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Potassium in PDB 6et9: Structure of the Acetoacetyl-Coa-Thiolase/Hmg-Coa-Synthase Complex From Methanothermococcus Thermolithotrophicus at 2.75 A

Enzymatic activity of Structure of the Acetoacetyl-Coa-Thiolase/Hmg-Coa-Synthase Complex From Methanothermococcus Thermolithotrophicus at 2.75 A

All present enzymatic activity of Structure of the Acetoacetyl-Coa-Thiolase/Hmg-Coa-Synthase Complex From Methanothermococcus Thermolithotrophicus at 2.75 A:
2.3.1.9; 2.3.3.10;

Protein crystallography data

The structure of Structure of the Acetoacetyl-Coa-Thiolase/Hmg-Coa-Synthase Complex From Methanothermococcus Thermolithotrophicus at 2.75 A, PDB code: 6et9 was solved by S.Engilberge, B.Voegeli, E.Girard, F.Riobe, O.Maury, T.J.Erb, S.Shima, T.Wagner, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.39 / 2.75
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 106.617, 144.014, 230.585, 90.00, 90.00, 90.00
R / Rfree (%) 19 / 22.5

Other elements in 6et9:

The structure of Structure of the Acetoacetyl-Coa-Thiolase/Hmg-Coa-Synthase Complex From Methanothermococcus Thermolithotrophicus at 2.75 A also contains other interesting chemical elements:

Magnesium (Mg) 1 atom
Zinc (Zn) 4 atoms
Chlorine (Cl) 6 atoms
Sodium (Na) 3 atoms

Potassium Binding Sites:

The binding sites of Potassium atom in the Structure of the Acetoacetyl-Coa-Thiolase/Hmg-Coa-Synthase Complex From Methanothermococcus Thermolithotrophicus at 2.75 A (pdb code 6et9). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 8 binding sites of Potassium where determined in the Structure of the Acetoacetyl-Coa-Thiolase/Hmg-Coa-Synthase Complex From Methanothermococcus Thermolithotrophicus at 2.75 A, PDB code: 6et9:
Jump to Potassium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Potassium binding site 1 out of 8 in 6et9

Go back to Potassium Binding Sites List in 6et9
Potassium binding site 1 out of 8 in the Structure of the Acetoacetyl-Coa-Thiolase/Hmg-Coa-Synthase Complex From Methanothermococcus Thermolithotrophicus at 2.75 A


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 1 of Structure of the Acetoacetyl-Coa-Thiolase/Hmg-Coa-Synthase Complex From Methanothermococcus Thermolithotrophicus at 2.75 A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K405

b:0.7
occ:1.00
 OE1 A:GLU296 2.7 56.0 1.0
O A:HOH507 3.1 39.8 1.0
O A:THR255 3.3 50.2 1.0
OD1 A:ASP297 3.5 63.2 1.0
CD A:GLU296 3.8 57.6 1.0
CB A:GLU296 3.9 57.0 1.0
CB A:LYS303 3.9 91.4 1.0
CB A:THR256 3.9 50.5 1.0
C A:THR255 4.2 49.3 1.0
CG A:LYS303 4.3 96.3 1.0
CA A:LYS303 4.3 87.0 1.0
CA A:THR256 4.3 48.9 1.0
OG1 A:THR256 4.4 50.8 1.0
CD A:LYS303 4.4 99.6 1.0
CG A:GLU296 4.5 58.1 1.0
O A:ILE293 4.6 52.1 1.0
CG A:ASP297 4.6 60.0 1.0
N A:THR256 4.7 48.6 1.0
CE2 A:TYR152 4.8 52.8 1.0
CG2 A:ILE293 4.8 48.8 1.0
OE2 A:GLU296 4.8 58.8 1.0
OG1 A:THR255 4.9 51.8 1.0
N A:GLY304 5.0 73.8 1.0

Potassium binding site 2 out of 8 in 6et9

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Potassium binding site 2 out of 8 in the Structure of the Acetoacetyl-Coa-Thiolase/Hmg-Coa-Synthase Complex From Methanothermococcus Thermolithotrophicus at 2.75 A


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 2 of Structure of the Acetoacetyl-Coa-Thiolase/Hmg-Coa-Synthase Complex From Methanothermococcus Thermolithotrophicus at 2.75 A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K403

b:64.0
occ:1.00
 OD1 B:ASP36 2.3 35.6 1.0
NZ B:LYS354 2.9 55.2 1.0
CG B:ASP36 3.3 34.8 1.0
OD2 B:ASP36 3.6 34.0 1.0
OD2 B:ASP356 3.8 39.2 1.0
OE1 B:GLU232 3.8 47.3 1.0
O B:HOH516 4.1 37.5 1.0
CE B:LYS354 4.2 55.5 1.0
O B:ASP36 4.3 38.5 1.0
CB B:ASP36 4.6 34.8 1.0
O B:HOH511 4.6 35.5 1.0
OH B:TYR350 4.8 31.3 1.0
CA B:ASP36 4.9 35.3 1.0
CD B:GLU232 4.9 45.7 1.0
CG B:ASP356 4.9 39.1 1.0
C B:ASP36 4.9 37.3 1.0

Potassium binding site 3 out of 8 in 6et9

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Potassium binding site 3 out of 8 in the Structure of the Acetoacetyl-Coa-Thiolase/Hmg-Coa-Synthase Complex From Methanothermococcus Thermolithotrophicus at 2.75 A


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 3 of Structure of the Acetoacetyl-Coa-Thiolase/Hmg-Coa-Synthase Complex From Methanothermococcus Thermolithotrophicus at 2.75 A within 5.0Å range:
probe atom residue distance (Å) B Occ
C:K402

b:0.8
occ:1.00
 OD1 C:ASP36 2.9 71.9 1.0
OE1 C:GLU232 3.4 96.6 1.0
NZ C:LYS354 3.5 66.3 1.0
CG C:ASP36 3.9 68.0 1.0
OD2 C:ASP356 4.1 60.7 1.0
CD C:GLU232 4.1 89.6 1.0
OD2 C:ASP36 4.3 68.4 1.0
OE2 C:GLU232 4.3 97.4 1.0
CE C:LYS354 4.6 66.3 1.0
O C:ASP36 4.6 66.8 1.0

Potassium binding site 4 out of 8 in 6et9

Go back to Potassium Binding Sites List in 6et9
Potassium binding site 4 out of 8 in the Structure of the Acetoacetyl-Coa-Thiolase/Hmg-Coa-Synthase Complex From Methanothermococcus Thermolithotrophicus at 2.75 A


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 4 of Structure of the Acetoacetyl-Coa-Thiolase/Hmg-Coa-Synthase Complex From Methanothermococcus Thermolithotrophicus at 2.75 A within 5.0Å range:
probe atom residue distance (Å) B Occ
D:K404

b:62.0
occ:1.00
 O D:ASP36 2.6 45.2 1.0
OD1 D:ASP36 2.7 58.0 1.0
OE1 D:GLU232 3.6 69.1 1.0
C D:ASP36 3.7 40.2 1.0
CG D:ASP36 3.7 52.4 1.0
NZ D:LYS354 3.8 42.9 1.0
CA D:ASP36 4.2 41.1 1.0
OD2 D:ASP36 4.5 51.6 1.0
CB D:ASP36 4.6 45.2 1.0
O D:ILE7 4.7 32.2 1.0
CD D:GLU232 4.8 67.5 1.0
N D:ALA37 4.8 33.1 1.0
OH D:TYR350 5.0 35.8 1.0

Potassium binding site 5 out of 8 in 6et9

Go back to Potassium Binding Sites List in 6et9
Potassium binding site 5 out of 8 in the Structure of the Acetoacetyl-Coa-Thiolase/Hmg-Coa-Synthase Complex From Methanothermococcus Thermolithotrophicus at 2.75 A


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 5 of Structure of the Acetoacetyl-Coa-Thiolase/Hmg-Coa-Synthase Complex From Methanothermococcus Thermolithotrophicus at 2.75 A within 5.0Å range:
probe atom residue distance (Å) B Occ
I:K401

b:55.2
occ:1.00
 OE2 K:GLU111 2.5 50.5 1.0
OE2 I:GLU111 2.5 49.5 1.0
CD I:GLU111 3.3 47.2 1.0
CD K:GLU111 3.4 49.3 1.0
OE1 I:GLU111 3.4 52.4 1.0
OE1 K:GLU111 3.7 50.4 1.0
O K:HOH506 3.9 52.1 1.0
O K:ALA87 4.1 51.0 1.0
OE2 K:GLU193 4.2 75.0 1.0
O I:HOH533 4.3 33.7 1.0
O I:ALA87 4.5 35.0 1.0
OE1 I:GLU193 4.5 64.0 1.0
CG I:GLU111 4.8 38.5 1.0
CG K:GLU111 4.8 43.5 1.0
OE2 I:GLU193 4.8 61.8 1.0
CA K:ALA87 4.8 43.8 1.0
C K:ALA87 5.0 47.5 1.0

Potassium binding site 6 out of 8 in 6et9

Go back to Potassium Binding Sites List in 6et9
Potassium binding site 6 out of 8 in the Structure of the Acetoacetyl-Coa-Thiolase/Hmg-Coa-Synthase Complex From Methanothermococcus Thermolithotrophicus at 2.75 A


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 6 of Structure of the Acetoacetyl-Coa-Thiolase/Hmg-Coa-Synthase Complex From Methanothermococcus Thermolithotrophicus at 2.75 A within 5.0Å range:
probe atom residue distance (Å) B Occ
I:K402

b:92.7
occ:1.00
 OD2 I:ASP3 2.7 84.3 1.0
CG I:ASP3 3.8 82.5 1.0
O I:GLY129 3.9 36.6 1.0
O K:HOH535 4.0 44.5 1.0
O K:SER130 4.2 42.7 1.0
OD1 I:ASP3 4.5 83.4 1.0
C I:GLY129 4.7 35.2 1.0
CA I:GLY129 4.8 34.2 1.0
CB I:ASP3 4.8 78.6 1.0
C K:SER130 5.0 41.6 1.0
CA K:SER130 5.0 40.6 1.0

Potassium binding site 7 out of 8 in 6et9

Go back to Potassium Binding Sites List in 6et9
Potassium binding site 7 out of 8 in the Structure of the Acetoacetyl-Coa-Thiolase/Hmg-Coa-Synthase Complex From Methanothermococcus Thermolithotrophicus at 2.75 A


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 7 of Structure of the Acetoacetyl-Coa-Thiolase/Hmg-Coa-Synthase Complex From Methanothermococcus Thermolithotrophicus at 2.75 A within 5.0Å range:
probe atom residue distance (Å) B Occ
J:K402

b:61.0
occ:1.00
 OE2 L:GLU111 2.3 53.0 1.0
OE2 J:GLU111 2.5 43.5 1.0
CD L:GLU111 3.2 53.8 1.0
CD J:GLU111 3.2 42.3 1.0
OE1 J:GLU111 3.3 43.6 1.0
OE1 L:GLU111 3.5 56.1 1.0
O L:HOH512 3.8 44.8 1.0
O L:ALA87 4.3 47.0 1.0
O J:ALA87 4.5 47.4 1.0
CG L:GLU111 4.6 51.9 1.0
CG J:GLU111 4.7 41.2 1.0
O J:HOH503 4.7 54.1 1.0
OE1 J:GLU193 4.8 0.9 1.0
CA L:ALA87 4.9 44.3 1.0

Potassium binding site 8 out of 8 in 6et9

Go back to Potassium Binding Sites List in 6et9
Potassium binding site 8 out of 8 in the Structure of the Acetoacetyl-Coa-Thiolase/Hmg-Coa-Synthase Complex From Methanothermococcus Thermolithotrophicus at 2.75 A


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 8 of Structure of the Acetoacetyl-Coa-Thiolase/Hmg-Coa-Synthase Complex From Methanothermococcus Thermolithotrophicus at 2.75 A within 5.0Å range:
probe atom residue distance (Å) B Occ
K:K401

b:82.9
occ:1.00
 O K:GLU72 2.5 42.2 1.0
O K:ALA101 3.0 37.4 1.0
O K:ASP104 3.1 37.9 1.0
CB K:ASP104 3.4 41.1 1.0
C K:GLU72 3.6 40.9 1.0
C K:ASP104 3.7 37.7 1.0
N K:ASP104 3.7 39.0 1.0
CA K:ASP104 3.8 39.1 1.0
CA K:GLU72 4.0 43.7 1.0
O K:ILE74 4.0 36.1 1.0
C K:ALA101 4.2 36.9 1.0
OD2 K:ASP104 4.3 51.0 1.0
CG K:ASP104 4.3 47.0 1.0
CB K:GLU72 4.5 50.3 1.0
C K:THR102 4.6 38.9 1.0
O K:THR102 4.6 39.9 1.0
N K:PRO103 4.7 39.4 1.0
N K:LYS73 4.7 41.1 1.0
N K:LEU105 4.7 36.5 1.0
C K:PRO103 4.8 38.3 1.0
CA K:ALA101 4.9 36.5 1.0
CD K:PRO103 5.0 41.2 1.0

Reference:

B.Vogeli, S.Engilberge, E.Girard, F.Riobe, O.Maury, T.J.Erb, S.Shima, T.Wagner. Archaeal Acetoacetyl-Coa Thiolase/Hmg-Coa Synthase Complex Channels the Intermediate Via A Fused Coa-Binding Site. Proc. Natl. Acad. Sci. V. 115 3380 2018U.S.A..
ISSN: ESSN 1091-6490
PubMed: 29531083
DOI: 10.1073/PNAS.1718649115
Page generated: Mon Dec 14 00:36:10 2020

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