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

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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

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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

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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

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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: Mon Dec 14 23:43:11 2020

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