Magnesium in PDB 6ojf: Dimeric Structure of LRRK2 Gtpase Domain

All present enzymatic activity of Dimeric Structure of LRRK2 Gtpase Domain:
2.7.11.1;

The structure of Dimeric Structure of LRRK2 Gtpase Domain, PDB code: 6ojf 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)	43.82 / 1.60
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	44.634, 101.883, 44.610, 90.00, 100.95, 90.00
R / Rfree (%)	14.3 / 15.8

The binding sites of Magnesium atom in the Dimeric Structure of LRRK2 Gtpase Domain (pdb code 6ojf). 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: 6ojf:
Jump to Magnesium binding site number: 1; 2; 3; 4;

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:23.9 occ:1.00 O A:HOH1738 2.0 28.9 1.0 O1B A:GDP1602 2.0 21.1 1.0 O A:HOH1746 2.0 24.2 1.0 O A:HOH1756 2.1 25.3 1.0 OG1 A:THR1348 2.2 25.7 1.0 O B:HOH1711 2.2 23.4 1.0 PB A:GDP1602 3.2 21.2 1.0 CB A:THR1348 3.2 23.4 1.0 O2B A:GDP1602 3.5 22.8 1.0 O B:HOH1726 3.9 30.1 1.0 O B:HOH1761 4.0 34.6 1.0 N A:THR1348 4.0 22.0 1.0 O2A A:GDP1602 4.1 24.4 1.0 CB B:THR1368 4.2 27.6 1.0 CA A:THR1348 4.2 22.3 1.0 OD2 B:ASP1394 4.2 27.3 1.0 CG2 A:THR1348 4.2 25.4 1.0 O3B A:GDP1602 4.3 22.9 1.0 OG1 B:THR1368 4.3 30.8 1.0 O3A A:GDP1602 4.3 21.8 1.0 OD1 B:ASP1394 4.3 24.8 1.0 CG2 B:THR1368 4.4 27.6 1.0 NZ A:LYS1347 4.4 23.7 1.0 PA A:GDP1602 4.5 22.1 1.0 CG B:ASP1394 4.6 24.6 1.0 O1A A:GDP1602 4.6 23.1 1.0 O B:HOH1771 4.7 52.8 1.0 O A:HOH1703 4.8 26.4 1.0 CA B:ALA1396 4.8 23.3 1.0 O B:VAL1369 4.8 25.6 1.0

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:47.4 occ:1.00 O A:MET1409 2.1 36.0 1.0 OH A:TYR1415 2.6 33.9 1.0 C A:MET1409 3.2 41.7 1.0 CZ A:TYR1415 3.5 28.3 1.0 CB A:ALA1413 3.5 44.4 1.0 O A:HOH1764 3.5 32.2 1.0 CB A:ALA1442 3.6 32.3 1.0 CE1 A:TYR1415 3.6 27.6 1.0 CA A:THR1410 3.8 47.4 1.0 O A:THR1410 3.8 52.1 1.0 N A:THR1410 3.9 44.6 1.0 C A:THR1410 3.9 48.7 1.0 CE A:MET1338 3.9 32.1 1.0 CA A:MET1409 4.4 39.4 1.0 CG A:MET1338 4.4 31.0 1.0 O A:GLN1411 4.4 53.2 1.0 OG A:SER1445 4.6 33.0 1.0 N A:GLN1411 4.7 50.9 1.0 CG A:ARG1441 4.7 31.6 1.0 CE2 A:TYR1415 4.7 26.8 1.0 SD A:MET1338 4.7 31.1 1.0 CA A:ALA1442 4.8 30.5 1.0 CD1 A:TYR1415 4.9 27.6 1.0 CA A:ALA1413 4.9 45.3 1.0 O A:PHE1408 5.0 39.6 1.0

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:24.4 occ:1.00 OG1 B:THR1348 1.9 23.0 1.0 O3B B:GDP1602 2.1 23.0 1.0 O A:HOH1713 2.1 21.1 1.0 O A:HOH1737 2.1 25.1 1.0 O B:HOH1742 2.1 21.3 1.0 O A:HOH1723 2.2 22.8 1.0 CB B:THR1348 3.1 23.2 1.0 PB B:GDP1602 3.3 23.7 1.0 O2B B:GDP1602 3.6 24.1 1.0 OG1 A:THR1368 3.6 41.6 1.0 N B:THR1348 3.9 22.8 1.0 O A:HOH1730 3.9 28.8 1.0 CG2 B:THR1348 4.0 24.1 1.0 CA B:THR1348 4.0 22.9 1.0 OD2 A:ASP1394 4.1 29.2 1.0 OD1 A:ASP1394 4.2 27.8 1.0 O2A B:GDP1602 4.2 23.7 1.0 O1B B:GDP1602 4.4 24.7 1.0 NZ B:LYS1347 4.4 27.0 1.0 O3A B:GDP1602 4.4 22.8 1.0 CG2 A:THR1368 4.4 33.5 1.0 O A:HOH1754 4.4 34.5 1.0 CG A:ASP1394 4.5 25.9 1.0 PA B:GDP1602 4.6 23.9 1.0 CB A:THR1368 4.6 34.3 1.0 O1A B:GDP1602 4.7 23.2 1.0 CB B:LYS1347 4.9 24.0 1.0 CA A:ALA1396 4.9 25.4 1.0

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:45.6 occ:1.00 O B:MET1409 2.3 36.4 1.0 OH B:TYR1415 2.5 34.2 1.0 O B:HOH1750 3.0 35.2 1.0 C B:MET1409 3.5 34.7 1.0 NH1 B:ARG1441 3.7 34.3 1.0 CZ B:TYR1415 3.8 28.2 1.0 CE B:MET1338 3.8 33.2 0.5 CE B:MET1338 3.9 29.8 0.5 CD B:ARG1441 4.0 35.9 1.0 O B:HOH1713 4.2 35.3 1.0 CA B:THR1410 4.2 33.7 1.0 N B:THR1410 4.2 33.0 1.0 CG B:ARG1441 4.3 36.7 1.0 CB B:ALA1413 4.4 32.3 1.0 CB B:ARG1441 4.4 36.4 1.0 CE1 A:PHE1401 4.5 28.9 1.0 CA B:MET1409 4.5 33.1 1.0 CE2 B:TYR1415 4.5 28.5 1.0 CZ A:PHE1401 4.5 28.3 1.0 CE1 B:TYR1415 4.6 28.3 1.0 CG B:MET1338 4.6 28.8 0.5 CZ B:ARG1441 4.6 33.8 1.0 CB B:MET1409 4.7 33.1 1.0 CG B:MET1338 4.7 29.2 0.5 SD B:MET1338 4.7 30.3 0.5 NE B:ARG1441 4.8 35.1 1.0 CG2 B:THR1410 4.8 36.3 1.0 SD B:MET1338 4.9 31.0 0.5

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.