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Chlorine in PDB 3vad: Crystal Structure of I170F Mutant Branched-Chain Alpha-Ketoacid Dehydrogenase Kinase in Complex with 3,6-Dichlorobenzo[B]Thiophene-2- Carboxylic Acid

Enzymatic activity of Crystal Structure of I170F Mutant Branched-Chain Alpha-Ketoacid Dehydrogenase Kinase in Complex with 3,6-Dichlorobenzo[B]Thiophene-2- Carboxylic Acid

All present enzymatic activity of Crystal Structure of I170F Mutant Branched-Chain Alpha-Ketoacid Dehydrogenase Kinase in Complex with 3,6-Dichlorobenzo[B]Thiophene-2- Carboxylic Acid:
2.7.11.4;

Protein crystallography data

The structure of Crystal Structure of I170F Mutant Branched-Chain Alpha-Ketoacid Dehydrogenase Kinase in Complex with 3,6-Dichlorobenzo[B]Thiophene-2- Carboxylic Acid, PDB code: 3vad was solved by K.Ahmed, W.J.Gui, S.C.Tso, J.L.Chuang, R.M.Wynn, D.T.Chuang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.50 / 2.60
Space group P 42 21 2
Cell size a, b, c (Å), α, β, γ (°) 128.079, 128.079, 74.035, 90.00, 90.00, 90.00
R / Rfree (%) 22.6 / 27.6

Other elements in 3vad:

The structure of Crystal Structure of I170F Mutant Branched-Chain Alpha-Ketoacid Dehydrogenase Kinase in Complex with 3,6-Dichlorobenzo[B]Thiophene-2- Carboxylic Acid also contains other interesting chemical elements:

Magnesium (Mg) 1 atom
Potassium (K) 1 atom

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of I170F Mutant Branched-Chain Alpha-Ketoacid Dehydrogenase Kinase in Complex with 3,6-Dichlorobenzo[B]Thiophene-2- Carboxylic Acid (pdb code 3vad). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 4 binding sites of Chlorine where determined in the Crystal Structure of I170F Mutant Branched-Chain Alpha-Ketoacid Dehydrogenase Kinase in Complex with 3,6-Dichlorobenzo[B]Thiophene-2- Carboxylic Acid, PDB code: 3vad:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in 3vad

Go back to Chlorine Binding Sites List in 3vad
Chlorine binding site 1 out of 4 in the Crystal Structure of I170F Mutant Branched-Chain Alpha-Ketoacid Dehydrogenase Kinase in Complex with 3,6-Dichlorobenzo[B]Thiophene-2- Carboxylic Acid


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 I170F Mutant Branched-Chain Alpha-Ketoacid Dehydrogenase Kinase in Complex with 3,6-Dichlorobenzo[B]Thiophene-2- Carboxylic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl404

b:57.7
occ:0.42
 CL1 A:0F1404 0.0 57.7 0.4
C2 A:0F1404 1.8 62.5 0.4
CZ A:PHE170 2.7 66.1 0.5
C3 A:0F1404 2.8 61.8 0.4
C1 A:0F1404 2.8 61.2 0.4
CD1 A:LEU68 3.0 66.8 1.0
CE1 A:PHE170 3.1 69.3 0.5
CG2 A:VAL125 3.6 64.3 1.0
CE2 A:PHE170 3.7 65.4 0.5
CG1 A:VAL125 3.8 74.0 1.0
CD1 A:LEU128 3.8 48.7 1.0
CB A:VAL125 4.0 61.3 1.0
C4 A:0F1404 4.0 66.4 0.4
CA A:VAL125 4.1 60.8 1.0
C6 A:0F1404 4.1 65.5 0.4
CB A:ALA174 4.1 49.5 1.0
CG A:LEU68 4.4 63.5 1.0
CD1 A:PHE170 4.4 69.6 0.5
CD2 A:LEU106 4.5 71.0 1.0
C5 A:0F1404 4.6 70.2 0.4
CB A:LEU128 4.6 56.1 1.0
O A:VAL125 4.7 63.3 1.0
CG A:LEU128 4.8 47.0 1.0
CD2 A:PHE170 4.8 63.9 0.5
CD2 A:LEU68 4.8 60.4 1.0
CB A:LEU68 4.9 64.2 1.0
C A:VAL125 4.9 62.4 1.0
CD1 A:LEU106 5.0 72.7 1.0

Chlorine binding site 2 out of 4 in 3vad

Go back to Chlorine Binding Sites List in 3vad
Chlorine binding site 2 out of 4 in the Crystal Structure of I170F Mutant Branched-Chain Alpha-Ketoacid Dehydrogenase Kinase in Complex with 3,6-Dichlorobenzo[B]Thiophene-2- Carboxylic Acid


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 I170F Mutant Branched-Chain Alpha-Ketoacid Dehydrogenase Kinase in Complex with 3,6-Dichlorobenzo[B]Thiophene-2- Carboxylic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl404

b:69.0
occ:0.42
 CL2 A:0F1404 0.0 69.0 0.4
C7 A:0F1405 1.1 0.3 0.5
C8 A:0F1405 1.3 0.3 0.5
C8 A:0F1404 1.8 70.4 0.4
S A:0F1405 1.9 0.6 0.5
C5 A:0F1405 2.0 0.0 0.5
C4 A:0F1405 2.2 0.2 0.5
C9 A:0F1405 2.3 0.3 0.5
CL2 A:0F1405 2.8 0.3 0.5
O1 A:0F1405 2.9 0.2 0.5
C5 A:0F1404 2.9 70.2 0.4
C7 A:0F1404 3.0 65.0 0.4
O2 A:0F1404 3.0 65.0 0.4
O2 A:0F1405 3.2 0.2 0.5
C6 A:0F1405 3.2 1.0 0.5
CE2 A:TYR99 3.4 69.1 1.0
C9 A:0F1404 3.4 59.0 0.4
ND1 A:HIS132 3.4 79.2 1.0
C6 A:0F1404 3.4 65.5 0.4
C3 A:0F1405 3.5 0.2 0.5
CZ A:TYR99 3.6 78.2 1.0
CE1 A:HIS132 3.7 77.3 1.0
CD2 A:PHE170 3.7 68.0 0.5
OH A:TYR99 3.7 74.2 1.0
CD2 A:TYR99 4.1 63.7 1.0
CE2 A:PHE170 4.1 66.5 0.5
C4 A:0F1404 4.2 66.4 0.4
C1 A:0F1405 4.2 0.1 0.5
C2 A:0F1405 4.3 0.2 0.5
CG A:HIS132 4.3 75.4 1.0
S A:0F1404 4.4 64.4 0.4
CG1 A:ILE72 4.4 74.5 1.0
CE1 A:TYR99 4.4 66.0 1.0
CD2 A:PHE170 4.5 63.9 0.5
CG A:PHE170 4.6 65.3 0.5
NE2 A:HIS132 4.6 71.9 1.0
CE2 A:PHE170 4.6 65.4 0.5
O1 A:0F1404 4.7 55.3 0.4
CG A:PHE170 4.7 68.2 0.5
CG A:TYR99 4.8 62.0 1.0
CD1 A:PHE170 4.8 69.6 0.5
C1 A:0F1404 4.8 61.2 0.4
CZ A:PHE170 4.9 66.1 0.5
CD1 A:TYR99 4.9 65.5 1.0
CD1 A:ILE72 5.0 83.8 1.0
CB A:HIS132 5.0 64.7 1.0
CE1 A:PHE170 5.0 69.3 0.5
CD2 A:HIS132 5.0 75.9 1.0

Chlorine binding site 3 out of 4 in 3vad

Go back to Chlorine Binding Sites List in 3vad
Chlorine binding site 3 out of 4 in the Crystal Structure of I170F Mutant Branched-Chain Alpha-Ketoacid Dehydrogenase Kinase in Complex with 3,6-Dichlorobenzo[B]Thiophene-2- Carboxylic Acid


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 I170F Mutant Branched-Chain Alpha-Ketoacid Dehydrogenase Kinase in Complex with 3,6-Dichlorobenzo[B]Thiophene-2- Carboxylic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl405

b:0.2
occ:0.52
 CL1 A:0F1405 0.0 0.2 0.5
CZ A:PHE170 1.5 73.8 0.5
C2 A:0F1405 1.8 0.2 0.5
CE2 A:PHE170 2.2 66.5 0.5
CE1 A:PHE170 2.5 69.6 0.5
C3 A:0F1405 2.7 0.2 0.5
C1 A:0F1405 2.8 0.1 0.5
O A:ARG71 2.9 78.8 1.0
CB A:SER166 3.2 59.7 1.0
C A:ARG71 3.4 79.2 1.0
CD A:ARG75 3.4 57.5 1.0
CD2 A:PHE170 3.5 68.0 0.5
CB A:ARG71 3.5 85.5 1.0
CD1 A:PHE170 3.7 67.4 0.5
OG A:SER166 3.8 76.3 1.0
CA A:ARG71 3.9 81.0 1.0
CG A:ARG75 4.0 69.1 1.0
C4 A:0F1405 4.0 0.2 0.5
N A:ILE72 4.0 68.4 1.0
CG A:PHE170 4.1 68.2 0.5
C6 A:0F1405 4.1 1.0 0.5
CB A:ARG75 4.3 62.3 1.0
CA A:SER166 4.3 60.0 1.0
C A:SER166 4.3 60.7 1.0
O A:SER166 4.3 62.5 1.0
CA A:ILE72 4.5 70.0 1.0
NE A:ARG75 4.6 60.0 1.0
C5 A:0F1405 4.6 0.0 0.5
CG A:ARG71 4.7 94.8 1.0
N A:ARG167 4.9 44.5 1.0
N A:ARG75 4.9 56.5 1.0

Chlorine binding site 4 out of 4 in 3vad

Go back to Chlorine Binding Sites List in 3vad
Chlorine binding site 4 out of 4 in the Crystal Structure of I170F Mutant Branched-Chain Alpha-Ketoacid Dehydrogenase Kinase in Complex with 3,6-Dichlorobenzo[B]Thiophene-2- Carboxylic Acid


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 I170F Mutant Branched-Chain Alpha-Ketoacid Dehydrogenase Kinase in Complex with 3,6-Dichlorobenzo[B]Thiophene-2- Carboxylic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl405

b:0.3
occ:0.52
 CL2 A:0F1405 0.0 0.3 0.5
O2 A:0F1404 0.6 65.0 0.4
C9 A:0F1404 1.8 59.0 0.4
C8 A:0F1405 1.8 0.3 0.5
O1 A:0F1404 2.7 55.3 0.4
C7 A:0F1404 2.8 65.0 0.4
CL2 A:0F1404 2.8 69.0 0.4
OH A:TYR99 2.9 74.2 1.0
C7 A:0F1405 3.0 0.3 0.5
C5 A:0F1405 3.0 0.0 0.5
C8 A:0F1404 3.1 70.4 0.4
O2 A:0F1405 3.2 0.2 0.5
ND1 A:HIS132 3.2 79.2 1.0
C9 A:0F1405 3.3 0.3 0.5
NE A:ARG167 3.4 60.5 1.0
CG A:ARG167 3.4 43.4 1.0
CD A:ARG167 3.6 49.6 1.0
C6 A:0F1405 3.6 1.0 0.5
CZ A:TYR99 3.6 78.2 1.0
CB A:HIS132 3.7 64.7 1.0
CG A:HIS132 3.9 75.4 1.0
CB A:ARG167 4.1 47.5 1.0
CE1 A:TYR99 4.1 66.0 1.0
C4 A:0F1405 4.2 0.2 0.5
CE1 A:HIS132 4.3 77.3 1.0
CG1 A:VAL135 4.3 60.6 1.0
O1 A:0F1405 4.3 0.2 0.5
CE2 A:TYR99 4.4 69.1 1.0
S A:0F1404 4.4 64.4 0.4
S A:0F1405 4.4 0.6 0.5
CZ A:ARG167 4.4 53.8 1.0
O A:HIS132 4.5 65.0 1.0
CB A:VAL135 4.5 58.9 1.0
CG2 A:VAL135 4.5 60.8 1.0
C5 A:0F1404 4.6 70.2 0.4
NH2 A:ARG167 4.8 55.5 1.0
CA A:ARG167 4.9 47.8 1.0
CD2 A:PHE170 4.9 68.0 0.5
CA A:HIS132 5.0 67.8 1.0
C1 A:0F1405 5.0 0.1 0.5

Reference:

K.Ahmed, W.J.Gui, S.C.Tso, J.L.Chuang, R.M Wynn, D.T.Chuang. Crystal Structure of I170F Mutant Branched-Chain Alpha-Ketoacid Dehydrogenase Kinase in Complex with 3,6-Dichlorobenzo[B]Thiophene-2-Carboxylic Acid To Be Published.
Page generated: Sun Jul 21 06:46:48 2024

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