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Potassium in PDB 6pcd: Crystal Structure of Beta-Ketoadipyl-Coa Thiolase Mutant (C90S-H356A) in Complex Octanoyl Coenzyme A

Enzymatic activity of Crystal Structure of Beta-Ketoadipyl-Coa Thiolase Mutant (C90S-H356A) in Complex Octanoyl Coenzyme A

All present enzymatic activity of Crystal Structure of Beta-Ketoadipyl-Coa Thiolase Mutant (C90S-H356A) in Complex Octanoyl Coenzyme A:
2.3.1.16; 2.3.1.174;

Protein crystallography data

The structure of Crystal Structure of Beta-Ketoadipyl-Coa Thiolase Mutant (C90S-H356A) in Complex Octanoyl Coenzyme A, PDB code: 6pcd was solved by B.Sukritee, S.Panjikar, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.99 / 1.37
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 111.078, 116.621, 128.561, 90.00, 90.00, 90.00
R / Rfree (%) 14 / 17.3

Other elements in 6pcd:

The structure of Crystal Structure of Beta-Ketoadipyl-Coa Thiolase Mutant (C90S-H356A) in Complex Octanoyl Coenzyme A also contains other interesting chemical elements:

Chlorine (Cl) 5 atoms

Potassium Binding Sites:

The binding sites of Potassium atom in the Crystal Structure of Beta-Ketoadipyl-Coa Thiolase Mutant (C90S-H356A) in Complex Octanoyl Coenzyme A (pdb code 6pcd). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 3 binding sites of Potassium where determined in the Crystal Structure of Beta-Ketoadipyl-Coa Thiolase Mutant (C90S-H356A) in Complex Octanoyl Coenzyme A, PDB code: 6pcd:
Jump to Potassium binding site number: 1; 2; 3;

Potassium binding site 1 out of 3 in 6pcd

Go back to Potassium Binding Sites List in 6pcd
Potassium binding site 1 out of 3 in the Crystal Structure of Beta-Ketoadipyl-Coa Thiolase Mutant (C90S-H356A) in Complex Octanoyl Coenzyme A


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 1 of Crystal Structure of Beta-Ketoadipyl-Coa Thiolase Mutant (C90S-H356A) in Complex Octanoyl Coenzyme A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K505

b:36.1
occ:0.45
 O B:ALA9 2.7 20.1 1.0
O B:HOH922 2.8 47.6 1.0
O B:GLU203 2.9 18.3 0.5
O B:GLU203 3.1 17.6 0.5
NH2 B:ARG40 3.5 17.9 1.0
CA B:GLU204 3.8 15.7 1.0
C B:GLU203 3.9 18.3 0.5
C B:ALA9 3.9 14.6 1.0
C B:GLU203 3.9 15.7 0.5
CD1 B:ILE10 4.0 23.8 1.0
O B:HOH631 4.2 28.9 1.0
N B:GLU204 4.3 16.0 1.0
CZ B:ARG40 4.4 16.8 1.0
C B:GLU204 4.4 15.2 1.0
O B:GLU204 4.4 16.4 1.0
O B:HOH758 4.5 18.1 1.0
OD1 B:ASP8 4.5 18.2 1.0
CA B:ILE10 4.6 15.9 1.0
N B:ILE10 4.7 14.7 1.0
O B:HOH628 4.8 38.1 1.0
CB B:GLU204 4.8 18.3 1.0
NH1 B:ARG40 4.8 18.4 1.0
N B:ALA9 4.9 14.6 1.0
CA B:ALA9 4.9 14.5 1.0
CG B:GLU204 4.9 17.0 1.0

Potassium binding site 2 out of 3 in 6pcd

Go back to Potassium Binding Sites List in 6pcd
Potassium binding site 2 out of 3 in the Crystal Structure of Beta-Ketoadipyl-Coa Thiolase Mutant (C90S-H356A) in Complex Octanoyl Coenzyme A


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 2 of Crystal Structure of Beta-Ketoadipyl-Coa Thiolase Mutant (C90S-H356A) in Complex Octanoyl Coenzyme A within 5.0Å range:
probe atom residue distance (Å) B Occ
C:K504

b:34.4
occ:0.75
 OD1 C:ASP95 2.5 17.5 0.5
O B:HOH706 2.6 21.5 1.0
O C:HOH784 2.9 17.7 1.0
OD1 C:ASP95 3.1 16.8 0.5
OD2 C:ASP95 3.1 17.5 0.5
CG C:ASP95 3.1 16.5 0.5
NH2 C:ARG88 3.6 17.8 1.0
OG1 C:THR99 3.6 15.4 1.0
CE2 B:PHE53 3.7 18.8 1.0
CG1 B:VAL84 3.8 16.2 1.0
NH1 C:ARG102 3.9 16.6 1.0
CE C:MET284 4.0 17.9 1.0
CG C:ASP95 4.1 16.1 0.5
CG2 B:VAL84 4.4 18.1 1.0
CD2 B:PHE53 4.5 17.6 1.0
CZ B:PHE53 4.5 19.4 1.0
CB B:VAL84 4.5 15.0 1.0
CB C:ASP95 4.6 14.0 0.5
OE2 B:GLU51 4.6 19.6 1.0
CB C:ASP95 4.6 16.3 0.5
CZ C:ARG88 4.8 16.5 1.0
O C:ASP95 4.8 13.1 0.5
CB C:THR99 5.0 14.6 1.0
OD2 C:ASP95 5.0 17.7 0.5

Potassium binding site 3 out of 3 in 6pcd

Go back to Potassium Binding Sites List in 6pcd
Potassium binding site 3 out of 3 in the Crystal Structure of Beta-Ketoadipyl-Coa Thiolase Mutant (C90S-H356A) in Complex Octanoyl Coenzyme A


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 3 of Crystal Structure of Beta-Ketoadipyl-Coa Thiolase Mutant (C90S-H356A) in Complex Octanoyl Coenzyme A within 5.0Å range:
probe atom residue distance (Å) B Occ
C:K505

b:57.7
occ:0.85
 O C:ARG136 2.9 21.3 1.0
O D:HOH861 3.1 40.3 1.0
O C:MET138 3.2 23.8 1.0
O D:HOH742 3.7 40.0 1.0
N C:MET138 3.7 23.4 1.0
CE2 D:PHE125 3.8 19.2 1.0
CA C:ASN137 4.0 23.5 1.0
C C:ARG136 4.0 19.4 1.0
C C:MET138 4.2 19.8 1.0
C C:ASN137 4.2 27.2 1.0
O D:HOH656 4.3 34.0 1.0
CB D:ASP142 4.4 17.0 1.0
N C:ASN137 4.4 21.9 1.0
CD2 D:PHE125 4.5 17.3 1.0
CA C:MET138 4.5 20.2 1.0
N D:ASP142 4.7 17.8 1.0
CZ D:PHE125 4.7 20.4 1.0
O D:LEU140 5.0 20.0 1.0

Reference:

S.Bhaskar, D.Steer, R.Anand, S.Panjikar. Structural Basis For Differentiation Between Two Classes of Thiolase: Degradative Vs Biosynthetic Thiolase J Struct Biol X 2020.
ISSN: ESSN 2590-1524
DOI: 10.1016/J.YJSBX.2019.100018
Page generated: Mon Aug 12 17:07:34 2024

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