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Sodium in PDB 6esq: Structure of the Acetoacetyl-Coa Thiolase/Hmg-Coa Synthase Complex From Methanothermococcus Thermolithotrophicus Soaked with Acetyl-Coa

Enzymatic activity of Structure of the Acetoacetyl-Coa Thiolase/Hmg-Coa Synthase Complex From Methanothermococcus Thermolithotrophicus Soaked with Acetyl-Coa

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

Resolution Low / High (Å) 49.29 / 2.95
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 107.603, 145.176, 230.891, 90.00, 90.00, 90.00
R / Rfree (%) 18.2 / 23

Other elements in 6esq:

The structure of Structure of the Acetoacetyl-Coa Thiolase/Hmg-Coa Synthase Complex From Methanothermococcus Thermolithotrophicus Soaked with Acetyl-Coa also contains other interesting chemical elements:

Potassium (K) 4 atoms
Zinc (Zn) 4 atoms
Chlorine (Cl) 3 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 Soaked with Acetyl-Coa (pdb code 6esq). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the Structure of the Acetoacetyl-Coa Thiolase/Hmg-Coa Synthase Complex From Methanothermococcus Thermolithotrophicus Soaked with Acetyl-Coa, PDB code: 6esq:

Sodium binding site 1 out of 1 in 6esq

Go back to Sodium Binding Sites List in 6esq
Sodium binding site 1 out of 1 in the Structure of the Acetoacetyl-Coa Thiolase/Hmg-Coa Synthase Complex From Methanothermococcus Thermolithotrophicus Soaked with Acetyl-Coa


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 Soaked with Acetyl-Coa within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Na401

b:63.0
occ:1.00
O I:VAL88 2.1 87.8 1.0
HA K:PHE112 2.5 72.5 1.0
H K:ALA113 2.5 81.1 1.0
HB3 K:GLU111 2.7 67.2 1.0
HD3 I:PRO90 3.1 72.0 1.0
N K:PHE112 3.2 73.7 1.0
CA K:PHE112 3.2 72.2 1.0
C K:GLU111 3.3 73.0 1.0
C I:VAL88 3.3 82.5 1.0
HB3 I:PRO90 3.3 62.9 1.0
N K:ALA113 3.4 78.5 1.0
HA I:VAL88 3.4 75.0 1.0
HA I:PRO90 3.5 62.6 1.0
H K:PHE112 3.6 75.1 1.0
O K:GLU111 3.7 70.3 1.0
CB K:GLU111 3.7 66.0 1.0
N I:PRO90 3.7 67.2 1.0
C K:PHE112 3.8 76.0 1.0
CD I:PRO90 3.8 70.1 1.0
HB2 I:ASP109 3.9 67.4 1.0
CA I:VAL88 3.9 76.0 1.0
C I:LYS89 4.0 73.5 1.0
CA I:PRO90 4.0 63.3 1.0
CA K:GLU111 4.0 65.0 1.0
CB I:PRO90 4.0 63.5 1.0
HB2 K:GLU111 4.1 65.6 1.0
HA K:GLU111 4.2 64.8 1.0
HA I:LYS89 4.3 67.8 1.0
N I:LYS89 4.3 68.3 1.0
HG13 I:VAL88 4.3 74.1 1.0
CG I:PRO90 4.4 71.5 1.0
HG3 I:PRO90 4.4 73.5 1.0
CA I:LYS89 4.4 70.1 1.0
O I:LYS89 4.5 74.2 1.0
CB K:PHE112 4.6 73.7 1.0
CA K:ALA113 4.6 79.5 1.0
HA K:ALA113 4.6 82.2 1.0
OD2 I:ASP109 4.7 88.5 1.0
HB2 K:ALA113 4.7 83.6 1.0
O I:ALA87 4.7 83.5 1.0
HB2 K:PHE112 4.8 75.2 1.0
HD2 I:PRO90 4.8 73.6 1.0
HG12 I:VAL88 4.8 75.8 1.0
CG K:GLU111 4.8 80.1 1.0
N I:VAL88 4.8 76.7 1.0
CB I:ASP109 4.9 64.6 1.0
HG2 K:GLU111 4.9 79.4 1.0
CG1 I:VAL88 4.9 75.7 1.0
OE1 K:GLU111 4.9 70.9 1.0
HB2 I:PRO90 5.0 60.7 1.0
H I:ASP109 5.0 66.6 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 Dec 15 12:12:20 2020

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