Chlorine 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:

Potassium (K) 3 atoms

Chlorine Binding Sites:

The binding sites of Chlorine 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 Chlorine atom.
In total 5 binding sites of Chlorine where determined in the Crystal Structure of Beta-Ketoadipyl-Coa Thiolase Mutant (C90S-H356A) in Complex Octanoyl Coenzyme A, PDB code: 6pcd:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5;

Chlorine binding site 1 out of 5 in 6pcd

Go back to Chlorine Binding Sites List in 6pcd
Chlorine binding site 1 out of 5 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 Chlorine with other atoms in the Cl 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
A:Cl504

b:19.3
occ:0.70
 O A:HOH820 3.1 18.5 1.0
ND2 A:ASN322 3.1 33.1 1.0
O A:HOH767 3.2 19.4 1.0
NH1 A:ARG364 3.4 21.1 1.0
CB A:SER361 3.8 21.3 0.5
CB A:SER361 3.8 17.9 0.5
CD2 A:LEU365 3.8 24.2 1.0
CB A:ALA351 3.9 18.5 1.0
CB A:ASN322 3.9 22.2 1.0
CG A:LEU365 4.0 19.4 1.0
CG A:ASN322 4.0 28.8 1.0
OG A:SER361 4.0 23.0 0.5
CA A:ASN322 4.2 19.1 1.0
O A:SER361 4.2 16.1 0.5
CD1 A:LEU365 4.3 22.2 1.0
CZ A:ARG364 4.4 20.5 1.0
O A:SER361 4.4 18.6 0.5
NE A:ARG364 4.5 17.3 1.0
CE A:MET385 4.5 17.6 0.5
CA A:SER361 4.5 18.3 0.5
OG A:SER361 4.6 18.7 0.5
CA A:SER361 4.6 17.3 0.5
CB A:ALA356 4.6 23.5 1.0
C A:SER361 4.6 15.6 0.5
C A:SER361 4.7 16.8 0.5
N A:GLU323 4.8 18.0 1.0
N A:ALA351 4.8 17.4 1.0
CA A:ALA351 4.8 17.8 1.0
O A:GLY355 4.8 19.4 1.0
O A:HOH821 5.0 25.2 1.0

Chlorine binding site 2 out of 5 in 6pcd

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Chlorine binding site 2 out of 5 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 Chlorine with other atoms in the Cl 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
B:Cl503

b:21.4
occ:1.00
 O B:HOH827 3.1 17.4 1.0
OD1 B:ASN322 3.1 34.0 1.0
O B:HOH771 3.2 18.6 1.0
NH2 B:ARG364 3.4 20.0 1.0
CB B:SER361 3.8 15.4 0.5
CB B:SER361 3.8 20.4 0.5
CD2 B:LEU365 3.8 22.3 1.0
CB B:ALA351 3.9 18.5 1.0
CG B:ASN322 3.9 29.7 1.0
CB B:ASN322 4.0 18.6 1.0
CG B:LEU365 4.0 17.0 1.0
OG B:SER361 4.0 22.5 0.5
CA B:ASN322 4.2 17.2 1.0
O B:SER361 4.2 15.5 0.5
CD1 B:LEU365 4.3 20.4 1.0
O B:HOH701 4.3 51.2 1.0
CZ B:ARG364 4.4 16.9 1.0
O B:SER361 4.4 17.4 0.5
NE B:ARG364 4.5 16.7 1.0
OG B:SER361 4.5 15.1 0.5
CA B:SER361 4.6 17.3 0.5
CA B:SER361 4.6 14.9 0.5
CB B:ALA356 4.6 23.3 1.0
C B:SER361 4.7 14.6 0.5
CE B:MET385 4.7 19.3 1.0
C B:SER361 4.7 15.8 0.5
CA B:ALA351 4.7 16.7 1.0
N B:ALA351 4.7 16.3 1.0
N B:GLU323 4.8 16.9 1.0
O B:GLY355 4.9 18.6 1.0
O B:HOH802 5.0 21.6 1.0

Chlorine binding site 3 out of 5 in 6pcd

Go back to Chlorine Binding Sites List in 6pcd
Chlorine binding site 3 out of 5 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 Chlorine with other atoms in the Cl 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
B:Cl504

b:35.9
occ:1.00
 O3 C:GOL502 2.7 37.0 1.0
NE B:ARG65 3.2 21.0 1.0
O B:HOH640 3.2 30.2 1.0
N C:GLY146 3.2 17.4 1.0
C3 C:GOL502 3.4 34.6 1.0
CG1 C:ILE145 3.7 21.9 1.0
CD B:ARG65 3.8 19.2 1.0
CA C:GLY146 3.9 17.7 1.0
CD1 C:LEU358 4.0 21.7 1.0
CZ B:ARG65 4.1 21.4 1.0
C C:ILE145 4.2 17.0 1.0
NH2 B:ARG65 4.2 24.8 1.0
CA C:ILE145 4.2 16.0 1.0
CG B:ARG65 4.3 17.2 1.0
CD2 C:LEU89 4.5 17.5 1.0
CB C:ILE145 4.6 17.2 1.0
C2 C:GOL502 4.7 35.9 1.0
C C:GLY146 4.7 17.0 1.0
CD1 C:ILE145 4.7 25.3 1.0
O C:GLY146 4.7 18.9 1.0
NH2 C:ARG148 4.7 19.4 1.0
CD1 C:LEU89 4.8 17.6 1.0

Chlorine binding site 4 out of 5 in 6pcd

Go back to Chlorine Binding Sites List in 6pcd
Chlorine binding site 4 out of 5 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 Chlorine with other atoms in the Cl binding site number 4 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:Cl503

b:18.8
occ:1.00
 O C:HOH823 3.1 16.1 1.0
ND2 C:ASN322 3.1 29.4 1.0
O C:HOH782 3.1 16.9 1.0
NH2 C:ARG364 3.4 18.0 1.0
CD2 C:LEU365 3.7 22.0 1.0
CB C:SER361 3.8 19.2 0.5
CB C:SER361 3.8 13.1 0.5
CB C:ALA351 3.9 15.2 1.0
CB C:ASN322 4.0 18.1 1.0
CG C:LEU365 4.0 16.5 1.0
CG C:ASN322 4.0 26.8 1.0
OG C:SER361 4.1 21.9 0.5
CD1 C:LEU365 4.2 21.4 1.0
CA C:ASN322 4.2 14.2 1.0
O C:SER361 4.2 14.6 0.5
CZ C:ARG364 4.4 15.7 1.0
O C:SER361 4.4 16.1 0.5
NE C:ARG364 4.5 16.7 1.0
CA C:SER361 4.5 16.3 0.5
CE C:MET385 4.6 21.0 1.0
OG C:SER361 4.6 13.7 0.5
CA C:SER361 4.6 13.7 0.5
C C:SER361 4.7 13.5 0.5
C C:SER361 4.7 15.1 0.5
N C:GLU323 4.7 14.7 1.0
CA C:ALA351 4.7 13.6 1.0
N C:ALA351 4.7 15.0 1.0
O C:GLY355 4.8 16.2 1.0
CB C:ALA356 4.8 21.7 1.0
O C:HOH760 4.9 21.1 1.0

Chlorine binding site 5 out of 5 in 6pcd

Go back to Chlorine Binding Sites List in 6pcd
Chlorine binding site 5 out of 5 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 Chlorine with other atoms in the Cl binding site number 5 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
D:Cl504

b:19.9
occ:1.00
 O D:HOH823 3.1 16.4 1.0
O D:HOH808 3.2 17.7 1.0
ND2 D:ASN322 3.2 27.1 1.0
NH1 D:ARG364 3.4 19.6 1.0
CB D:SER361 3.8 14.7 0.5
CD2 D:LEU365 3.8 21.7 1.0
CB D:ALA351 3.8 15.3 1.0
CB D:SER361 3.9 20.4 0.5
CB D:ASN322 4.0 17.9 1.0
CG D:LEU365 4.0 16.7 1.0
OG D:SER361 4.0 23.0 0.5
CG D:ASN322 4.1 24.0 1.0
CA D:ASN322 4.2 15.2 1.0
O D:SER361 4.2 15.6 0.5
CD1 D:LEU365 4.3 19.6 1.0
CZ D:ARG364 4.3 17.0 1.0
O D:SER361 4.4 17.1 0.5
NE D:ARG364 4.5 16.7 1.0
OG D:SER361 4.5 14.8 0.5
CA D:SER361 4.6 14.6 0.5
CA D:SER361 4.6 17.6 0.5
CB D:ALA356 4.6 23.2 1.0
C D:SER361 4.7 14.9 0.5
CE D:MET385 4.7 20.1 1.0
CA D:ALA351 4.7 14.3 1.0
C D:SER361 4.7 16.8 0.5
N D:GLU323 4.7 16.0 1.0
N D:ALA351 4.8 15.0 1.0
O D:GLY355 4.8 16.2 1.0
O D:HOH798 4.9 21.8 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: Sat Dec 12 13:29:36 2020

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