Potassium in PDB 7b80: Deampylation Complex of Monomeric Ficd and Ampylated Bip (State 2)

Enzymatic activity of Deampylation Complex of Monomeric Ficd and Ampylated Bip (State 2)

All present enzymatic activity of Deampylation Complex of Monomeric Ficd and Ampylated Bip (State 2):
3.6.4.10;

Protein crystallography data

The structure of Deampylation Complex of Monomeric Ficd and Ampylated Bip (State 2), PDB code: 7b80 was solved by L.A.Perera, D.Ron, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 52.40 / 1.87
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 95, 103.89, 104.79, 90, 90, 90
R / Rfree (%) 20.1 / 22.8

Other elements in 7b80:

The structure of Deampylation Complex of Monomeric Ficd and Ampylated Bip (State 2) also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms

Potassium Binding Sites:

The binding sites of Potassium atom in the Deampylation Complex of Monomeric Ficd and Ampylated Bip (State 2) (pdb code 7b80). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 3 binding sites of Potassium where determined in the Deampylation Complex of Monomeric Ficd and Ampylated Bip (State 2), PDB code: 7b80:
Jump to Potassium binding site number: 1; 2; 3;

Potassium binding site 1 out of 3 in 7b80

Go back to Potassium Binding Sites List in 7b80
Potassium binding site 1 out of 3 in the Deampylation Complex of Monomeric Ficd and Ampylated Bip (State 2)


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 1 of Deampylation Complex of Monomeric Ficd and Ampylated Bip (State 2) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K604

b:26.4
occ:1.00
 O B:HOH705 2.7 27.3 1.0
O B:ALA229 2.7 27.1 1.0
OD1 B:ASP224 2.7 28.7 1.0
O B:HOH778 2.7 25.2 1.0
O3 B:PO4603 2.7 28.2 1.0
O B:ASP224 3.1 23.2 1.0
CG B:ASP224 3.2 28.0 1.0
O2 B:PO4603 3.3 31.1 1.0
N B:GLY226 3.4 28.4 1.0
P B:PO4603 3.5 31.4 1.0
C B:ALA229 3.7 26.0 1.0
CA B:GLY226 3.7 28.9 1.0
O B:HOH807 3.7 26.4 1.0
OD2 B:ASP224 3.7 29.2 1.0
MG B:MG602 3.7 27.1 1.0
C B:ASP224 3.8 25.2 1.0
OE1 B:GLU201 3.8 27.0 1.0
O1 B:PO4603 3.9 29.7 1.0
CB B:ASP224 4.0 26.7 1.0
C B:LEU225 4.2 27.7 1.0
N B:LEU225 4.4 26.0 1.0
CA B:LEU225 4.5 26.8 1.0
CA B:ASP224 4.5 25.9 1.0
N B:PHE230 4.5 24.7 1.0
CB B:ALA229 4.5 26.2 1.0
CA B:ALA229 4.5 26.3 1.0
CA B:PHE230 4.6 24.4 1.0
N B:ASP231 4.7 24.2 1.0
N B:ALA229 4.8 26.4 1.0
O4 B:PO4603 4.9 30.5 1.0
C B:GLY226 4.9 29.3 1.0
O B:HOH758 5.0 27.2 1.0
CD B:GLU201 5.0 26.6 1.0
OD2 B:ASP231 5.0 25.0 1.0

Potassium binding site 2 out of 3 in 7b80

Go back to Potassium Binding Sites List in 7b80
Potassium binding site 2 out of 3 in the Deampylation Complex of Monomeric Ficd and Ampylated Bip (State 2)


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 2 of Deampylation Complex of Monomeric Ficd and Ampylated Bip (State 2) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K605

b:34.8
occ:0.50
 O B:HOH970 2.7 38.3 1.0
ND1 B:HIS252 2.7 34.7 1.0
O B:HOH985 2.7 40.2 1.0
OE1 B:GLN110 2.7 43.7 1.0
O B:HIS252 2.7 34.6 1.0
OD1 B:ASP257 2.7 33.6 1.0
O B:HOH979 3.3 46.2 1.0
CE1 B:HIS252 3.4 34.8 1.0
CG B:ASP257 3.6 30.2 1.0
CD B:GLN110 3.6 43.6 1.0
K B:K606 3.6 36.6 0.5
NE2 B:GLN110 3.7 44.5 1.0
C B:HIS252 3.8 30.6 1.0
CG B:HIS252 3.8 32.8 1.0
OD2 B:ASP257 4.0 28.6 1.0
O B:HOH1013 4.2 36.5 1.0
CB B:HIS252 4.2 31.5 1.0
NH2 B:ARG97 4.3 32.7 1.0
CA B:HIS252 4.5 30.6 1.0
NE2 B:HIS252 4.6 34.3 1.0
CB B:ASP257 4.7 29.5 1.0
N B:LEU253 4.7 29.1 1.0
NH1 B:ARG97 4.8 31.4 1.0
CD2 B:HIS252 4.8 33.4 1.0
CZ B:ARG97 4.9 32.2 1.0
CA B:LEU253 5.0 27.9 1.0

Potassium binding site 3 out of 3 in 7b80

Go back to Potassium Binding Sites List in 7b80
Potassium binding site 3 out of 3 in the Deampylation Complex of Monomeric Ficd and Ampylated Bip (State 2)


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 3 of Deampylation Complex of Monomeric Ficd and Ampylated Bip (State 2) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K606

b:36.6
occ:0.50
 O B:HOH985 2.7 40.2 1.0
O B:HOH988 2.7 43.8 1.0
O B:HOH1013 2.7 36.5 1.0
OD2 B:ASP250 2.7 32.1 1.0
O B:HOH792 2.7 39.6 1.0
O B:HIS252 2.7 34.6 1.0
CG B:ASP250 3.3 28.8 1.0
OD1 B:ASP250 3.3 28.2 1.0
K B:K605 3.6 34.8 0.5
C B:HIS252 3.7 30.6 1.0
O B:HOH970 3.8 38.3 1.0
CB B:HIS252 4.4 31.5 1.0
CB B:LEU253 4.4 28.1 1.0
O B:HOH871 4.4 33.0 1.0
N B:LEU253 4.5 29.1 1.0
O B:HOH879 4.5 30.5 1.0
CA B:HIS252 4.5 30.6 1.0
CB B:ASP250 4.7 27.6 1.0
CA B:LEU253 4.7 27.9 1.0
ND1 B:HIS252 4.9 34.7 1.0
N B:HIS252 5.0 29.1 1.0

Reference:

L.A.Perera, D.Ron. Structures of A Deampylation Complex Rationalise the Switch Between Antagonistic Catalytic Activities of Ficd Nat Commun 2021.
ISSN: ESSN 2041-1723
Page generated: Sat Jul 10 16:25:56 2021

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