7
|
37.9
|
1.0
|
CG
|
B:MET1338
|
4.9
|
40.6
|
1.0
|
CB
|
B:THR1410
|
4.9
|
45.4
|
1.0
|
SD
|
B:MET1338
|
4.9
|
44.3
|
1.0
|
CZ
|
B:ARG1441
|
5.0
|
38.9
|
1.0
|
|
Reference:
C.X.Wu,
J.Liao,
Y.Park,
N.C.Hoang,
V.A.Engel,
R.Sanishvili,
Y.Takagi,
S.M.Johnson,
M.Wang,
M.Federici,
R.J.Nichols,
M.R.Cookson,
Q.Q.Hoang.
Structural Basis For Conformational Plasticity in the Gtpase Domain of the Parkinson'S Disease-Associated Protein LRRK2 To Be Published.
Page generated: Tue Oct 1 13:24:19 2024
|