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Zinc 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
Chlorine (Cl) 6 atoms
Sodium (Na) 3 atoms

Zinc Binding Sites:

The binding sites of Zinc 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 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 at 2.75 A, PDB code: 6et9:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 6et9

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Zinc binding site 1 out of 4 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 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 at 2.75 A within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn201

b:93.1
occ:1.00
 SG E:CYS23 2.3 77.9 1.0
SG E:CYS37 2.4 81.8 1.0
SG E:CYS20 2.5 80.3 1.0
SG E:CYS34 2.5 76.9 1.0
CB E:CYS20 3.3 77.9 1.0
CB E:CYS23 3.3 80.3 1.0
CB E:CYS37 3.5 82.5 1.0
N E:CYS23 3.6 82.9 1.0
CB E:CYS34 3.7 77.1 1.0
CA E:CYS23 4.1 81.8 1.0
N E:CYS37 4.1 79.7 1.0
CB E:THR22 4.3 86.3 1.0
CA E:CYS37 4.5 81.8 1.0
C E:THR22 4.6 85.4 1.0
CA E:CYS20 4.7 78.5 1.0
CA E:GLY41 4.8 87.6 1.0
OH E:TYR27 4.8 74.5 1.0
CB E:ASP36 4.8 85.6 1.0
CA E:THR22 4.8 86.5 1.0
CG2 E:THR22 4.9 87.7 1.0
N E:THR22 4.9 85.4 1.0
C E:CYS23 4.9 80.6 1.0
O E:CYS20 4.9 80.0 1.0
C E:CYS20 5.0 80.4 1.0
N E:GLY24 5.0 89.2 1.0

Zinc binding site 2 out of 4 in 6et9

Go back to Zinc Binding Sites List in 6et9
Zinc binding site 2 out of 4 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 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 at 2.75 A within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn201

b:81.5
occ:1.00
 SG F:CYS20 2.4 77.7 1.0
SG F:CYS23 2.4 65.8 1.0
SG F:CYS34 2.4 69.4 1.0
SG F:CYS37 2.6 82.2 1.0
CB F:CYS20 3.4 72.7 1.0
CB F:CYS23 3.4 68.8 1.0
CB F:CYS37 3.4 83.8 1.0
CB F:CYS34 3.5 70.8 1.0
N F:CYS23 3.7 71.9 1.0
N F:CYS37 4.0 82.4 1.0
CA F:CYS23 4.1 70.2 1.0
CB F:THR22 4.2 78.2 1.0
CA F:CYS37 4.3 84.8 1.0
CA F:GLY41 4.6 0.1 1.0
C F:THR22 4.6 75.3 1.0
CB F:ASP36 4.7 85.8 1.0
OH F:TYR27 4.7 70.4 1.0
CA F:CYS20 4.7 71.8 1.0
CG2 F:THR22 4.8 80.7 1.0
CA F:THR22 4.8 77.2 1.0
C F:ASP36 4.9 88.1 1.0
CA F:CYS34 4.9 69.8 1.0
N F:THR22 4.9 75.1 1.0

Zinc binding site 3 out of 4 in 6et9

Go back to Zinc Binding Sites List in 6et9
Zinc binding site 3 out of 4 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 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 at 2.75 A within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Zn201

b:61.1
occ:1.00
 SG G:CYS23 2.4 61.9 1.0
SG G:CYS34 2.5 59.2 1.0
SG G:CYS20 2.5 65.8 1.0
SG G:CYS37 2.5 67.2 1.0
CB G:CYS20 3.4 63.6 1.0
CB G:CYS23 3.4 63.4 1.0
CB G:CYS37 3.4 65.9 1.0
CB G:CYS34 3.6 58.5 1.0
N G:CYS23 3.7 68.1 1.0
N G:CYS37 4.1 61.0 1.0
CA G:CYS23 4.1 64.0 1.0
CB G:THR22 4.2 78.9 1.0
CA G:CYS37 4.4 63.2 1.0
C G:THR22 4.6 76.4 1.0
CA G:GLY41 4.6 78.8 1.0
CA G:CYS20 4.8 62.8 1.0
CA G:THR22 4.8 80.5 1.0
CG2 G:THR22 4.8 80.0 1.0
OH G:TYR27 4.9 54.3 1.0
N G:THR22 4.9 82.7 1.0
CB G:ASP36 4.9 66.4 1.0
O G:CYS20 4.9 69.2 1.0
C G:CYS20 5.0 66.9 1.0
C G:CYS23 5.0 59.9 1.0

Zinc binding site 4 out of 4 in 6et9

Go back to Zinc Binding Sites List in 6et9
Zinc binding site 4 out of 4 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 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 at 2.75 A within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Zn201

b:0.2
occ:1.00
 SG H:CYS34 2.4 98.1 1.0
SG H:CYS23 2.5 0.1 1.0
SG H:CYS37 2.5 0.1 1.0
SG H:CYS20 2.6 0.3 1.0
CB H:CYS37 3.4 0.8 1.0
CB H:CYS20 3.4 0.6 1.0
CB H:CYS23 3.5 0.6 1.0
CB H:CYS34 3.6 98.2 1.0
N H:CYS23 3.8 0.4 1.0
N H:CYS37 3.9 0.5 1.0
CA H:CYS23 4.3 0.8 1.0
CA H:CYS37 4.3 0.7 1.0
CB H:THR22 4.4 1.0 1.0
CB H:ASP36 4.5 0.3 1.0
OH H:TYR27 4.6 0.8 1.0
CA H:GLY41 4.7 0.3 1.0
C H:THR22 4.8 0.7 1.0
C H:ASP36 4.8 0.2 1.0
CA H:CYS20 4.9 0.6 1.0
CG2 H:THR22 4.9 0.2 1.0
CA H:CYS34 5.0 95.1 1.0
CA H:THR22 5.0 0.7 1.0
CE1 H:TYR27 5.0 0.7 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 20:20:28 2024

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