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Potassium in PDB 5tvv: Computationally Designed Fentanyl Binder - FEN49* Apo

Enzymatic activity of Computationally Designed Fentanyl Binder - FEN49* Apo

All present enzymatic activity of Computationally Designed Fentanyl Binder - FEN49* Apo:
3.2.1.8;

Protein crystallography data

The structure of Computationally Designed Fentanyl Binder - FEN49* Apo, PDB code: 5tvv was solved by M.J.Bick, P.J.Greisen, K.J.Morey, A.S.Antunes, D.La, B.Sankaran, L.Reymond, K.Johnsson, J.I.Medford, D.Baker, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.86 / 1.79
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 54.760, 73.259, 137.558, 90.00, 90.00, 90.00
R / Rfree (%) 20.4 / 22.5

Potassium Binding Sites:

The binding sites of Potassium atom in the Computationally Designed Fentanyl Binder - FEN49* Apo (pdb code 5tvv). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 3 binding sites of Potassium where determined in the Computationally Designed Fentanyl Binder - FEN49* Apo, PDB code: 5tvv:
Jump to Potassium binding site number: 1; 2; 3;

Potassium binding site 1 out of 3 in 5tvv

Go back to Potassium Binding Sites List in 5tvv
Potassium binding site 1 out of 3 in the Computationally Designed Fentanyl Binder - FEN49* Apo


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 1 of Computationally Designed Fentanyl Binder - FEN49* Apo within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K201

b:17.2
occ:1.00
O B:HOH390 2.7 15.7 0.9
OH B:TYR94 2.7 19.0 1.0
OD1 B:ASP106 2.7 14.9 1.0
O A:GLY21 2.8 19.1 1.0
O A:ASN20 2.8 19.3 1.0
OD1 A:ASN20 2.8 14.9 1.0
HH B:TYR94 3.0 22.8 1.0
HE21 B:GLN133 3.1 21.8 1.0
HG22 B:THR97 3.4 18.9 1.0
CG A:ASN20 3.4 15.2 1.0
HG21 B:THR97 3.4 18.9 1.0
CZ B:TYR94 3.4 17.5 1.0
C A:GLY21 3.4 22.2 1.0
C A:ASN20 3.5 18.6 1.0
HE22 B:GLN133 3.5 21.8 1.0
HG23 B:THR97 3.6 18.9 1.0
HE1 B:TYR94 3.6 20.6 1.0
NE2 B:GLN133 3.6 18.2 1.0
CG2 B:THR97 3.7 15.8 1.0
CG B:ASP106 3.7 15.4 1.0
CE1 B:TYR94 3.8 17.2 1.0
HA A:SER22 3.9 28.0 0.3
HB3 A:ASN20 3.9 20.0 1.0
HA A:SER22 3.9 28.0 0.5
HA A:SER22 3.9 28.1 0.2
HZ3 A:LYS40 4.0 24.7 1.0
N A:GLY21 4.0 18.6 1.0
HA2 A:GLY21 4.0 24.4 1.0
CA A:GLY21 4.1 20.4 1.0
ND2 A:ASN20 4.1 15.4 1.0
CB A:ASN20 4.1 16.6 1.0
HD21 A:ASN20 4.1 18.4 1.0
O B:HOH312 4.2 20.5 1.0
OD2 B:ASP106 4.2 16.5 1.0
N A:SER22 4.3 23.6 0.3
N A:SER22 4.3 23.5 0.5
N A:SER22 4.3 23.6 0.2
CE2 B:TYR94 4.4 17.8 1.0
CA A:ASN20 4.4 17.5 1.0
CA A:SER22 4.5 23.4 0.3
HE2 B:TYR94 4.5 21.4 1.0
CA A:SER22 4.6 23.4 0.5
CA A:SER22 4.6 23.4 0.2
HD22 A:ASN20 4.7 18.4 1.0
O A:HOH362 4.7 27.0 0.8
H A:GLY21 4.7 22.4 1.0
HA B:ASP106 4.7 14.8 1.0
HB3 B:ASP106 4.7 15.7 1.0
O A:HOH337 4.8 22.5 1.0
NZ A:LYS40 4.8 20.6 1.0
CB B:ASP106 4.8 13.1 1.0
O A:HOH414 4.8 31.6 0.9
CD B:GLN133 4.9 17.9 1.0
HA A:ASN20 4.9 21.0 1.0
HZ2 A:LYS40 4.9 24.7 1.0
HG2 B:GLN133 4.9 21.1 1.0
H A:SER22 4.9 28.2 0.5
H A:SER22 4.9 28.3 0.3
H A:SER22 4.9 28.3 0.2
CD1 B:TYR94 5.0 16.0 1.0
HB2 A:ASN20 5.0 20.0 1.0
HE2 A:LYS40 5.0 23.5 1.0
HA3 A:GLY21 5.0 24.4 1.0

Potassium binding site 2 out of 3 in 5tvv

Go back to Potassium Binding Sites List in 5tvv
Potassium binding site 2 out of 3 in the Computationally Designed Fentanyl Binder - FEN49* Apo


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 2 of Computationally Designed Fentanyl Binder - FEN49* Apo within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K201

b:21.2
occ:1.00
O B:ASN20 2.8 15.7 1.0
O B:GLY21 2.8 16.6 1.0
OD1 B:ASN20 3.0 16.3 1.0
CG B:ASN20 3.5 16.2 1.0
C B:GLY21 3.5 16.9 1.0
C B:ASN20 3.5 15.6 1.0
HA B:SER22 3.9 25.8 1.0
ND2 B:ASN20 4.0 17.5 1.0
HD21 B:ASN20 4.0 21.0 1.0
HZ3 B:LYS40 4.1 19.7 1.0
HB3 B:ASN20 4.1 19.5 1.0
N B:GLY21 4.1 16.1 1.0
HA2 B:GLY21 4.1 20.1 1.0
CA B:GLY21 4.1 16.7 1.0
O B:HOH351 4.2 23.5 1.0
CB B:ASN20 4.2 16.3 1.0
N B:SER22 4.3 20.0 1.0
CA B:ASN20 4.5 14.9 1.0
CA B:SER22 4.5 21.5 1.0
HD22 B:ASN20 4.6 21.0 1.0
O B:HOH443 4.7 31.5 1.0
H B:GLY21 4.8 19.4 1.0
NZ B:LYS40 4.9 16.4 1.0
H B:GLY23 4.9 24.2 1.0
HZ2 B:LYS40 4.9 19.7 1.0
H B:SER22 4.9 24.0 1.0

Potassium binding site 3 out of 3 in 5tvv

Go back to Potassium Binding Sites List in 5tvv
Potassium binding site 3 out of 3 in the Computationally Designed Fentanyl Binder - FEN49* Apo


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 3 of Computationally Designed Fentanyl Binder - FEN49* Apo within 5.0Å range:
probe atom residue distance (Å) B Occ
C:K201

b:42.0
occ:1.00
O C:GLY21 2.7 34.3 1.0
O C:ASN20 2.7 26.9 1.0
OD1 C:ASN20 2.9 24.4 1.0
C C:GLY21 3.3 38.0 1.0
HA C:SER22 3.3 57.6 1.0
C C:ASN20 3.5 26.6 1.0
CG C:ASN20 3.6 25.7 1.0
HZ1 C:LYS40 3.8 30.3 1.0
N C:SER22 3.9 44.4 1.0
HB3 C:ASN20 4.0 32.7 1.0
CA C:SER22 4.1 48.0 1.0
CA C:GLY21 4.1 35.7 1.0
N C:GLY21 4.1 34.5 1.0
HA2 C:GLY21 4.2 42.9 1.0
O C:HOH320 4.2 31.0 1.0
CB C:ASN20 4.2 27.3 1.0
ND2 C:ASN20 4.4 25.7 1.0
HD21 C:ASN20 4.5 30.8 1.0
H C:GLY23 4.5 52.3 1.0
CA C:ASN20 4.5 26.1 1.0
H C:SER22 4.6 53.2 1.0
NZ C:LYS40 4.7 25.2 1.0
HZ3 C:LYS40 4.8 30.3 1.0
H C:GLY21 4.8 41.4 1.0
C C:SER22 4.8 46.5 1.0
N C:GLY23 4.9 43.5 1.0

Reference:

M.J.Bick, P.J.Greisen, K.J.Morey, M.S.Antunes, D.La, B.Sankaran, L.Reymond, K.Johnsson, J.I.Medford, D.Baker. Computational Design of Environmental Sensors For the Potent Opioid Fentanyl. Elife V. 6 2017.
ISSN: ESSN 2050-084X
PubMed: 28925919
DOI: 10.7554/ELIFE.28909
Page generated: Mon Dec 14 00:07:58 2020

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