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Chlorine in PDB 6tmy: Crystal Structure of Isoform Cbd of the Basic Phospholipase A2 Subunit of Crotoxin From Crotalus Durissus Terrificus

Enzymatic activity of Crystal Structure of Isoform Cbd of the Basic Phospholipase A2 Subunit of Crotoxin From Crotalus Durissus Terrificus

All present enzymatic activity of Crystal Structure of Isoform Cbd of the Basic Phospholipase A2 Subunit of Crotoxin From Crotalus Durissus Terrificus:
3.1.1.4;

Protein crystallography data

The structure of Crystal Structure of Isoform Cbd of the Basic Phospholipase A2 Subunit of Crotoxin From Crotalus Durissus Terrificus, PDB code: 6tmy was solved by D.Nemecz, M.Ostrowski, F.A.Saul, G.Faure, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.50 / 1.80
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 149.626, 75.592, 109.012, 90.00, 121.85, 90.00
R / Rfree (%) 19.2 / 21.4

Other elements in 6tmy:

The structure of Crystal Structure of Isoform Cbd of the Basic Phospholipase A2 Subunit of Crotoxin From Crotalus Durissus Terrificus also contains other interesting chemical elements:

Sodium (Na) 12 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of Isoform Cbd of the Basic Phospholipase A2 Subunit of Crotoxin From Crotalus Durissus Terrificus (pdb code 6tmy). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 7 binding sites of Chlorine where determined in the Crystal Structure of Isoform Cbd of the Basic Phospholipase A2 Subunit of Crotoxin From Crotalus Durissus Terrificus, PDB code: 6tmy:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7;

Chlorine binding site 1 out of 7 in 6tmy

Go back to Chlorine Binding Sites List in 6tmy
Chlorine binding site 1 out of 7 in the Crystal Structure of Isoform Cbd of the Basic Phospholipase A2 Subunit of Crotoxin From Crotalus Durissus Terrificus


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 Isoform Cbd of the Basic Phospholipase A2 Subunit of Crotoxin From Crotalus Durissus Terrificus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl204

b:25.9
occ:1.00
 O A:HOH339 3.2 21.6 1.0
O A:HOH392 3.2 23.2 1.0
N B:TYR66 3.3 23.6 1.0
O B:HOH310 3.3 27.4 1.0
O A:TYR66 3.4 21.7 1.0
O B:TYR66 3.4 24.5 1.0
N A:TYR66 3.4 22.2 1.0
CA A:ARG65 3.6 20.8 1.0
CA B:ARG65 3.6 24.3 1.0
NH1 B:ARG65 3.6 43.1 1.0
CD B:ARG65 3.9 53.1 1.0
C B:ARG65 3.9 27.3 1.0
CB A:ARG65 4.0 19.7 1.0
O B:TYR64 4.0 26.8 1.0
CG A:ARG65 4.0 22.8 1.0
C A:ARG65 4.0 23.3 1.0
O A:TYR64 4.1 24.1 1.0
C B:TYR66 4.3 27.1 1.0
C A:TYR66 4.3 22.5 1.0
CA B:TYR66 4.4 23.1 1.0
CB B:ARG65 4.4 27.6 1.0
CG B:ARG65 4.5 44.6 1.0
CA A:TYR66 4.5 20.7 1.0
CD1 B:TYR66 4.5 21.8 1.0
CZ B:ARG65 4.6 62.0 1.0
N B:ARG65 4.6 24.8 1.0
CD1 A:TYR66 4.7 22.8 1.0
N A:ARG65 4.7 20.3 1.0
NE B:ARG65 4.7 50.9 1.0
C B:TYR64 4.7 28.1 1.0
C A:TYR64 4.8 22.8 1.0
NE2 B:GLN4 4.9 22.2 1.0
CE1 B:TYR66 4.9 21.1 1.0

Chlorine binding site 2 out of 7 in 6tmy

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Chlorine binding site 2 out of 7 in the Crystal Structure of Isoform Cbd of the Basic Phospholipase A2 Subunit of Crotoxin From Crotalus Durissus Terrificus


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 Isoform Cbd of the Basic Phospholipase A2 Subunit of Crotoxin From Crotalus Durissus Terrificus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl205

b:26.1
occ:1.00
 NE2 B:HIS1 3.1 20.7 1.0
O B:HOH346 3.1 31.9 1.0
NE2 A:HIS1 3.1 22.5 1.0
CD2 B:HIS1 3.8 20.4 1.0
CE1 A:HIS1 3.8 22.3 1.0
CE1 B:HIS1 4.2 21.2 1.0
CD2 A:HIS1 4.3 23.0 1.0
CD1 A:LEU3 4.9 27.8 1.0
CE3 B:TRP61 4.9 27.6 1.0

Chlorine binding site 3 out of 7 in 6tmy

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Chlorine binding site 3 out of 7 in the Crystal Structure of Isoform Cbd of the Basic Phospholipase A2 Subunit of Crotoxin From Crotalus Durissus Terrificus


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 Isoform Cbd of the Basic Phospholipase A2 Subunit of Crotoxin From Crotalus Durissus Terrificus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl206

b:37.2
occ:1.00
 O A:HOH389 3.0 28.5 1.0
O A:HOH457 3.0 48.6 1.0
N A:TRP80 3.1 26.4 1.0
O F:HOH374 3.2 38.6 1.0
C6 A:PG4203 3.6 67.5 1.0
CB A:TRP80 3.7 26.9 1.0
OH F:TYR105 3.7 31.1 1.0
CA A:THR79 3.8 23.9 1.0
CB A:THR79 3.8 28.8 1.0
CZ F:PHE20 3.8 30.4 1.0
CE1 F:PHE20 3.9 31.6 1.0
C A:THR79 3.9 27.5 1.0
CA A:TRP80 4.0 26.4 1.0
CE1 F:TYR105 4.0 31.0 1.0
C7 A:PG4203 4.1 71.4 1.0
CZ F:TYR105 4.1 32.4 1.0
O4 A:PG4203 4.4 70.8 1.0
CG2 A:THR79 4.5 29.6 1.0
O F:HOH387 4.7 49.2 1.0
C5 A:PG4203 4.7 66.2 1.0
C8 A:PG4203 4.8 71.6 1.0
N A:CYS81 4.8 23.8 1.0
OG1 A:THR79 4.9 25.9 1.0
CE2 F:PHE20 4.9 32.2 1.0
C A:TRP80 5.0 26.2 1.0

Chlorine binding site 4 out of 7 in 6tmy

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Chlorine binding site 4 out of 7 in the Crystal Structure of Isoform Cbd of the Basic Phospholipase A2 Subunit of Crotoxin From Crotalus Durissus Terrificus


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 Isoform Cbd of the Basic Phospholipase A2 Subunit of Crotoxin From Crotalus Durissus Terrificus within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl205

b:32.6
occ:1.00
 O C:HOH373 3.1 28.6 1.0
O C:HOH303 3.4 35.7 1.0
N C:TYR66 3.4 27.4 1.0
O C:TYR66 3.5 28.1 1.0
NH1 C:ARG65 3.6 46.6 1.0
CA C:ARG65 3.7 31.5 1.0
CD C:ARG65 4.0 58.8 1.0
O C:TYR64 4.0 31.2 1.0
C C:ARG65 4.1 32.6 1.0
C C:TYR66 4.4 29.2 1.0
CB C:ARG65 4.5 37.3 1.0
CA C:TYR66 4.5 26.2 1.0
CG C:ARG65 4.5 46.3 1.0
CD1 C:TYR66 4.6 27.5 1.0
CZ C:ARG65 4.6 66.9 1.0
N C:ARG65 4.7 31.0 1.0
NE C:ARG65 4.8 57.3 1.0
C C:TYR64 4.8 32.2 1.0
NE2 C:GLN4 4.9 24.1 1.0
CE1 C:TYR66 4.9 27.2 1.0

Chlorine binding site 5 out of 7 in 6tmy

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Chlorine binding site 5 out of 7 in the Crystal Structure of Isoform Cbd of the Basic Phospholipase A2 Subunit of Crotoxin From Crotalus Durissus Terrificus


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 Isoform Cbd of the Basic Phospholipase A2 Subunit of Crotoxin From Crotalus Durissus Terrificus within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl203

b:28.6
occ:1.00
 NE2 D:HIS1 3.1 25.7 1.0
CE1 D:HIS1 3.8 26.0 1.0
CD2 D:HIS1 4.3 25.7 1.0
CD1 D:LEU3 4.9 30.1 1.0

Chlorine binding site 6 out of 7 in 6tmy

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Chlorine binding site 6 out of 7 in the Crystal Structure of Isoform Cbd of the Basic Phospholipase A2 Subunit of Crotoxin From Crotalus Durissus Terrificus


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 Isoform Cbd of the Basic Phospholipase A2 Subunit of Crotoxin From Crotalus Durissus Terrificus within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Cl204

b:26.1
occ:1.00
 NE2 E:HIS1 3.1 26.3 1.0
CE1 E:HIS1 3.8 26.3 1.0
CD2 E:HIS1 4.3 26.0 1.0
CD1 E:LEU3 4.8 30.5 1.0

Chlorine binding site 7 out of 7 in 6tmy

Go back to Chlorine Binding Sites List in 6tmy
Chlorine binding site 7 out of 7 in the Crystal Structure of Isoform Cbd of the Basic Phospholipase A2 Subunit of Crotoxin From Crotalus Durissus Terrificus


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 Isoform Cbd of the Basic Phospholipase A2 Subunit of Crotoxin From Crotalus Durissus Terrificus within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Cl205

b:27.2
occ:1.00
 O F:HOH364 3.2 26.8 1.0
O F:HOH309 3.4 25.5 1.0
N F:TYR66 3.4 26.0 1.0
NH1 F:ARG65 3.4 44.2 1.0
O F:TYR66 3.5 26.0 1.0
CA F:ARG65 3.6 26.5 1.0
CD F:ARG65 3.8 48.7 1.0
C F:ARG65 4.0 27.8 1.0
O F:TYR64 4.1 30.2 1.0
C F:TYR66 4.4 26.0 1.0
CG F:ARG65 4.4 42.5 1.0
CB F:ARG65 4.4 30.9 1.0
CZ F:ARG65 4.4 59.9 1.0
CA F:TYR66 4.5 24.3 1.0
NE F:ARG65 4.6 46.0 1.0
CD1 F:TYR66 4.7 24.6 1.0
N F:ARG65 4.7 25.9 1.0
C F:TYR64 4.8 29.2 1.0
NE2 F:GLN4 5.0 21.9 1.0

Reference:

D.Nemecz, M.Ostrowski, M.Ravatin, F.Saul, G.Faure. Crystal Structure of Isoform Cbd of the Basic Phospholipase A 2 Subunit of Crotoxin: Description of the Structural Framework of Cb For Interaction with Protein Targets. Molecules V. 25 2020.
ISSN: ESSN 1420-3049
PubMed: 33202772
DOI: 10.3390/MOLECULES25225290
Page generated: Mon Jul 29 15:30:26 2024

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