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Zinc 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
Chlorine (Cl) 3 atoms
Sodium (Na) 1 atom

Zinc Binding Sites:

The binding sites of Zinc 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 Zinc atom.
In total 4 binding sites of Zinc where determined in the Structure of the Acetoacetyl-Coa Thiolase/Hmg-Coa Synthase Complex From Methanothermococcus Thermolithotrophicus Soaked with Acetyl-Coa, PDB code: 6esq:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 6esq

Go back to Zinc Binding Sites List in 6esq
Zinc binding site 1 out of 4 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 Zinc with other atoms in the Zn 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
E:Zn201

b:0.8
occ:0.30
 HG E:CYS37 1.8 0.5 1.0
HG E:CYS23 1.8 0.8 1.0
SG E:CYS34 2.3 0.3 1.0
SG E:CYS37 2.5 0.7 1.0
SG E:CYS20 2.7 0.1 1.0
SG E:CYS23 2.8 0.2 1.0
HB2 E:CYS20 3.4 1.0 1.0
HB2 E:ASP36 3.4 0.1 1.0
H E:CYS37 3.4 0.8 1.0
CB E:CYS20 3.5 0.0 1.0
HB3 E:CYS20 3.5 0.1 1.0
HH E:TYR27 3.5 0.3 1.0
HB2 E:CYS37 3.6 0.4 1.0
CB E:CYS34 3.7 0.9 1.0
HE2 E:TYR27 3.7 1.0 1.0
CB E:CYS37 3.7 0.9 1.0
HB2 E:CYS34 3.8 0.6 1.0
HB3 E:CYS34 3.9 0.8 1.0
HB2 E:CYS23 3.9 0.5 1.0
CB E:CYS23 4.1 0.0 1.0
N E:CYS37 4.2 0.6 1.0
H E:CYS23 4.3 0.4 1.0
H E:ASP36 4.3 0.8 1.0
OH E:TYR27 4.4 0.8 1.0
HA3 E:GLY41 4.4 1.0 1.0
CB E:ASP36 4.5 0.5 1.0
HB E:THR22 4.5 0.9 1.0
HB3 E:CYS37 4.5 0.9 1.0
CA E:CYS37 4.6 0.7 1.0
CE2 E:TYR27 4.6 0.4 1.0
OD2 E:ASP36 4.7 0.2 1.0
HB3 E:CYS23 4.7 0.1 1.0
HB3 E:ASP36 4.9 0.9 1.0
CA E:CYS20 4.9 0.3 1.0
HB3 E:LYS25 5.0 0.8 1.0
CZ E:TYR27 5.0 0.5 1.0
N E:CYS23 5.0 0.5 1.0
CA E:CYS34 5.0 0.6 1.0
HD2 E:PRO35 5.0 0.6 1.0

Zinc binding site 2 out of 4 in 6esq

Go back to Zinc Binding Sites List in 6esq
Zinc binding site 2 out of 4 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 Zinc with other atoms in the Zn binding site number 2 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
F:Zn201

b:0.4
occ:0.40
 SG F:CYS34 2.3 0.3 1.0
SG F:CYS23 2.4 0.4 1.0
H F:CYS37 2.5 0.2 1.0
HG F:CYS20 2.5 0.6 1.0
HB2 F:CYS37 2.6 1.0 1.0
HB2 F:ASP36 2.7 0.3 1.0
HG F:CYS37 2.8 0.0 1.0
SG F:CYS37 2.9 0.5 1.0
CB F:CYS37 3.2 0.1 1.0
SG F:CYS20 3.3 0.6 1.0
N F:CYS37 3.3 0.0 1.0
HH F:TYR27 3.7 0.7 1.0
CB F:CYS34 3.7 0.8 1.0
HB3 F:CYS34 3.8 0.5 1.0
CB F:ASP36 3.8 0.5 1.0
H F:ASP36 3.8 0.1 1.0
CA F:CYS37 3.9 0.2 1.0
HA3 F:GLY41 4.0 0.5 1.0
CB F:CYS23 4.0 0.1 1.0
HB2 F:CYS34 4.1 0.8 1.0
HB3 F:CYS37 4.1 0.4 1.0
HB3 F:CYS20 4.1 1.0 1.0
HB2 F:CYS23 4.1 0.8 1.0
HB F:THR22 4.2 0.0 1.0
HB3 F:ASP36 4.2 0.6 1.0
CB F:CYS20 4.2 0.2 1.0
HB2 F:CYS20 4.3 0.3 1.0
H F:CYS23 4.3 0.3 1.0
C F:ASP36 4.3 0.2 1.0
HE2 F:TYR27 4.3 0.3 1.0
HA2 F:GLY41 4.4 0.6 1.0
OD2 F:ASP36 4.4 0.8 1.0
CA F:ASP36 4.4 0.7 1.0
N F:ASP36 4.5 0.5 1.0
HA F:CYS37 4.6 0.2 1.0
HB3 F:CYS23 4.6 1.0 1.0
OH F:TYR27 4.6 0.8 1.0
CG F:ASP36 4.6 0.1 1.0
H F:ARG38 4.6 0.4 1.0
CA F:GLY41 4.7 0.3 1.0
N F:CYS23 4.8 0.4 1.0
C F:CYS37 5.0 0.4 1.0

Zinc binding site 3 out of 4 in 6esq

Go back to Zinc Binding Sites List in 6esq
Zinc binding site 3 out of 4 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 Zinc with other atoms in the Zn binding site number 3 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
G:Zn201

b:0.2
occ:0.50
 HG G:CYS20 2.1 0.8 1.0
SG G:CYS34 2.4 0.7 1.0
SG G:CYS20 2.7 0.4 1.0
HG G:CYS37 2.7 0.1 1.0
HB2 G:ASP36 3.0 0.0 1.0
H G:CYS37 3.1 0.0 1.0
SG G:CYS37 3.2 0.1 1.0
HG G:CYS23 3.6 0.5 1.0
HB G:THR22 3.6 0.9 1.0
SG G:CYS23 3.7 0.2 1.0
CB G:CYS34 3.7 0.4 1.0
HB3 G:CYS34 3.7 0.5 1.0
CB G:CYS20 3.8 0.6 1.0
HH G:TYR27 3.8 0.4 1.0
HB2 G:CYS20 3.8 0.5 1.0
HB3 G:CYS20 3.8 0.4 1.0
HB2 G:CYS34 4.0 0.7 1.0
HA2 G:GLY41 4.1 0.4 1.0
N G:CYS37 4.1 0.8 1.0
H G:ASP36 4.1 0.5 1.0
CB G:ASP36 4.1 0.5 1.0
HA3 G:GLY41 4.2 0.2 1.0
HE2 G:TYR27 4.2 0.2 1.0
HG1 G:THR22 4.4 0.3 1.0
HB3 G:ASP36 4.5 0.1 1.0
OD2 G:ASP36 4.6 0.5 1.0
CB G:THR22 4.6 0.3 1.0
CA G:GLY41 4.7 0.1 1.0
H G:CYS23 4.7 0.1 1.0
CB G:CYS37 4.7 0.1 1.0
OH G:TYR27 4.7 1.0 1.0
OG1 G:THR22 4.8 0.9 1.0
CA G:ASP36 4.8 0.3 1.0
O G:CYS37 4.8 0.1 1.0
N G:ASP36 4.8 0.9 1.0
CA G:CYS37 4.9 0.0 1.0
C G:ASP36 4.9 0.9 1.0
CG G:ASP36 4.9 0.2 1.0

Zinc binding site 4 out of 4 in 6esq

Go back to Zinc Binding Sites List in 6esq
Zinc binding site 4 out of 4 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 Zinc with other atoms in the Zn binding site number 4 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
H:Zn201

b:0.6
occ:0.40
 SG H:CYS34 2.2 0.5 1.0
HG H:CYS37 2.3 0.8 1.0
HG H:CYS20 2.4 0.4 1.0
SG H:CYS23 2.5 0.2 1.0
H H:CYS37 2.6 0.9 1.0
HB2 H:CYS37 2.8 1.0 1.0
SG H:CYS37 2.9 0.5 1.0
HB2 H:ASP36 2.9 0.9 1.0
SG H:CYS20 3.0 0.4 1.0
CB H:CYS37 3.3 0.8 1.0
N H:CYS37 3.4 0.1 1.0
CB H:CYS34 3.5 0.6 1.0
HB3 H:CYS34 3.6 0.4 1.0
H H:ASP36 3.8 0.0 1.0
HB2 H:CYS34 3.8 0.5 1.0
HB3 H:CYS20 3.9 0.4 1.0
CB H:CYS20 3.9 0.1 1.0
HE2 H:TYR27 4.0 0.8 1.0
CB H:ASP36 4.0 0.5 1.0
CB H:CYS23 4.0 0.1 1.0
CA H:CYS37 4.0 0.8 1.0
HB2 H:CYS23 4.0 0.9 1.0
HB2 H:CYS20 4.0 0.4 1.0
HB H:THR22 4.1 0.0 1.0
H H:CYS23 4.2 0.9 1.0
OH H:TYR27 4.2 0.8 1.0
HB3 H:CYS37 4.3 0.2 1.0
HH H:TYR27 4.3 0.9 1.0
C H:ASP36 4.4 0.8 1.0
HA3 H:GLY41 4.4 0.3 1.0
HB3 H:ASP36 4.4 0.5 1.0
H H:ARG38 4.5 0.2 1.0
CA H:ASP36 4.5 0.8 1.0
N H:ASP36 4.6 0.2 1.0
OD2 H:ASP36 4.6 0.4 1.0
HA H:CYS37 4.6 0.4 1.0
HB3 H:CYS23 4.6 0.7 1.0
CE2 H:TYR27 4.7 0.5 1.0
N H:CYS23 4.8 0.4 1.0
CA H:CYS34 4.8 0.8 1.0
CG H:ASP36 4.8 0.1 1.0
CZ H:TYR27 4.8 0.7 1.0
CA H:CYS23 5.0 0.6 1.0
HD2 H:PRO35 5.0 0.6 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: Mon Oct 28 20:20:37 2024

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