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Chlorine in PDB 3mpj: Structure of the Glutaryl-Coenzyme A Dehydrogenase

Enzymatic activity of Structure of the Glutaryl-Coenzyme A Dehydrogenase

All present enzymatic activity of Structure of the Glutaryl-Coenzyme A Dehydrogenase:
1.3.99.7;

Protein crystallography data

The structure of Structure of the Glutaryl-Coenzyme A Dehydrogenase, PDB code: 3mpj was solved by S.Wischgoll, E.Warkentin, M.Boll, U.Ermler, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 2.10
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 152.400, 250.600, 62.800, 90.00, 90.00, 90.00
R / Rfree (%) 18.1 / 22.5

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Structure of the Glutaryl-Coenzyme A Dehydrogenase (pdb code 3mpj). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 6 binding sites of Chlorine where determined in the Structure of the Glutaryl-Coenzyme A Dehydrogenase, PDB code: 3mpj:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6;

Chlorine binding site 1 out of 6 in 3mpj

Go back to Chlorine Binding Sites List in 3mpj
Chlorine binding site 1 out of 6 in the Structure of the Glutaryl-Coenzyme A Dehydrogenase


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Structure of the Glutaryl-Coenzyme A Dehydrogenase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl401

b:32.6
occ:1.00
 O A:HOH8012 3.0 38.5 1.0
O A:HOH7136 3.1 26.5 1.0
ND2 A:ASN35 3.2 44.2 1.0
NZ A:LYS204 3.2 19.1 1.0
ND1 A:HIS208 3.3 27.4 1.0
N A:LYS204 3.5 21.7 1.0
O A:HOH7142 3.9 19.6 1.0
CB A:LYS204 4.0 19.0 1.0
CE A:LYS204 4.0 17.9 1.0
CA A:HIS208 4.0 24.7 1.0
CG A:LYS204 4.1 19.5 1.0
CA A:GLU203 4.1 27.3 1.0
O A:LEU202 4.1 28.5 1.0
CE1 A:HIS208 4.1 28.8 1.0
CA A:LYS204 4.2 19.9 1.0
C A:GLU203 4.3 23.3 1.0
CG A:HIS208 4.3 28.3 1.0
O A:LYS204 4.4 19.2 1.0
CB A:HIS208 4.4 25.8 1.0
CG A:ASN35 4.5 43.6 1.0
O A:GLY206 4.6 19.5 1.0
CD A:LYS204 4.6 18.5 1.0
O A:HIS208 4.7 24.9 1.0
C A:LYS204 4.8 20.0 1.0
N A:HIS208 4.8 23.8 1.0
C A:HIS208 4.9 24.8 1.0
O A:SER207 4.9 24.0 1.0
C A:LEU202 5.0 26.9 1.0
CB A:GLU203 5.0 31.4 1.0
N A:GLU203 5.0 27.1 1.0

Chlorine binding site 2 out of 6 in 3mpj

Go back to Chlorine Binding Sites List in 3mpj
Chlorine binding site 2 out of 6 in the Structure of the Glutaryl-Coenzyme A Dehydrogenase


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Structure of the Glutaryl-Coenzyme A Dehydrogenase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl401

b:32.4
occ:1.00
 O B:HOH7361 3.0 35.6 1.0
ND1 B:HIS208 3.3 28.4 1.0
NZ B:LYS204 3.4 21.8 1.0
O B:HOH7966 3.4 36.7 1.0
N B:LYS204 3.4 22.7 1.0
ND2 B:ASN35 3.5 37.1 1.0
O B:HOH7111 3.7 24.7 1.0
CB B:LYS204 4.0 20.2 1.0
CA B:HIS208 4.1 24.0 1.0
CA B:GLU203 4.1 28.2 1.0
CE1 B:HIS208 4.1 27.1 1.0
O B:LEU202 4.1 23.5 1.0
CG B:LYS204 4.2 21.2 1.0
CA B:LYS204 4.2 21.7 1.0
CE B:LYS204 4.2 19.3 1.0
C B:GLU203 4.2 26.3 1.0
CG B:HIS208 4.3 28.4 1.0
O B:LYS204 4.4 19.1 1.0
CB B:HIS208 4.4 26.5 1.0
O B:HIS208 4.6 27.4 1.0
O B:GLY206 4.6 22.4 1.0
C B:LYS204 4.7 20.4 1.0
CG B:ASN35 4.8 35.3 1.0
CD B:LYS204 4.8 19.6 1.0
C B:HIS208 4.8 26.0 1.0
O B:SER207 4.9 22.3 1.0
O B:HOH7924 4.9 47.2 1.0
CB B:GLU203 4.9 32.6 1.0
N B:HIS208 4.9 24.0 1.0
CG B:GLU203 5.0 47.7 1.0
C B:LEU202 5.0 25.2 1.0

Chlorine binding site 3 out of 6 in 3mpj

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Chlorine binding site 3 out of 6 in the Structure of the Glutaryl-Coenzyme A Dehydrogenase


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Structure of the Glutaryl-Coenzyme A Dehydrogenase within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl401

b:45.5
occ:1.00
 NZ D:LYS204 3.1 43.7 1.0
ND1 D:HIS208 3.5 43.9 1.0
O D:HOH7610 3.5 44.4 1.0
N D:LYS204 3.5 38.8 1.0
CE D:LYS204 3.6 41.7 1.0
CG D:LYS204 3.8 39.7 1.0
CB D:LYS204 3.9 38.2 1.0
CA D:HIS208 4.0 45.9 1.0
O D:LEU202 4.0 41.2 1.0
ND2 D:ASN35 4.1 63.5 1.0
CA D:LYS204 4.2 37.2 1.0
CB D:HIS208 4.3 47.2 1.0
CA D:GLU203 4.3 43.0 1.0
CG D:HIS208 4.3 46.1 1.0
CD D:LYS204 4.3 39.4 1.0
O D:LYS204 4.4 36.5 1.0
C D:GLU203 4.4 39.7 1.0
O D:HIS208 4.5 44.8 1.0
CE1 D:HIS208 4.5 44.0 1.0
O D:GLY206 4.5 34.4 1.0
C D:HIS208 4.7 46.8 1.0
O D:SER207 4.7 46.8 1.0
C D:LYS204 4.8 36.1 1.0
N D:HIS208 4.8 44.2 1.0

Chlorine binding site 4 out of 6 in 3mpj

Go back to Chlorine Binding Sites List in 3mpj
Chlorine binding site 4 out of 6 in the Structure of the Glutaryl-Coenzyme A Dehydrogenase


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Structure of the Glutaryl-Coenzyme A Dehydrogenase within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Cl401

b:54.5
occ:1.00
 ND1 E:HIS208 3.4 50.6 1.0
ND2 E:ASN35 3.4 77.2 1.0
NZ E:LYS204 3.5 52.5 1.0
CG E:LYS204 3.6 49.9 1.0
N E:LYS204 3.7 52.5 1.0
CA E:HIS208 3.9 49.4 1.0
O E:LEU202 4.2 62.1 1.0
CG E:HIS208 4.2 48.6 1.0
CB E:HIS208 4.2 49.7 1.0
CE E:LYS204 4.2 49.8 1.0
CE1 E:HIS208 4.3 48.1 1.0
CG E:ASN35 4.4 72.8 1.0
CA E:GLU203 4.4 60.2 1.0
O E:LYS204 4.4 46.7 1.0
CD E:LYS204 4.5 49.8 1.0
C E:GLU203 4.5 56.4 1.0
CA E:LYS204 4.5 50.5 1.0
O E:HIS208 4.5 53.1 1.0
CB E:LYS204 4.6 49.5 1.0
O E:GLY206 4.6 44.8 1.0
C E:HIS208 4.7 50.9 1.0
OD1 E:ASN35 4.7 78.5 1.0
O E:SER210 4.8 57.1 1.0
N E:HIS208 4.8 46.5 1.0
C E:LYS204 4.8 48.1 1.0
O E:SER207 4.9 45.4 1.0

Chlorine binding site 5 out of 6 in 3mpj

Go back to Chlorine Binding Sites List in 3mpj
Chlorine binding site 5 out of 6 in the Structure of the Glutaryl-Coenzyme A Dehydrogenase


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Structure of the Glutaryl-Coenzyme A Dehydrogenase within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Cl401

b:36.5
occ:1.00
 O F:HOH7527 3.0 31.3 1.0
NZ F:LYS204 3.0 24.9 1.0
ND1 F:HIS208 3.5 28.9 1.0
CG F:LYS204 3.5 26.6 1.0
ND2 F:ASN35 3.6 40.9 1.0
N F:LYS204 3.6 27.3 1.0
O F:HOH7528 3.7 31.6 1.0
CE F:LYS204 3.9 24.1 1.0
CA F:HIS208 4.0 26.8 1.0
CA F:GLU203 4.2 30.6 1.0
O F:LEU202 4.2 28.7 1.0
CD F:LYS204 4.3 25.0 1.0
O F:LYS204 4.3 23.8 1.0
C F:GLU203 4.3 29.2 1.0
CG F:HIS208 4.4 27.8 1.0
CE1 F:HIS208 4.4 28.0 1.0
CB F:HIS208 4.4 27.3 1.0
CA F:LYS204 4.4 26.6 1.0
CB F:LYS204 4.4 26.6 1.0
O F:HIS208 4.5 29.0 1.0
O F:GLY206 4.5 24.1 1.0
C F:LYS204 4.7 24.6 1.0
C F:HIS208 4.7 28.0 1.0
N F:HIS208 4.8 25.5 1.0
CG F:ASN35 4.9 43.4 1.0
O F:SER207 4.9 26.2 1.0
CB F:GLU203 5.0 33.1 1.0

Chlorine binding site 6 out of 6 in 3mpj

Go back to Chlorine Binding Sites List in 3mpj
Chlorine binding site 6 out of 6 in the Structure of the Glutaryl-Coenzyme A Dehydrogenase


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Structure of the Glutaryl-Coenzyme A Dehydrogenase within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Cl401

b:38.7
occ:1.00
 O G:HOH7567 3.2 34.0 1.0
NZ G:LYS204 3.3 26.9 1.0
ND1 G:HIS208 3.3 29.4 1.0
N G:LYS204 3.5 31.5 1.0
CG G:LYS204 3.6 28.9 1.0
O G:HOH7998 3.7 35.4 1.0
ND2 G:ASN35 3.9 44.1 1.0
CA G:GLU203 3.9 38.8 1.0
CA G:HIS208 4.1 29.8 1.0
O G:LEU202 4.1 36.3 1.0
C G:GLU203 4.2 35.1 1.0
CG G:HIS208 4.2 29.5 1.0
CD G:LYS204 4.2 28.3 1.0
CB G:HIS208 4.2 30.0 1.0
CE G:LYS204 4.3 28.1 1.0
CE1 G:HIS208 4.3 27.9 1.0
O G:LYS204 4.3 29.1 1.0
CA G:LYS204 4.4 29.8 1.0
CB G:LYS204 4.6 28.8 1.0
O G:GLY206 4.6 28.1 1.0
CB G:GLU203 4.7 40.8 1.0
O G:HIS208 4.7 30.3 1.0
C G:LYS204 4.7 31.0 1.0
N G:HIS208 4.9 29.6 1.0
C G:HIS208 4.9 30.5 1.0
O G:SER207 4.9 30.3 1.0
N G:GLU203 4.9 38.8 1.0
C G:LEU202 4.9 37.3 1.0

Reference:

S.Wischgoll, U.Demmer, E.Warkentin, R.Gunther, M.Boll, U.Ermler. Structural Basis For Promoting and Preventing Decarboxylation in Glutaryl-Coenzyme A Dehydrogenases. Biochemistry V. 49 5350 2010.
ISSN: ISSN 0006-2960
PubMed: 20486657
DOI: 10.1021/BI100317M
Page generated: Sun Jul 21 00:18:18 2024

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