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Chlorine in PDB 6p02: Crystal Structure of Mtb Aspartate Decarboxylase, 6-Chlorine Pyrazinoic Acid Complex

Enzymatic activity of Crystal Structure of Mtb Aspartate Decarboxylase, 6-Chlorine Pyrazinoic Acid Complex

All present enzymatic activity of Crystal Structure of Mtb Aspartate Decarboxylase, 6-Chlorine Pyrazinoic Acid Complex:
4.1.1.11;

Protein crystallography data

The structure of Crystal Structure of Mtb Aspartate Decarboxylase, 6-Chlorine Pyrazinoic Acid Complex, PDB code: 6p02 was solved by Q.Sun, X.Li, J.C.Sacchettini, Tb Structural Genomics Consortium (Tbsgc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 21.89 / 2.25
Space group P 31
Cell size a, b, c (Å), α, β, γ (°) 143.679, 143.679, 59.838, 90.00, 90.00, 120.00
R / Rfree (%) 13.4 / 16.4

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 Mtb Aspartate Decarboxylase, 6-Chlorine Pyrazinoic Acid Complex (pdb code 6p02). 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 Mtb Aspartate Decarboxylase, 6-Chlorine Pyrazinoic Acid Complex, PDB code: 6p02:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Chlorine binding site 1 out of 12 in 6p02

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Chlorine binding site 1 out of 12 in the Crystal Structure of Mtb Aspartate Decarboxylase, 6-Chlorine Pyrazinoic Acid Complex


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 Mtb Aspartate Decarboxylase, 6-Chlorine Pyrazinoic Acid Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl201

b:74.4
occ:1.00
 CL07 B:NMJ201 0.0 74.4 1.0
C04 B:NMJ201 1.7 57.0 1.0
N03 B:NMJ201 2.6 54.1 1.0
C05 B:NMJ201 2.7 58.2 1.0
OH H:TYR90 3.4 43.0 1.0
OG1 B:THR57 3.7 49.4 1.0
CA B:THR57 3.8 45.5 1.0
C02 B:NMJ201 3.8 56.5 1.0
CG1 H:ILE88 3.8 55.1 1.0
NH2 H:ARG54 3.9 49.7 1.0
N06 B:NMJ201 4.0 56.2 1.0
O B:VAL56 4.1 31.9 1.0
CD2 B:TYR58 4.1 51.5 1.0
CB B:THR57 4.2 49.3 1.0
CG2 H:ILE88 4.4 54.0 1.0
CD1 H:ILE88 4.4 58.6 1.0
C01 B:NMJ201 4.4 58.1 1.0
N B:TYR58 4.4 40.6 1.0
CB H:ILE88 4.4 47.7 1.0
C B:THR57 4.5 44.4 1.0
CE2 B:TYR58 4.5 52.5 1.0
CZ H:TYR90 4.6 57.1 1.0
CG1 H:VAL47 4.7 39.6 1.0
N B:THR57 4.8 44.9 1.0
C B:VAL56 4.8 33.1 1.0
O10 B:NMJ201 4.9 50.1 1.0
C08 B:NMJ201 5.0 48.0 1.0

Chlorine binding site 2 out of 12 in 6p02

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Chlorine binding site 2 out of 12 in the Crystal Structure of Mtb Aspartate Decarboxylase, 6-Chlorine Pyrazinoic Acid Complex


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 Mtb Aspartate Decarboxylase, 6-Chlorine Pyrazinoic Acid Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl201

b:57.5
occ:1.00
 CL07 D:NMJ201 0.0 57.5 1.0
C04 D:NMJ201 1.7 50.6 1.0
N03 D:NMJ201 2.6 62.6 1.0
C05 D:NMJ201 2.7 60.7 1.0
OH B:TYR90 3.5 42.2 1.0
NH2 B:ARG54 3.7 41.5 1.0
CG1 B:ILE88 3.7 61.0 1.0
C02 D:NMJ201 3.8 55.1 1.0
O D:VAL56 3.9 34.5 1.0
N06 D:NMJ201 3.9 52.5 1.0
CA D:THR57 4.1 37.2 1.0
OG1 D:THR57 4.1 34.5 1.0
CG2 B:VAL47 4.2 47.9 1.0
CB B:ILE88 4.4 45.7 1.0
C01 D:NMJ201 4.4 50.7 1.0
CD1 B:ILE88 4.4 53.0 1.0
CG2 B:THR45 4.5 38.1 1.0
CG2 B:ILE88 4.5 54.6 1.0
CB D:THR57 4.6 43.5 1.0
CZ B:TYR90 4.7 44.9 1.0
CD2 D:TYR58 4.7 39.3 1.0
C D:VAL56 4.8 38.0 1.0
CZ B:ARG54 4.8 35.1 1.0
C D:THR57 5.0 36.9 1.0
N D:THR57 5.0 34.8 1.0

Chlorine binding site 3 out of 12 in 6p02

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Chlorine binding site 3 out of 12 in the Crystal Structure of Mtb Aspartate Decarboxylase, 6-Chlorine Pyrazinoic Acid Complex


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 Mtb Aspartate Decarboxylase, 6-Chlorine Pyrazinoic Acid Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Cl201

b:69.8
occ:1.00
 CL07 F:NMJ201 0.0 69.8 1.0
C04 F:NMJ201 1.8 62.7 1.0
N03 F:NMJ201 2.6 54.0 1.0
C05 F:NMJ201 2.8 55.9 1.0
OH D:TYR90 3.5 37.2 1.0
NH2 D:ARG54 3.5 40.3 1.0
O F:VAL56 3.7 34.5 1.0
C02 F:NMJ201 3.8 55.0 1.0
CA F:THR57 3.9 33.7 1.0
OG1 F:THR57 3.9 34.7 1.0
CG1 D:ILE88 4.0 50.4 1.0
N06 F:NMJ201 4.0 48.5 1.0
CB F:THR57 4.3 38.9 1.0
C01 F:NMJ201 4.4 52.4 1.0
CB D:ILE88 4.5 41.4 1.0
CG1 D:VAL47 4.5 44.1 1.0
CG2 D:ILE88 4.5 49.0 1.0
C F:VAL56 4.6 33.0 1.0
CD2 F:TYR58 4.6 37.5 1.0
CZ D:TYR90 4.7 44.1 1.0
N F:THR57 4.7 36.0 1.0
C F:THR57 4.7 39.6 1.0
CD1 D:ILE88 4.7 56.8 1.0
CG2 D:THR45 4.7 39.7 1.0
CZ D:ARG54 4.7 38.4 1.0
N F:TYR58 4.8 35.4 1.0
C08 F:NMJ201 4.8 37.3 1.0
CE2 F:TYR58 5.0 41.6 1.0

Chlorine binding site 4 out of 12 in 6p02

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Chlorine binding site 4 out of 12 in the Crystal Structure of Mtb Aspartate Decarboxylase, 6-Chlorine Pyrazinoic Acid Complex


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 Mtb Aspartate Decarboxylase, 6-Chlorine Pyrazinoic Acid Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Cl201

b:67.0
occ:1.00
 CL07 H:NMJ201 0.0 67.0 1.0
C04 H:NMJ201 1.8 53.6 1.0
N03 H:NMJ201 2.6 61.9 1.0
C05 H:NMJ201 2.8 56.5 1.0
NH2 F:ARG54 3.5 43.3 1.0
CD1 F:ILE88 3.6 67.8 1.0
OH F:TYR90 3.7 38.7 1.0
OG1 H:THR57 3.7 60.2 1.0
O H:VAL56 3.8 34.7 1.0
C02 H:NMJ201 3.9 57.0 1.0
CA H:THR57 3.9 39.9 1.0
N06 H:NMJ201 4.1 51.8 1.0
CG1 F:ILE88 4.2 55.2 1.0
CB H:THR57 4.3 44.4 1.0
CG2 F:VAL47 4.3 43.0 1.0
C01 H:NMJ201 4.5 54.7 1.0
CD2 H:TYR58 4.5 46.1 1.0
CZ F:ARG54 4.7 36.2 1.0
C H:VAL56 4.7 38.9 1.0
C H:THR57 4.7 39.0 1.0
N H:TYR58 4.7 32.3 1.0
N H:THR57 4.8 36.7 1.0
CB F:ILE88 4.8 51.8 1.0
CG2 F:ILE88 4.8 64.0 1.0
CE2 H:TYR58 4.9 41.2 1.0
CZ F:TYR90 4.9 33.8 1.0
C08 H:NMJ201 5.0 62.3 1.0
O10 H:NMJ201 5.0 60.0 1.0

Chlorine binding site 5 out of 12 in 6p02

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Chlorine binding site 5 out of 12 in the Crystal Structure of Mtb Aspartate Decarboxylase, 6-Chlorine Pyrazinoic Acid Complex


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 Mtb Aspartate Decarboxylase, 6-Chlorine Pyrazinoic Acid Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Cl201

b:59.5
occ:1.00
 CL07 J:NMJ201 0.0 59.5 1.0
C04 J:NMJ201 1.7 59.0 1.0
N03 J:NMJ201 2.6 53.1 1.0
C05 J:NMJ201 2.7 60.1 1.0
NH2 P:ARG54 3.5 39.3 1.0
O J:VAL56 3.7 38.2 1.0
OH P:TYR90 3.7 35.0 1.0
C02 J:NMJ201 3.8 56.8 1.0
CG1 P:ILE88 3.9 59.0 1.0
OG1 J:THR57 3.9 49.2 1.0
CA J:THR57 3.9 47.9 1.0
N06 J:NMJ201 4.0 63.6 1.0
CG1 P:VAL47 4.3 39.3 1.0
CB J:THR57 4.3 46.0 1.0
C01 J:NMJ201 4.4 63.0 1.0
CB P:ILE88 4.5 49.5 1.0
C J:VAL56 4.6 32.1 1.0
CG2 P:ILE88 4.6 48.4 1.0
CD1 P:ILE88 4.6 55.9 1.0
CD1 J:TYR58 4.6 41.2 1.0
CZ P:ARG54 4.7 39.9 1.0
N J:THR57 4.7 42.6 1.0
CG2 P:THR45 4.7 36.8 1.0
C J:THR57 4.8 56.2 1.0
N J:TYR58 4.9 39.8 1.0
CZ P:TYR90 4.9 39.7 1.0
C08 J:NMJ201 5.0 56.7 1.0
CE1 J:TYR58 5.0 41.5 1.0

Chlorine binding site 6 out of 12 in 6p02

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Chlorine binding site 6 out of 12 in the Crystal Structure of Mtb Aspartate Decarboxylase, 6-Chlorine Pyrazinoic Acid Complex


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 Mtb Aspartate Decarboxylase, 6-Chlorine Pyrazinoic Acid Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Cl201

b:70.7
occ:1.00
 CL07 L:NMJ201 0.0 70.7 1.0
C04 L:NMJ201 1.8 55.2 1.0
C05 L:NMJ201 2.7 41.5 1.0
N03 L:NMJ201 2.7 57.0 1.0
OH J:TYR90 3.4 37.2 1.0
NH2 J:ARG54 3.8 38.1 1.0
O L:VAL56 3.8 39.5 1.0
CG1 J:ILE88 3.8 61.5 1.0
CA L:THR57 3.9 39.0 1.0
N06 L:NMJ201 4.0 41.8 1.0
C02 L:NMJ201 4.0 51.6 1.0
OG1 L:THR57 4.0 41.5 1.0
CG2 J:VAL47 4.4 32.8 1.0
CB J:ILE88 4.4 43.1 1.0
CG2 J:ILE88 4.4 57.5 1.0
CB L:THR57 4.4 45.4 1.0
C01 L:NMJ201 4.5 49.5 1.0
CZ J:TYR90 4.5 40.8 1.0
CG2 J:THR45 4.5 40.4 1.0
CD2 L:TYR58 4.6 53.1 1.0
CD1 J:ILE88 4.6 64.7 1.0
C L:VAL56 4.6 41.5 1.0
C L:THR57 4.7 43.1 1.0
N L:THR57 4.7 39.6 1.0
N L:TYR58 4.8 41.1 1.0
CZ J:ARG54 4.9 32.8 1.0
CE2 J:TYR90 4.9 29.1 1.0

Chlorine binding site 7 out of 12 in 6p02

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Chlorine binding site 7 out of 12 in the Crystal Structure of Mtb Aspartate Decarboxylase, 6-Chlorine Pyrazinoic Acid Complex


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 Mtb Aspartate Decarboxylase, 6-Chlorine Pyrazinoic Acid Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Cl201

b:61.7
occ:1.00
 CL07 N:NMJ201 0.0 61.7 1.0
C04 N:NMJ201 1.8 62.2 1.0
N03 N:NMJ201 2.6 66.0 1.0
C05 N:NMJ201 2.7 42.9 1.0
OH L:TYR90 3.2 33.7 1.0
O N:VAL56 3.5 34.5 1.0
NH2 L:ARG54 3.7 43.0 1.0
CA N:THR57 3.7 41.1 1.0
C02 N:NMJ201 3.9 61.7 1.0
OG1 N:THR57 3.9 45.5 1.0
N06 N:NMJ201 4.0 69.3 1.0
CG1 L:ILE88 4.0 54.2 1.0
CB N:THR57 4.2 39.9 1.0
C N:VAL56 4.3 38.0 1.0
CZ L:TYR90 4.3 38.0 1.0
C01 N:NMJ201 4.4 60.7 1.0
N N:THR57 4.5 37.7 1.0
CG2 L:ILE88 4.5 51.1 1.0
C N:THR57 4.5 39.5 1.0
CB L:ILE88 4.5 46.6 1.0
CG1 L:VAL47 4.5 40.9 1.0
CD2 N:TYR58 4.6 36.9 1.0
N N:TYR58 4.6 40.1 1.0
CG2 L:THR45 4.6 39.9 1.0
CD1 L:ILE88 4.8 57.4 1.0
CE2 L:TYR90 4.8 33.3 1.0
CZ L:ARG54 4.9 34.0 1.0

Chlorine binding site 8 out of 12 in 6p02

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Chlorine binding site 8 out of 12 in the Crystal Structure of Mtb Aspartate Decarboxylase, 6-Chlorine Pyrazinoic Acid Complex


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 Mtb Aspartate Decarboxylase, 6-Chlorine Pyrazinoic Acid Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Cl201

b:57.3
occ:1.00
 CL07 P:NMJ201 0.0 57.3 1.0
C04 P:NMJ201 1.8 48.3 1.0
N03 P:NMJ201 2.7 46.2 1.0
C05 P:NMJ201 2.8 49.7 1.0
NH2 N:ARG54 3.4 45.4 1.0
OH N:TYR90 3.4 49.0 1.0
O P:VAL56 3.5 41.5 1.0
CD1 N:ILE88 3.7 62.8 1.0
C02 P:NMJ201 3.9 62.4 1.0
CA P:THR57 3.9 48.8 1.0
N06 P:NMJ201 4.0 64.5 1.0
OG1 P:THR57 4.1 58.1 1.0
CG2 N:VAL47 4.2 40.8 1.0
CG1 N:ILE88 4.3 54.2 1.0
CG2 N:THR45 4.4 41.2 1.0
C P:VAL56 4.4 45.7 1.0
CB P:THR57 4.4 50.9 1.0
C01 P:NMJ201 4.5 55.7 1.0
CZ N:ARG54 4.5 34.5 1.0
CZ N:TYR90 4.6 38.1 1.0
N P:THR57 4.6 46.6 1.0
CG2 N:ILE88 4.7 45.8 1.0
CB N:ILE88 4.8 46.2 1.0
C P:THR57 4.8 41.0 1.0
CD2 P:TYR58 4.9 48.2 1.0
CE2 N:TYR90 5.0 47.4 1.0
N P:TYR58 5.0 41.5 1.0

Chlorine binding site 9 out of 12 in 6p02

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Chlorine binding site 9 out of 12 in the Crystal Structure of Mtb Aspartate Decarboxylase, 6-Chlorine Pyrazinoic Acid Complex


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 Mtb Aspartate Decarboxylase, 6-Chlorine Pyrazinoic Acid Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
R:Cl201

b:66.1
occ:1.00
 CL07 R:NMJ201 0.0 66.1 1.0
C04 R:NMJ201 1.8 68.2 1.0
N03 R:NMJ201 2.6 64.0 1.0
C05 R:NMJ201 2.8 69.0 1.0
OH X:TYR90 3.6 40.7 1.0
NH2 X:ARG54 3.7 46.0 1.0
OG1 R:THR57 3.8 49.6 1.0
C02 R:NMJ201 3.9 68.2 1.0
O R:VAL56 3.9 43.6 1.0
CG1 X:ILE88 3.9 54.3 1.0
CA R:THR57 4.0 41.1 1.0
N06 R:NMJ201 4.0 55.5 1.0
CG1 X:VAL47 4.3 55.5 1.0
CB R:THR57 4.4 44.8 1.0
C01 R:NMJ201 4.5 67.3 1.0
CD1 X:ILE88 4.5 57.0 1.0
CB X:ILE88 4.6 55.8 1.0
CD2 R:TYR58 4.6 41.3 1.0
CG2 X:ILE88 4.7 55.1 1.0
C R:VAL56 4.7 43.0 1.0
CZ X:TYR90 4.8 44.9 1.0
C R:THR57 4.8 39.9 1.0
CZ X:ARG54 4.8 42.5 1.0
N R:THR57 4.9 37.3 1.0
N R:TYR58 4.9 40.4 1.0
CG2 X:THR45 4.9 48.0 1.0
CE2 R:TYR58 4.9 41.4 1.0
C08 R:NMJ201 5.0 58.8 1.0

Chlorine binding site 10 out of 12 in 6p02

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Chlorine binding site 10 out of 12 in the Crystal Structure of Mtb Aspartate Decarboxylase, 6-Chlorine Pyrazinoic Acid Complex


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 Mtb Aspartate Decarboxylase, 6-Chlorine Pyrazinoic Acid Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
T:Cl201

b:72.8
occ:1.00
 CL07 T:NMJ201 0.0 72.8 1.0
C04 T:NMJ201 1.8 58.6 1.0
N03 T:NMJ201 2.6 58.7 1.0
C05 T:NMJ201 2.8 54.7 1.0
NH2 R:ARG54 3.2 44.8 1.0
O T:VAL56 3.2 44.4 1.0
OH R:TYR90 3.4 57.6 1.0
CA T:THR57 3.7 43.8 1.0
C02 T:NMJ201 3.9 59.5 1.0
OG1 T:THR57 3.9 60.0 1.0
N06 T:NMJ201 4.0 62.5 1.0
CG1 R:VAL47 4.1 52.9 1.0
C T:VAL56 4.2 33.4 1.0
CB T:THR57 4.2 42.1 1.0
CG1 R:ILE88 4.2 54.5 1.0
CZ R:ARG54 4.4 42.8 1.0
N T:THR57 4.4 43.2 1.0
CG2 R:THR45 4.4 46.1 1.0
C01 T:NMJ201 4.5 60.0 1.0
C T:THR57 4.6 51.6 1.0
CZ R:TYR90 4.7 54.5 1.0
CB R:ILE88 4.8 49.7 1.0
N T:TYR58 4.9 48.8 1.0
CG2 R:ILE88 4.9 49.9 1.0
C08 T:NMJ201 5.0 63.3 1.0
CD2 T:TYR58 5.0 54.5 1.0

Reference:

Q.Sun, X.Li, L.M.Perez, W.Shi, Y.Zhang, J.C.Sacchettini. The Molecular Basis of Pyrazinamide Activity on Mycobacterium Tuberculosis Pand. Nat Commun V. 11 339 2020.
ISSN: ESSN 2041-1723
PubMed: 31953389
DOI: 10.1038/S41467-019-14238-3
Page generated: Mon Jul 29 12:55:45 2024

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