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Sodium 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
Potassium (K) 8 atoms
Zinc (Zn) 4 atoms
Chlorine (Cl) 6 atoms

Sodium Binding Sites:

The binding sites of Sodium 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 Sodium atom.
In total 3 binding sites of Sodium 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 Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in 6et9

Go back to Sodium Binding Sites List in 6et9
Sodium binding site 1 out of 3 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 Sodium with other atoms in the Na 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:Na401

b:58.3
occ:1.00
O A:ARG316 2.3 83.4 1.0
O A:LYS314 2.4 73.9 1.0
O A:TYR319 2.6 99.0 1.0
O A:PHE322 3.1 81.3 1.0
O A:VAL323 3.3 68.7 1.0
C A:ARG316 3.4 81.5 1.0
OG1 A:THR324 3.4 71.6 1.0
CB A:TYR319 3.5 99.4 1.0
C A:ILE315 3.5 69.8 1.0
C A:LYS314 3.5 73.4 1.0
C A:TYR319 3.6 0.5 1.0
N A:ARG316 3.7 72.2 1.0
O A:ILE315 3.8 68.5 1.0
C A:PHE322 3.8 80.2 1.0
C A:VAL323 3.8 68.5 1.0
CA A:TYR319 3.9 0.8 1.0
CA A:ILE315 4.0 68.8 1.0
CA A:THR324 4.0 67.2 1.0
N A:THR324 4.1 67.8 1.0
CA A:ARG316 4.1 77.1 1.0
N A:ILE315 4.2 70.9 1.0
N A:TYR319 4.2 0.0 1.0
CB A:THR324 4.3 68.7 1.0
O A:ILE317 4.3 80.0 1.0
N A:ILE317 4.4 74.5 1.0
CB A:PHE322 4.4 85.0 1.0
CG A:TYR319 4.4 0.6 1.0
CD1 A:TYR319 4.5 0.0 1.0
CA A:PHE322 4.5 85.4 1.0
N A:PHE322 4.5 90.7 1.0
C A:ILE317 4.6 79.1 1.0
CA A:ILE317 4.6 75.7 1.0
N A:VAL323 4.6 71.4 1.0
CA A:LYS314 4.6 75.8 1.0
N A:ASP320 4.7 0.8 1.0
CA A:VAL323 4.8 69.2 1.0
CG2 A:THR324 4.9 68.5 1.0
O A:GLY313 4.9 90.8 1.0

Sodium binding site 2 out of 3 in 6et9

Go back to Sodium Binding Sites List in 6et9
Sodium binding site 2 out of 3 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 Sodium with other atoms in the Na 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
D:Na402

b:42.2
occ:1.00
OG1 D:THR341 2.7 29.3 1.0
O D:GLY335 2.8 31.8 1.0
NE D:ARG344 2.9 31.4 1.0
NH1 D:ARG344 3.3 36.1 1.0
CG2 D:THR341 3.4 30.0 1.0
CB D:THR341 3.4 28.9 1.0
CZ D:ARG344 3.5 34.4 1.0
CA D:THR341 3.6 28.0 1.0
CG D:LEU331 3.8 32.4 1.0
CD1 D:LEU331 3.9 34.3 1.0
CD D:ARG344 3.9 27.2 1.0
CE2 D:PHE14 3.9 38.1 1.0
C D:GLY335 4.0 30.8 1.0
CA D:HIS336 4.1 26.9 1.0
CA D:LEU331 4.4 33.8 1.0
O D:THR341 4.5 25.0 1.0
N D:HIS336 4.5 27.6 1.0
CD2 D:PHE14 4.5 39.8 1.0
ND1 D:HIS336 4.5 27.1 1.0
C D:THR341 4.5 26.1 1.0
CB D:LEU331 4.6 33.0 1.0
CB D:ARG344 4.6 25.3 1.0
N D:THR341 4.7 28.6 1.0
N D:ALA337 4.8 27.0 1.0
NH2 D:ARG344 4.8 33.2 1.0
CB D:HIS336 4.9 27.0 1.0
CD2 D:LEU331 4.9 32.0 1.0
CG D:ARG344 4.9 25.8 1.0
CZ D:PHE14 4.9 37.1 1.0
N D:LEU331 5.0 33.7 1.0
C D:HIS336 5.0 27.1 1.0

Sodium binding site 3 out of 3 in 6et9

Go back to Sodium Binding Sites List in 6et9
Sodium binding site 3 out of 3 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 Sodium with other atoms in the Na 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
J:Na401

b:58.9
occ:1.00
O J:ASP150 2.5 42.3 1.0
O J:GLY149 2.8 45.6 1.0
C J:GLY149 3.1 45.0 1.0
O J:PRO148 3.1 42.5 1.0
C J:ASP150 3.3 42.8 1.0
N J:ASP150 3.4 42.6 1.0
CE2 J:TYR154 3.4 43.9 1.0
OE1 J:GLU153 3.5 41.0 1.0
CD1 J:TRP27 3.8 43.0 1.0
CA J:ASP150 3.8 43.0 1.0
CA J:GLY149 3.9 44.3 1.0
OH J:TYR154 3.9 44.7 1.0
CZ J:TYR154 3.9 44.1 1.0
C J:PRO148 4.1 41.5 1.0
CD2 J:TYR154 4.2 43.4 1.0
N J:ALA151 4.2 43.5 1.0
CG J:TRP27 4.2 43.8 1.0
CB J:GLU153 4.2 40.4 1.0
NE1 J:TRP27 4.2 42.4 1.0
CG2 J:ILE23 4.2 42.2 1.0
N J:GLY149 4.5 42.2 1.0
CD J:GLU153 4.6 40.4 1.0
CA J:ALA151 4.6 43.7 1.0
CB J:TRP27 4.6 44.8 1.0
O J:ALA147 4.8 40.8 1.0
CE2 J:TRP27 4.8 42.9 1.0
CD2 J:TRP27 4.9 43.7 1.0
CG J:GLU153 4.9 40.1 1.0
CE1 J:TYR154 5.0 44.0 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: Tue Oct 8 08:31:44 2024

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