Atomistry » Platinum » PDB 5yky-7bpr » 6yk8
Atomistry »
  Platinum »
    PDB 5yky-7bpr »
      6yk8 »

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

Go back to Platinum Binding Sites List in 6yk8
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

Go back to Platinum Binding Sites List in 6yk8
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

Go back to Platinum Binding Sites List in 6yk8
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

Go back to Platinum Binding Sites List in 6yk8
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

Go back to Platinum Binding Sites List in 6yk8
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

Go back to Platinum Binding Sites List in 6yk8
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

Go back to Platinum Binding Sites List in 6yk8
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

Go back to Platinum Binding Sites List in 6yk8
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

Go back to Platinum Binding Sites List in 6yk8
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

Go back to Platinum Binding Sites List in 6yk8
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: Thu Oct 10 11:48:20 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy