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Platinum in PDB 6dlp: Crystal Structure of LRRK2 WD40 Domain Dimer

Enzymatic activity of Crystal Structure of LRRK2 WD40 Domain Dimer

All present enzymatic activity of Crystal Structure of LRRK2 WD40 Domain Dimer:
2.7.11.1;

Protein crystallography data

The structure of Crystal Structure of LRRK2 WD40 Domain Dimer, PDB code: 6dlp was solved by P.Zhang, H.Ru, L.Wang, H.Wu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 76.26 / 4.00
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 79.293, 103.590, 112.664, 90.00, 90.00, 90.00
R / Rfree (%) 22.8 / 26.3

Platinum Binding Sites:

The binding sites of Platinum atom in the Crystal Structure of LRRK2 WD40 Domain Dimer (pdb code 6dlp). This binding sites where shown within 5.0 Angstroms radius around Platinum atom.
In total 6 binding sites of Platinum where determined in the Crystal Structure of LRRK2 WD40 Domain Dimer, PDB code: 6dlp:
Jump to Platinum binding site number: 1; 2; 3; 4; 5; 6;

Platinum binding site 1 out of 6 in 6dlp

Go back to Platinum Binding Sites List in 6dlp
Platinum binding site 1 out of 6 in the Crystal Structure of LRRK2 WD40 Domain Dimer


Mono view


Stereo pair view

A full contact list of Platinum with other atoms in the Pt binding site number 1 of Crystal Structure of LRRK2 WD40 Domain Dimer within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Pt2601

b:0.8
occ:1.00
SG B:CYS2201 2.6 75.8 1.0
CB B:CYS2154 3.4 0.4 1.0
CB B:CYS2201 3.9 50.1 1.0
CA B:CYS2201 4.0 43.9 1.0
CA B:CYS2154 4.2 66.9 1.0
N B:LEU2202 4.3 34.2 1.0
O B:LEU2200 4.4 68.7 1.0
N B:MET2155 4.6 52.7 1.0
C B:CYS2201 4.7 34.0 1.0
O B:LEU2202 4.8 60.4 1.0
SG B:CYS2154 4.9 0.1 1.0
C B:CYS2154 5.0 54.2 1.0

Platinum binding site 2 out of 6 in 6dlp

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Platinum binding site 2 out of 6 in the Crystal Structure of LRRK2 WD40 Domain Dimer


Mono view


Stereo pair view

A full contact list of Platinum with other atoms in the Pt binding site number 2 of Crystal Structure of LRRK2 WD40 Domain Dimer within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Pt2602

b:0.9
occ:1.00
SG B:CYS2302 2.1 73.8 1.0
CB B:CYS2302 3.5 49.4 1.0
O B:LEU2303 3.5 0.2 1.0
CA B:CYS2302 3.7 51.9 1.0
N B:LEU2303 3.7 67.4 1.0
C B:CYS2302 4.2 55.7 1.0
C B:LEU2303 4.4 88.8 1.0
O B:MET2301 4.6 66.1 1.0
CA B:LEU2303 4.7 69.4 1.0
OG1 B:THR2356 4.9 81.0 1.0
O B:ILE2355 4.9 74.1 1.0
N B:CYS2302 4.9 41.7 1.0

Platinum binding site 3 out of 6 in 6dlp

Go back to Platinum Binding Sites List in 6dlp
Platinum binding site 3 out of 6 in the Crystal Structure of LRRK2 WD40 Domain Dimer


Mono view


Stereo pair view

A full contact list of Platinum with other atoms in the Pt binding site number 3 of Crystal Structure of LRRK2 WD40 Domain Dimer within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Pt2603

b:0.9
occ:1.00
SG B:CYS2418 2.5 59.4 1.0
CB B:CYS2418 3.9 57.4 1.0
CA B:CYS2418 4.1 57.2 1.0
N B:THR2460 4.4 89.5 1.0
CA B:MET2459 4.4 52.1 1.0
O B:LEU2417 4.6 46.8 1.0
O B:MET2458 4.6 66.0 1.0
N B:LEU2419 4.6 70.5 1.0
OG1 B:THR2460 4.8 37.3 1.0
CB B:MET2459 4.8 57.3 1.0
C B:MET2459 4.8 76.1 1.0
C B:CYS2418 4.9 72.0 1.0
CB B:THR2460 5.0 38.1 1.0

Platinum binding site 4 out of 6 in 6dlp

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Platinum binding site 4 out of 6 in the Crystal Structure of LRRK2 WD40 Domain Dimer


Mono view


Stereo pair view

A full contact list of Platinum with other atoms in the Pt binding site number 4 of Crystal Structure of LRRK2 WD40 Domain Dimer within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Pt2601

b:0.3
occ:1.00
SG A:CYS2418 2.8 77.1 1.0
CB A:CYS2418 3.7 66.3 1.0
N A:THR2460 3.8 80.9 1.0
CA A:CYS2418 3.9 55.3 1.0
CA A:MET2459 3.9 51.7 1.0
N A:LEU2419 4.1 44.3 1.0
OG1 A:THR2460 4.2 40.0 1.0
O A:MET2458 4.3 86.1 1.0
C A:MET2459 4.3 62.6 1.0
CB A:THR2460 4.4 51.8 1.0
C A:CYS2418 4.5 49.6 1.0
CB A:MET2459 4.6 54.3 1.0
O A:LEU2417 4.7 30.3 1.0
O A:LEU2419 4.7 41.2 1.0
CA A:THR2460 4.7 73.1 1.0
N A:MET2459 4.9 44.6 1.0
C A:MET2458 5.0 56.8 1.0

Platinum binding site 5 out of 6 in 6dlp

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Platinum binding site 5 out of 6 in the Crystal Structure of LRRK2 WD40 Domain Dimer


Mono view


Stereo pair view

A full contact list of Platinum with other atoms in the Pt binding site number 5 of Crystal Structure of LRRK2 WD40 Domain Dimer within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Pt2602

b:0.4
occ:1.00
SG A:CYS2302 2.1 81.0 1.0
CB A:CYS2302 3.5 54.3 1.0
O A:LEU2303 3.7 48.7 1.0
CA A:CYS2302 3.8 45.5 1.0
N A:LEU2303 3.9 39.0 1.0
C A:CYS2302 4.4 28.1 1.0
C A:LEU2303 4.6 40.0 1.0
OG1 A:THR2356 4.7 49.0 1.0
O A:MET2301 4.7 55.1 1.0
CA A:LEU2303 4.9 37.0 1.0

Platinum binding site 6 out of 6 in 6dlp

Go back to Platinum Binding Sites List in 6dlp
Platinum binding site 6 out of 6 in the Crystal Structure of LRRK2 WD40 Domain Dimer


Mono view


Stereo pair view

A full contact list of Platinum with other atoms in the Pt binding site number 6 of Crystal Structure of LRRK2 WD40 Domain Dimer within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Pt2603

b:0.6
occ:1.00
SG A:CYS2201 2.6 37.0 1.0
CB A:CYS2154 3.2 0.5 1.0
CB A:CYS2201 3.9 45.8 1.0
CA A:CYS2154 3.9 58.9 1.0
CA A:CYS2201 4.0 37.9 1.0
N A:MET2155 4.1 41.8 1.0
N A:LEU2202 4.4 38.9 1.0
O A:LEU2200 4.6 58.0 1.0
C A:CYS2154 4.6 39.5 1.0
O A:MET2155 4.6 49.3 1.0
C A:CYS2201 4.8 37.8 1.0
O A:GLU2153 4.8 44.4 1.0
SG A:CYS2154 4.8 0.6 1.0

Reference:

P.Zhang, Y.Fan, H.Ru, L.Wang, V.G.Magupalli, S.S.Taylor, D.R.Alessi, H.Wu. Crystal Structure of the WD40 Domain Dimer of LRRK2. Proc. Natl. Acad. Sci. V. 116 1579 2019U.S.A..
ISSN: ESSN 1091-6490
PubMed: 30635421
DOI: 10.1073/PNAS.1817889116
Page generated: Wed Dec 16 02:05:32 2020

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