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Platinum in PDB 6yk8: Otu-Like Deubiquitinase From Legionella -LPG2529

Protein crystallography data

The structure of Otu-Like Deubiquitinase From Legionella -LPG2529, PDB code: 6yk8 was solved by D.Shin, I.Dikic, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 44.53 / 2.42
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 38.534, 140.979, 57.437, 90, 90, 90
R / Rfree (%) 22.9 / 28.3

Platinum Binding Sites:

The binding sites of Platinum atom in the Otu-Like Deubiquitinase From Legionella -LPG2529 (pdb code 6yk8). This binding sites where shown within 5.0 Angstroms radius around Platinum atom.
In total 10 binding sites of Platinum where determined in the Otu-Like Deubiquitinase From Legionella -LPG2529, PDB code: 6yk8:
Jump to Platinum binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Platinum binding site 1 out of 10 in 6yk8

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Platinum binding site 1 out of 10 in the Otu-Like Deubiquitinase From Legionella -LPG2529


Mono view


Stereo pair view

A full contact list of Platinum with other atoms in the Pt binding site number 1 of Otu-Like Deubiquitinase From Legionella -LPG2529 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Pt401

b:209.3
occ:1.00
 C A:CYS16 3.5 82.8 1.0
N A:LEU17 3.6 75.8 1.0
CA A:CYS16 3.7 83.2 1.0
N A:TYR18 3.9 59.9 1.0
N A:TYR19 4.0 69.1 1.0
O A:CYS16 4.1 84.2 1.0
CB A:CYS16 4.3 91.7 1.0
CD2 A:TYR18 4.4 72.4 1.0
CB A:TYR19 4.4 64.7 1.0
C A:LEU17 4.5 68.7 1.0
CB A:TYR18 4.6 65.8 1.0
CA A:LEU17 4.6 73.4 1.0
CA A:TYR18 4.6 71.0 1.0
NH2 A:ARG85 4.6 86.2 1.0
C A:TYR18 4.8 71.8 1.0
CA A:TYR19 4.9 61.3 1.0
N A:CYS16 4.9 84.5 1.0
CG A:TYR18 5.0 63.0 1.0

Platinum binding site 2 out of 10 in 6yk8

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Platinum binding site 2 out of 10 in the Otu-Like Deubiquitinase From Legionella -LPG2529


Mono view


Stereo pair view

A full contact list of Platinum with other atoms in the Pt binding site number 2 of Otu-Like Deubiquitinase From Legionella -LPG2529 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Pt402

b:273.4
occ:1.00
 CE A:MET240 2.9 151.0 1.0
OE2 A:GLU236 3.4 114.1 1.0
CG A:GLU236 3.4 88.5 1.0
CD A:GLU236 3.9 107.0 1.0
CG A:MET240 3.9 99.4 1.0
SD A:MET240 4.2 120.9 1.0
CB A:GLU236 4.5 72.5 1.0
PT A:PT403 4.7 260.0 1.0
O A:GLU236 4.7 79.5 1.0

Platinum binding site 3 out of 10 in 6yk8

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Platinum binding site 3 out of 10 in the Otu-Like Deubiquitinase From Legionella -LPG2529


Mono view


Stereo pair view

A full contact list of Platinum with other atoms in the Pt binding site number 3 of Otu-Like Deubiquitinase From Legionella -LPG2529 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Pt403

b:260.0
occ:1.00
 CG A:MET240 3.4 99.4 1.0
CB A:MET240 3.7 84.6 1.0
NH1 A:ARG244 3.8 63.8 1.0
SD A:MET240 3.8 120.9 1.0
CE A:MET240 3.9 151.0 1.0
PT A:PT404 4.0 257.0 1.0
PT A:PT402 4.7 273.4 1.0
CZ A:ARG244 5.0 62.6 1.0
CA A:MET240 5.0 69.8 1.0

Platinum binding site 4 out of 10 in 6yk8

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Platinum binding site 4 out of 10 in the Otu-Like Deubiquitinase From Legionella -LPG2529


Mono view


Stereo pair view

A full contact list of Platinum with other atoms in the Pt binding site number 4 of Otu-Like Deubiquitinase From Legionella -LPG2529 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Pt404

b:257.0
occ:1.00
 SD A:MET240 3.0 120.9 1.0
CE A:MET240 3.4 151.0 1.0
PT A:PT403 4.0 260.0 1.0
CG A:MET240 4.3 99.4 1.0
CB A:MET240 4.8 84.6 1.0

Platinum binding site 5 out of 10 in 6yk8

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Platinum binding site 5 out of 10 in the Otu-Like Deubiquitinase From Legionella -LPG2529


Mono view


Stereo pair view

A full contact list of Platinum with other atoms in the Pt binding site number 5 of Otu-Like Deubiquitinase From Legionella -LPG2529 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Pt405

b:227.2
occ:1.00
 CB A:MET251 3.1 108.1 1.0
CA A:MET251 4.5 112.8 1.0

Platinum binding site 6 out of 10 in 6yk8

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Platinum binding site 6 out of 10 in the Otu-Like Deubiquitinase From Legionella -LPG2529


Mono view


Stereo pair view

A full contact list of Platinum with other atoms in the Pt binding site number 6 of Otu-Like Deubiquitinase From Legionella -LPG2529 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Pt401

b:192.6
occ:1.00
 C B:CYS16 3.4 86.2 1.0
N B:LEU17 3.5 74.3 1.0
CA B:CYS16 3.5 87.1 1.0
N B:TYR18 3.9 64.5 1.0
O B:CYS16 4.0 83.1 1.0
N B:TYR19 4.1 75.3 1.0
CG B:TYR19 4.2 78.3 1.0
N B:CYS16 4.3 89.8 1.0
CD1 B:TYR19 4.4 90.1 1.0
CB B:TYR19 4.4 66.4 1.0
CD2 B:TYR19 4.5 88.8 1.0
CA B:LEU17 4.6 75.8 1.0
C B:LEU17 4.6 71.3 1.0
CD1 B:TYR18 4.6 72.2 1.0
CB B:CYS16 4.6 90.2 1.0
CB B:TYR18 4.6 67.5 1.0
CA B:TYR18 4.7 69.8 1.0
CE1 B:TYR19 4.8 95.1 1.0
CA B:TYR19 4.9 64.6 1.0
NH2 B:ARG85 4.9 85.5 1.0
C B:TYR18 4.9 75.1 1.0
CE2 B:TYR19 5.0 93.1 1.0

Platinum binding site 7 out of 10 in 6yk8

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Platinum binding site 7 out of 10 in the Otu-Like Deubiquitinase From Legionella -LPG2529


Mono view


Stereo pair view

A full contact list of Platinum with other atoms in the Pt binding site number 7 of Otu-Like Deubiquitinase From Legionella -LPG2529 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Pt402

b:235.8
occ:1.00
 CG B:MET240 2.5 102.7 1.0
SD B:MET240 2.7 101.7 1.0
CB B:MET240 3.3 82.7 1.0
CE B:MET240 4.4 96.7 1.0
NH1 B:ARG244 4.5 65.3 1.0
CA B:MET240 4.7 75.8 1.0

Platinum binding site 8 out of 10 in 6yk8

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Platinum binding site 8 out of 10 in the Otu-Like Deubiquitinase From Legionella -LPG2529


Mono view


Stereo pair view

A full contact list of Platinum with other atoms in the Pt binding site number 8 of Otu-Like Deubiquitinase From Legionella -LPG2529 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Pt403

b:296.7
occ:1.00
 OE1 B:GLU236 3.0 113.7 1.0
CG B:GLU236 3.2 101.2 1.0
CB B:GLU236 3.2 85.3 1.0
CD B:GLU236 3.2 114.3 1.0
O B:GLU236 3.5 77.0 1.0
C B:GLU236 3.8 79.4 1.0
CA B:GLU236 3.9 71.3 1.0
NH1 B:ARG273 4.0 101.8 1.0
OE2 B:GLU236 4.1 113.5 1.0
CG B:MET240 4.4 102.7 1.0
N B:GLU237 4.6 84.3 1.0
CD2 B:LEU239 4.7 73.1 1.0
CG2 B:VAL271 5.0 78.8 1.0

Platinum binding site 9 out of 10 in 6yk8

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Platinum binding site 9 out of 10 in the Otu-Like Deubiquitinase From Legionella -LPG2529


Mono view


Stereo pair view

A full contact list of Platinum with other atoms in the Pt binding site number 9 of Otu-Like Deubiquitinase From Legionella -LPG2529 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Pt404

b:334.1
occ:1.00
 CE B:MET240 3.6 96.7 1.0
SD B:MET240 3.7 101.7 1.0
O B:LEU269 3.7 86.2 1.0
CD1 B:LEU269 4.3 81.2 1.0
C B:LEU269 4.5 83.1 1.0
CB B:LEU269 4.8 77.6 1.0

Platinum binding site 10 out of 10 in 6yk8

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Platinum binding site 10 out of 10 in the Otu-Like Deubiquitinase From Legionella -LPG2529


Mono view


Stereo pair view

A full contact list of Platinum with other atoms in the Pt binding site number 10 of Otu-Like Deubiquitinase From Legionella -LPG2529 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Pt405

b:276.3
occ:1.00
 CE B:MET251 2.3 118.0 1.0
CG B:MET251 2.5 130.6 1.0
CB B:MET251 2.6 126.8 1.0
SD B:MET251 2.7 125.6 1.0
CA B:MET251 4.0 118.4 1.0
C B:MET251 4.6 113.7 1.0
N B:PRO261 5.0 118.0 1.0

Reference:

D.Shin, A.Bhattacharya, Y.L.Cheng, M.C.Alonso, A.R.Mehdipour, G.J.Van Der Heden Van Noort, H.Ovaa, G.Hummer, I.Dikic. Bacterial Otu Deubiquitinases Regulate Substrate Ubiquitination Upon Legionella Infection. Elife V. 9 2020.
ISSN: ESSN 2050-084X
PubMed: 33185526
DOI: 10.7554/ELIFE.58277
Page generated: Wed Mar 3 15:42:50 2021

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