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Chlorine in PDB 2ii3: Crystal Structure of A Cubic Core of the Dihydrolipoamide Acyltransferase (E2B) Component in the Branched-Chain Alpha-Ketoacid Dehydrogenase Complex (Bckdc), Oxidized Coenzyme A-Bound Form

Enzymatic activity of Crystal Structure of A Cubic Core of the Dihydrolipoamide Acyltransferase (E2B) Component in the Branched-Chain Alpha-Ketoacid Dehydrogenase Complex (Bckdc), Oxidized Coenzyme A-Bound Form

All present enzymatic activity of Crystal Structure of A Cubic Core of the Dihydrolipoamide Acyltransferase (E2B) Component in the Branched-Chain Alpha-Ketoacid Dehydrogenase Complex (Bckdc), Oxidized Coenzyme A-Bound Form:
2.3.1.168;

Protein crystallography data

The structure of Crystal Structure of A Cubic Core of the Dihydrolipoamide Acyltransferase (E2B) Component in the Branched-Chain Alpha-Ketoacid Dehydrogenase Complex (Bckdc), Oxidized Coenzyme A-Bound Form, PDB code: 2ii3 was solved by M.Kato, R.M.Wynn, J.L.Chuang, C.A.Brautigam, M.Custorio, D.T.Chuang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 2.17
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 194.915, 194.915, 171.997, 90.00, 90.00, 120.00
R / Rfree (%) 20.2 / 25.9

Chlorine Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Chlorine atom in the Crystal Structure of A Cubic Core of the Dihydrolipoamide Acyltransferase (E2B) Component in the Branched-Chain Alpha-Ketoacid Dehydrogenase Complex (Bckdc), Oxidized Coenzyme A-Bound Form (pdb code 2ii3). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 12 binding sites of Chlorine where determined in the Crystal Structure of A Cubic Core of the Dihydrolipoamide Acyltransferase (E2B) Component in the Branched-Chain Alpha-Ketoacid Dehydrogenase Complex (Bckdc), Oxidized Coenzyme A-Bound Form, PDB code: 2ii3:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Chlorine binding site 1 out of 12 in 2ii3

Go back to Chlorine Binding Sites List in 2ii3
Chlorine binding site 1 out of 12 in the Crystal Structure of A Cubic Core of the Dihydrolipoamide Acyltransferase (E2B) Component in the Branched-Chain Alpha-Ketoacid Dehydrogenase Complex (Bckdc), Oxidized Coenzyme A-Bound Form


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 A Cubic Core of the Dihydrolipoamide Acyltransferase (E2B) Component in the Branched-Chain Alpha-Ketoacid Dehydrogenase Complex (Bckdc), Oxidized Coenzyme A-Bound Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl802

b:67.9
occ:1.00
 O B:HOH853 2.5 37.3 1.0
NZ A:LYS349 3.1 52.3 1.0
O A:HOH892 3.2 52.5 1.0
N B:HIS214 4.1 36.4 1.0
O A:HOH822 4.1 34.1 1.0
CE1 A:HIS214 4.2 28.2 1.0
CA B:PRO213 4.2 35.0 1.0
CD2 A:LEU210 4.3 31.6 1.0
ND1 A:HIS214 4.3 29.4 1.0
O B:HIS214 4.4 40.3 1.0
O A:ALA209 4.5 30.5 1.0
C B:PRO213 4.5 35.9 1.0
NE2 A:HIS214 4.6 29.7 1.0
CE A:LYS349 4.6 47.1 1.0
O B:HOH873 4.7 42.5 1.0
CB B:PRO213 4.7 34.5 1.0
CG A:HIS214 4.8 32.4 1.0
CA A:LEU210 4.8 33.2 1.0
CG1 A:VAL351 4.8 32.9 1.0
C A:ALA209 4.9 31.4 1.0
CD2 A:HIS214 4.9 29.9 1.0
CG2 A:VAL351 4.9 33.1 1.0

Chlorine binding site 2 out of 12 in 2ii3

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Chlorine binding site 2 out of 12 in the Crystal Structure of A Cubic Core of the Dihydrolipoamide Acyltransferase (E2B) Component in the Branched-Chain Alpha-Ketoacid Dehydrogenase Complex (Bckdc), Oxidized Coenzyme A-Bound Form


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 A Cubic Core of the Dihydrolipoamide Acyltransferase (E2B) Component in the Branched-Chain Alpha-Ketoacid Dehydrogenase Complex (Bckdc), Oxidized Coenzyme A-Bound Form within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl801

b:63.5
occ:1.00
 O C:HOH847 2.6 41.3 1.0
NZ B:LYS349 3.3 59.1 1.0
O B:HOH873 3.6 42.5 1.0
N C:HIS214 4.0 34.2 1.0
CE1 B:HIS214 4.1 30.6 1.0
O C:HIS214 4.1 36.7 1.0
ND1 B:HIS214 4.2 34.6 1.0
CA C:PRO213 4.3 34.8 1.0
CE B:LYS349 4.4 54.7 1.0
NE2 B:HIS214 4.4 34.1 1.0
C C:PRO213 4.5 34.3 1.0
CG2 B:VAL351 4.6 31.0 1.0
CG1 B:VAL351 4.6 31.5 1.0
O B:HOH853 4.6 37.3 1.0
O B:ALA209 4.6 32.5 1.0
CG B:HIS214 4.7 34.3 1.0
CD2 B:LEU210 4.7 33.1 1.0
CB C:PRO213 4.7 35.5 1.0
CD2 B:HIS214 4.8 34.8 1.0
C C:HIS214 4.9 35.9 1.0
C B:ALA209 5.0 32.2 1.0
O C:HOH867 5.0 47.4 1.0

Chlorine binding site 3 out of 12 in 2ii3

Go back to Chlorine Binding Sites List in 2ii3
Chlorine binding site 3 out of 12 in the Crystal Structure of A Cubic Core of the Dihydrolipoamide Acyltransferase (E2B) Component in the Branched-Chain Alpha-Ketoacid Dehydrogenase Complex (Bckdc), Oxidized Coenzyme A-Bound Form


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 A Cubic Core of the Dihydrolipoamide Acyltransferase (E2B) Component in the Branched-Chain Alpha-Ketoacid Dehydrogenase Complex (Bckdc), Oxidized Coenzyme A-Bound Form within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl803

b:62.0
occ:1.00
 O A:HOH822 2.8 34.1 1.0
NZ C:LYS349 2.9 52.1 1.0
O C:HOH867 3.5 47.4 1.0
N A:HIS214 4.1 35.5 1.0
CA A:PRO213 4.2 35.6 1.0
CE1 C:HIS214 4.2 31.4 1.0
O A:HIS214 4.2 40.0 1.0
ND1 C:HIS214 4.3 30.6 1.0
CD2 C:LEU210 4.3 27.6 1.0
CE C:LYS349 4.3 48.6 1.0
C A:PRO213 4.5 36.6 1.0
O C:HOH847 4.5 41.3 1.0
CB A:PRO213 4.6 35.9 1.0
O C:ALA209 4.6 31.9 1.0
NE2 C:HIS214 4.7 29.9 1.0
O A:HOH892 4.7 52.5 1.0
CG1 C:VAL351 4.9 31.9 1.0
CG C:HIS214 4.9 30.7 1.0
CA C:LEU210 4.9 31.4 1.0
CG2 C:VAL351 4.9 30.6 1.0

Chlorine binding site 4 out of 12 in 2ii3

Go back to Chlorine Binding Sites List in 2ii3
Chlorine binding site 4 out of 12 in the Crystal Structure of A Cubic Core of the Dihydrolipoamide Acyltransferase (E2B) Component in the Branched-Chain Alpha-Ketoacid Dehydrogenase Complex (Bckdc), Oxidized Coenzyme A-Bound Form


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 A Cubic Core of the Dihydrolipoamide Acyltransferase (E2B) Component in the Branched-Chain Alpha-Ketoacid Dehydrogenase Complex (Bckdc), Oxidized Coenzyme A-Bound Form within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl807

b:62.2
occ:1.00
 O B:HOH912 2.8 54.0 1.0
NH2 C:ARG370 3.4 40.3 1.0
NH2 B:ARG370 3.7 34.0 1.0
NH2 A:ARG370 3.7 40.2 1.0
NH1 C:ARG370 3.9 40.4 1.0
NH1 B:ARG370 4.0 34.9 1.0
CZ C:ARG370 4.1 40.5 1.0
NH1 A:ARG370 4.2 37.3 1.0
CZ B:ARG370 4.3 36.5 1.0
CZ A:ARG370 4.4 39.2 1.0
CD1 B:LEU368 4.6 29.4 1.0
O C:HOH821 4.8 28.9 1.0
CD1 C:LEU368 4.9 33.8 1.0
O B:HOH840 5.0 33.1 1.0

Chlorine binding site 5 out of 12 in 2ii3

Go back to Chlorine Binding Sites List in 2ii3
Chlorine binding site 5 out of 12 in the Crystal Structure of A Cubic Core of the Dihydrolipoamide Acyltransferase (E2B) Component in the Branched-Chain Alpha-Ketoacid Dehydrogenase Complex (Bckdc), Oxidized Coenzyme A-Bound Form


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 A Cubic Core of the Dihydrolipoamide Acyltransferase (E2B) Component in the Branched-Chain Alpha-Ketoacid Dehydrogenase Complex (Bckdc), Oxidized Coenzyme A-Bound Form within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl805

b:59.9
occ:1.00
 O E:HOH837 2.9 33.2 1.0
NZ D:LYS349 3.0 52.7 1.0
O D:HOH860 3.3 40.6 1.0
CE1 D:HIS214 4.0 35.2 1.0
N E:HIS214 4.1 35.8 1.0
CA E:PRO213 4.1 36.2 1.0
ND1 D:HIS214 4.2 33.5 1.0
CD2 D:LEU210 4.2 29.0 1.0
O D:ALA209 4.3 31.4 1.0
O E:HIS214 4.4 36.4 1.0
CE D:LYS349 4.5 51.5 1.0
CB E:PRO213 4.5 36.3 1.0
NE2 D:HIS214 4.5 33.2 1.0
C E:PRO213 4.5 36.0 1.0
O D:HOH849 4.6 38.7 1.0
C D:ALA209 4.7 32.4 1.0
CA D:LEU210 4.7 33.7 1.0
CG D:HIS214 4.7 34.8 1.0
CG1 D:VAL351 4.8 36.0 1.0
N D:LEU210 4.8 32.4 1.0
CG2 D:VAL351 4.9 30.3 1.0
O E:HOH886 4.9 46.5 1.0
CD2 D:HIS214 4.9 32.8 1.0

Chlorine binding site 6 out of 12 in 2ii3

Go back to Chlorine Binding Sites List in 2ii3
Chlorine binding site 6 out of 12 in the Crystal Structure of A Cubic Core of the Dihydrolipoamide Acyltransferase (E2B) Component in the Branched-Chain Alpha-Ketoacid Dehydrogenase Complex (Bckdc), Oxidized Coenzyme A-Bound Form


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Crystal Structure of A Cubic Core of the Dihydrolipoamide Acyltransferase (E2B) Component in the Branched-Chain Alpha-Ketoacid Dehydrogenase Complex (Bckdc), Oxidized Coenzyme A-Bound Form within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Cl806

b:68.5
occ:1.00
 O F:HOH864 3.0 41.4 1.0
NZ E:LYS349 3.0 52.1 1.0
O E:HOH886 3.3 46.5 1.0
CE1 E:HIS214 4.1 34.4 1.0
ND1 E:HIS214 4.2 34.8 1.0
CA F:PRO213 4.2 35.7 1.0
N F:HIS214 4.2 35.0 1.0
O E:ALA209 4.3 32.3 1.0
CD2 E:LEU210 4.3 28.4 1.0
O F:HIS214 4.4 36.3 1.0
CE E:LYS349 4.4 49.7 1.0
O E:HOH837 4.4 33.2 1.0
NE2 E:HIS214 4.6 33.1 1.0
C F:PRO213 4.6 36.1 1.0
CB F:PRO213 4.6 36.7 1.0
CG1 E:VAL351 4.6 32.9 1.0
CA E:LEU210 4.8 31.6 1.0
CG E:HIS214 4.8 33.5 1.0
C E:ALA209 4.8 31.7 1.0
CG2 E:VAL351 4.8 32.7 1.0
O F:HOH847 4.9 38.7 1.0
CD2 E:HIS214 5.0 30.8 1.0

Chlorine binding site 7 out of 12 in 2ii3

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Chlorine binding site 7 out of 12 in the Crystal Structure of A Cubic Core of the Dihydrolipoamide Acyltransferase (E2B) Component in the Branched-Chain Alpha-Ketoacid Dehydrogenase Complex (Bckdc), Oxidized Coenzyme A-Bound Form


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of Crystal Structure of A Cubic Core of the Dihydrolipoamide Acyltransferase (E2B) Component in the Branched-Chain Alpha-Ketoacid Dehydrogenase Complex (Bckdc), Oxidized Coenzyme A-Bound Form within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Cl804

b:63.3
occ:1.00
 O D:HOH849 3.0 38.7 1.0
O F:HOH847 3.3 38.7 1.0
NZ F:LYS349 3.3 52.9 1.0
CE1 F:HIS214 4.0 32.8 1.0
ND1 F:HIS214 4.1 35.0 1.0
O F:ALA209 4.2 29.9 1.0
O F:HOH864 4.2 41.4 1.0
N D:HIS214 4.3 36.6 1.0
CA D:PRO213 4.3 37.2 1.0
CD2 F:LEU210 4.4 32.2 1.0
NE2 F:HIS214 4.5 32.5 1.0
C F:ALA209 4.5 31.2 1.0
O D:HIS214 4.5 38.5 1.0
CA F:LEU210 4.5 32.1 1.0
N F:LEU210 4.6 31.4 1.0
C D:PRO213 4.7 36.4 1.0
CE F:LYS349 4.7 49.0 1.0
CG F:HIS214 4.7 32.3 1.0
CG1 F:VAL351 4.7 32.8 1.0
CB D:PRO213 4.8 38.2 1.0
O D:HOH860 4.9 40.6 1.0
CD2 F:HIS214 4.9 28.7 1.0

Chlorine binding site 8 out of 12 in 2ii3

Go back to Chlorine Binding Sites List in 2ii3
Chlorine binding site 8 out of 12 in the Crystal Structure of A Cubic Core of the Dihydrolipoamide Acyltransferase (E2B) Component in the Branched-Chain Alpha-Ketoacid Dehydrogenase Complex (Bckdc), Oxidized Coenzyme A-Bound Form


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 8 of Crystal Structure of A Cubic Core of the Dihydrolipoamide Acyltransferase (E2B) Component in the Branched-Chain Alpha-Ketoacid Dehydrogenase Complex (Bckdc), Oxidized Coenzyme A-Bound Form within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Cl808

b:66.5
occ:1.00
 O E:HOH906 2.9 59.4 1.0
NH2 F:ARG370 3.4 40.5 1.0
NH2 D:ARG370 3.6 41.5 1.0
NH2 E:ARG370 3.7 41.0 1.0
NH1 D:ARG370 3.9 42.0 1.0
NH1 F:ARG370 4.0 36.6 1.0
NH1 E:ARG370 4.1 33.9 1.0
CZ F:ARG370 4.1 39.1 1.0
CZ D:ARG370 4.2 41.0 1.0
CZ E:ARG370 4.3 38.7 1.0
CD1 E:LEU368 4.6 33.6 1.0
O E:HOH879 4.7 45.1 1.0
CD1 F:LEU368 4.8 33.2 1.0
CD1 D:LEU368 5.0 30.8 1.0

Chlorine binding site 9 out of 12 in 2ii3

Go back to Chlorine Binding Sites List in 2ii3
Chlorine binding site 9 out of 12 in the Crystal Structure of A Cubic Core of the Dihydrolipoamide Acyltransferase (E2B) Component in the Branched-Chain Alpha-Ketoacid Dehydrogenase Complex (Bckdc), Oxidized Coenzyme A-Bound Form


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 9 of Crystal Structure of A Cubic Core of the Dihydrolipoamide Acyltransferase (E2B) Component in the Branched-Chain Alpha-Ketoacid Dehydrogenase Complex (Bckdc), Oxidized Coenzyme A-Bound Form within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Cl810

b:66.1
occ:0.33
 NH2 G:ARG370 3.6 44.2 1.0
NH1 G:ARG370 3.8 41.1 1.0
CZ G:ARG370 4.1 41.8 1.0
CD1 G:LEU368 4.9 37.8 1.0

Chlorine binding site 10 out of 12 in 2ii3

Go back to Chlorine Binding Sites List in 2ii3
Chlorine binding site 10 out of 12 in the Crystal Structure of A Cubic Core of the Dihydrolipoamide Acyltransferase (E2B) Component in the Branched-Chain Alpha-Ketoacid Dehydrogenase Complex (Bckdc), Oxidized Coenzyme A-Bound Form


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 10 of Crystal Structure of A Cubic Core of the Dihydrolipoamide Acyltransferase (E2B) Component in the Branched-Chain Alpha-Ketoacid Dehydrogenase Complex (Bckdc), Oxidized Coenzyme A-Bound Form within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Cl811

b:69.1
occ:1.00
 NZ G:LYS349 3.4 51.6 1.0
O G:HOH876 3.6 54.4 1.0
CE1 G:HIS214 4.1 28.4 1.0
CD2 G:LEU210 4.1 30.3 1.0
ND1 G:HIS214 4.1 30.3 1.0
O G:ALA209 4.4 32.8 1.0
O G:HOH834 4.4 40.9 1.0
NE2 G:HIS214 4.6 31.2 1.0
CA G:LEU210 4.7 32.6 1.0
C G:ALA209 4.7 32.5 1.0
CG G:HIS214 4.8 33.4 1.0
N G:LEU210 4.8 32.1 1.0
CG1 G:VAL351 4.9 33.9 1.0
CE G:LYS349 4.9 48.1 1.0
CG2 G:VAL351 5.0 35.3 1.0

Reference:

M.Kato, R.M.Wynn, J.L.Chuang, C.A.Brautigam, M.Custorio, D.T.Chuang. A Synchronized Substrate-Gating Mechanism Revealed By Cubic-Core Structure of the Bovine Branched-Chain Alpha-Ketoacid Dehydrogenase Complex. Embo J. V. 25 5983 2006.
ISSN: ISSN 0261-4189
PubMed: 17124494
DOI: 10.1038/SJ.EMBOJ.7601444
Page generated: Sat Jul 20 08:16:18 2024

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