Chlorine in PDB 6pcb: Crystal Structure of Beta-Ketoadipyl-Coa Thiolase Mutant (H356A) in Complex with Coa

Enzymatic activity of Crystal Structure of Beta-Ketoadipyl-Coa Thiolase Mutant (H356A) in Complex with Coa

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

Protein crystallography data

The structure of Crystal Structure of Beta-Ketoadipyl-Coa Thiolase Mutant (H356A) in Complex with Coa, PDB code: 6pcb 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) 20.00 / 1.61
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 110.487, 115.958, 128.866, 90.00, 90.00, 90.00
R / Rfree (%) 16.1 / 19.6

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of Beta-Ketoadipyl-Coa Thiolase Mutant (H356A) in Complex with Coa (pdb code 6pcb). 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 (H356A) in Complex with Coa, PDB code: 6pcb:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5;

Chlorine binding site 1 out of 5 in 6pcb

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Chlorine binding site 1 out of 5 in the Crystal Structure of Beta-Ketoadipyl-Coa Thiolase Mutant (H356A) in Complex with Coa


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 (H356A) in Complex with Coa within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1003

b:35.0
occ:1.00
 ND2 A:ASN322 2.8 29.2 1.0
O A:HOH1228 2.9 21.0 1.0
O A:HOH1239 3.2 22.6 1.0
NH1 A:ARG364 3.3 23.6 1.0
CD2 A:LEU365 3.6 24.8 1.0
CG A:LEU365 3.8 23.7 1.0
CB A:ALA351 3.8 17.7 1.0
CB A:SER361 3.9 21.3 1.0
CG A:ASN322 3.9 30.6 1.0
CD1 A:LEU365 4.1 24.7 1.0
OG A:SER361 4.1 26.3 1.0
CA A:ASN322 4.1 20.5 1.0
CB A:ASN322 4.1 23.8 1.0
CZ A:ARG364 4.3 21.3 1.0
O A:SER361 4.4 18.8 1.0
NE A:ARG364 4.5 21.1 1.0
N A:GLU323 4.6 18.8 1.0
CA A:SER361 4.6 18.9 1.0
N A:ALA351 4.7 18.4 1.0
CA A:ALA351 4.7 20.4 1.0
CE A:MET385 4.7 22.1 1.0
C A:SER361 4.7 19.3 1.0
O A:HOH1283 4.9 26.7 1.0
C A:ASN322 4.9 19.9 1.0
O A:GLY355 5.0 21.2 1.0

Chlorine binding site 2 out of 5 in 6pcb

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Chlorine binding site 2 out of 5 in the Crystal Structure of Beta-Ketoadipyl-Coa Thiolase Mutant (H356A) in Complex with Coa


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 (H356A) in Complex with Coa within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl503

b:36.7
occ:1.00
 O C:HOH882 3.0 29.2 1.0
O B:HOH745 3.0 20.9 1.0
NE B:ARG65 3.1 16.7 0.5
N C:GLY146 3.2 18.9 1.0
CD B:ARG65 3.2 30.4 0.5
CD B:ARG65 3.4 16.4 0.5
NH1 C:ARG148 3.6 27.4 1.0
CD1 C:LEU358 3.7 20.7 1.0
CG B:ARG65 3.7 16.7 0.5
NH2 B:ARG65 3.8 32.0 0.5
CA C:ILE145 3.8 17.2 1.0
C C:ILE145 4.0 18.4 1.0
CG B:ARG65 4.0 27.7 0.5
CG1 C:ILE145 4.0 20.6 1.0
NE B:ARG65 4.1 28.2 0.5
CA C:GLY146 4.1 19.6 1.0
CZ B:ARG65 4.3 17.9 0.5
CZ B:ARG65 4.3 27.4 0.5
O C:GLY146 4.4 19.9 1.0
CB C:ILE145 4.6 17.9 1.0
NH1 B:ARG65 4.6 18.7 0.5
CZ C:ARG148 4.6 22.9 1.0
C C:GLY146 4.7 20.3 1.0
CD2 C:LEU89 4.7 20.0 1.0
NH2 C:ARG148 4.8 23.8 1.0
N C:ILE145 4.9 16.9 1.0

Chlorine binding site 3 out of 5 in 6pcb

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Chlorine binding site 3 out of 5 in the Crystal Structure of Beta-Ketoadipyl-Coa Thiolase Mutant (H356A) in Complex with Coa


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 (H356A) in Complex with Coa within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl503

b:39.6
occ:1.00
 O C:ALA356 2.7 18.6 1.0
O C:GLY254 2.8 19.1 1.0
N4P C:COA501 2.9 28.3 1.0
C6P C:COA501 3.5 28.8 1.0
CE C:MET120 3.5 16.7 1.0
SD C:MET120 3.6 16.6 1.0
C5P C:COA501 3.7 30.2 1.0
CD2 C:LEU358 3.7 21.8 1.0
C3P C:COA501 3.8 27.9 1.0
C C:ALA356 3.8 17.0 1.0
C C:GLY254 3.9 19.7 1.0
C2P C:COA501 3.9 28.2 1.0
CA C:VAL255 3.9 18.0 1.0
CB C:ALA356 3.9 19.0 1.0
CD1 C:ILE145 4.1 24.1 1.0
N C:VAL255 4.3 16.9 1.0
CA C:ALA356 4.4 18.1 1.0
CG C:LEU358 4.4 19.8 1.0
CG2 C:VAL255 4.5 24.9 1.0
N C:ASN256 4.7 14.7 1.0
OG C:SER253 4.7 14.1 0.5
N C:ALA356 4.8 16.5 1.0
C C:VAL255 4.8 17.0 1.0
CB C:VAL255 4.8 21.4 1.0
N C:LEU358 4.8 16.5 1.0
N C:PRO357 4.8 15.6 1.0
C7P C:COA501 4.9 28.0 1.0
O5P C:COA501 4.9 29.6 1.0
OG C:SER253 5.0 27.7 0.5
OD1 C:ASN256 5.0 17.7 1.0

Chlorine binding site 4 out of 5 in 6pcb

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Chlorine binding site 4 out of 5 in the Crystal Structure of Beta-Ketoadipyl-Coa Thiolase Mutant (H356A) in Complex with Coa


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 (H356A) in Complex with Coa within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl503

b:36.1
occ:1.00
 O D:HOH681 3.1 37.0 1.0
N D:MET163 3.2 21.2 1.0
O D:HOH863 3.4 30.6 1.0
CG D:MET163 3.5 33.8 1.0
CB D:MET163 3.8 26.3 1.0
CA D:GLY146 3.8 19.7 1.0
CD D:PRO164 3.9 20.7 1.0
CB D:SER162 4.0 21.4 1.0
CA D:SER162 4.1 19.6 1.0
CA D:MET163 4.1 23.0 1.0
CG1 D:ILE145 4.1 22.2 1.0
C D:SER162 4.2 19.7 1.0
N D:GLY146 4.3 19.5 1.0
CG2 D:ILE145 4.6 21.7 1.0
C D:ILE145 4.6 19.2 1.0
O D:ILE145 4.6 21.0 1.0
CD1 D:ILE145 4.7 26.2 1.0
O C:HOH830 4.7 36.0 1.0
CB D:ILE145 4.9 20.3 1.0
N D:PRO164 4.9 21.0 1.0
OG D:SER162 5.0 22.3 1.0
CE D:MET163 5.0 42.9 1.0

Chlorine binding site 5 out of 5 in 6pcb

Go back to Chlorine Binding Sites List in 6pcb
Chlorine binding site 5 out of 5 in the Crystal Structure of Beta-Ketoadipyl-Coa Thiolase Mutant (H356A) in Complex with Coa


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 (H356A) in Complex with Coa within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl504

b:36.5
occ:1.00
 O D:HOH858 3.0 22.4 1.0
N A:GLY146 3.1 21.4 1.0
NE D:ARG65 3.2 20.6 0.5
O A:HOH1343 3.3 27.7 1.0
NE D:ARG65 3.4 16.0 0.5
O A:HOH1262 3.4 43.5 1.0
CD D:ARG65 3.4 17.0 0.5
NH1 A:ARG148 3.6 27.2 1.0
CG D:ARG65 3.7 16.6 0.5
CD1 A:LEU358 3.9 24.1 1.0
CA A:ILE145 3.9 20.1 1.0
CG1 A:ILE145 4.0 23.0 1.0
CD D:ARG65 4.0 16.2 0.5
C A:ILE145 4.0 21.7 1.0
CA A:GLY146 4.1 20.0 1.0
CG D:ARG65 4.1 15.6 0.5
CZ D:ARG65 4.2 16.5 0.5
NH2 D:ARG65 4.3 16.6 0.5
O A:GLY146 4.3 21.9 1.0
CZ D:ARG65 4.4 21.1 0.5
CB A:ILE145 4.6 20.3 1.0
C A:GLY146 4.6 20.8 1.0
CD2 A:LEU89 4.7 21.2 1.0
NH2 D:ARG65 4.7 23.8 0.5
CZ A:ARG148 4.8 23.9 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 13:29:34 2020

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