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Sodium 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:

Chlorine (Cl) 7 atoms

Sodium Binding Sites:

Pages:

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

Binding sites:

The binding sites of Sodium 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 Sodium atom.
In total 12 binding sites of Sodium 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 Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Sodium binding site 1 out of 12 in 6tmy

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Sodium binding site 1 out of 12 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 Sodium with other atoms in the Na 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:Na201

b:27.1
occ:1.00
 O A:TYR27 2.2 24.1 1.0
O A:GLY31 2.3 33.2 1.0
O A:GLY29 2.3 31.5 1.0
OD2 A:ASP48 2.4 33.2 1.0
OD1 A:ASP48 2.6 35.5 1.0
CG A:ASP48 2.8 34.0 1.0
O A:HOH319 3.2 44.0 1.0
C A:GLY31 3.4 36.9 1.0
C A:TYR27 3.4 24.5 1.0
C A:GLY29 3.5 31.9 1.0
N A:GLY31 3.6 35.9 1.0
C A:TRP30 3.9 39.1 1.0
O A:HOH338 3.9 44.8 1.0
CA A:GLY31 4.0 36.0 1.0
CA A:TYR27 4.0 22.2 1.0
N A:GLY29 4.0 22.8 1.0
C A:CYS28 4.2 27.2 1.0
O1 A:PG4202 4.2 41.3 1.0
CA A:TRP30 4.2 40.9 1.0
N A:TRP30 4.3 36.6 1.0
CB A:ASP48 4.3 22.8 1.0
O A:TRP30 4.4 38.7 1.0
CA A:GLY29 4.4 23.4 1.0
N A:CYS28 4.4 22.0 1.0
N A:GLY32 4.4 34.1 1.0
CB A:TYR27 4.5 24.1 1.0
CA A:CYS28 4.5 22.4 1.0
O A:CYS28 4.5 28.5 1.0
O A:CYS44 4.7 21.2 1.0
CA A:GLY32 4.7 34.4 1.0
CD1 A:TYR27 4.8 27.2 1.0

Sodium binding site 2 out of 12 in 6tmy

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Sodium binding site 2 out of 12 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 Sodium with other atoms in the Na 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:Na207

b:53.1
occ:1.00
 O A:HOH321 2.4 35.3 1.0
O A:HOH307 2.5 29.7 1.0
O A:GLY25 2.6 27.0 1.0
O A:PHE23 2.7 26.7 1.0
O A:TYR110 2.9 32.4 1.0
O A:HOH401 3.3 55.4 1.0
C A:PHE23 3.5 26.6 1.0
C A:GLY25 3.8 28.0 1.0
C A:TYR110 3.9 33.3 1.0
CB A:TYR110 4.0 31.9 1.0
CA A:PHE23 4.1 22.3 1.0
N A:TYR110 4.2 29.0 1.0
CA A:TYR110 4.2 29.4 1.0
C A:TYR24 4.3 25.9 1.0
O A:TYR24 4.3 24.2 1.0
N A:GLY25 4.4 24.0 1.0
N A:TYR24 4.4 22.4 1.0
OD1 A:ASP112 4.5 56.6 1.0
O A:HOH358 4.5 36.9 1.0
CB A:PHE23 4.6 23.9 1.0
CA A:GLY25 4.7 24.2 1.0
N A:CYS26 4.8 25.4 1.0
CA A:TYR24 4.8 22.1 1.0
CA A:CYS26 4.8 26.9 1.0
O A:HOH338 4.8 44.8 1.0
O A:CYS28 4.9 28.5 1.0

Sodium binding site 3 out of 12 in 6tmy

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Sodium binding site 3 out of 12 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 Sodium with other atoms in the Na 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
B:Na201

b:31.2
occ:1.00
 O B:TYR27 2.2 29.2 1.0
O B:GLY29 2.3 30.3 1.0
O B:GLY31 2.3 39.3 1.0
OD2 B:ASP48 2.6 56.0 1.0
OD1 B:ASP48 2.7 56.0 1.0
CG B:ASP48 3.0 51.3 1.0
C B:TYR27 3.4 30.2 1.0
C B:GLY29 3.4 31.6 1.0
C B:GLY31 3.5 43.1 1.0
N B:GLY31 3.7 40.7 1.0
O B:HOH329 3.9 48.0 1.0
O1 B:PG4202 3.9 38.0 1.0
C B:TRP30 3.9 41.6 1.0
N B:GLY29 4.0 26.8 1.0
CA B:GLY31 4.1 41.6 1.0
CA B:TYR27 4.2 27.7 1.0
C B:CYS28 4.2 30.1 1.0
CA B:TRP30 4.2 36.8 1.0
N B:TRP30 4.3 34.0 1.0
O B:HOH308 4.3 43.5 1.0
CA B:GLY29 4.4 26.9 1.0
N B:CYS28 4.4 26.0 1.0
O B:TRP30 4.4 41.4 1.0
CA B:CYS28 4.5 26.5 1.0
CB B:ASP48 4.5 31.1 1.0
CB B:TYR27 4.6 29.8 1.0
N B:GLY32 4.6 37.6 1.0
O B:HOH323 4.6 56.4 1.0
O B:CYS28 4.6 29.4 1.0
O B:CYS44 4.7 28.3 1.0
CA B:GLY32 4.9 36.1 1.0
CD1 B:TYR27 4.9 35.2 1.0

Sodium binding site 4 out of 12 in 6tmy

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Sodium binding site 4 out of 12 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 Sodium with other atoms in the Na 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
B:Na204

b:52.8
occ:1.00
 O B:GLY25 2.3 28.8 1.0
O B:HOH355 2.4 45.3 1.0
O B:PHE23 2.4 31.2 1.0
O B:TYR110 2.5 40.9 1.0
O B:HOH398 2.5 51.3 1.0
O B:HOH335 2.6 32.6 1.0
CB B:TYR110 3.3 40.2 1.0
C B:TYR110 3.4 41.3 1.0
C B:PHE23 3.4 32.0 1.0
C B:GLY25 3.5 30.3 1.0
CA B:TYR110 3.6 38.5 1.0
N B:TYR110 3.6 38.5 1.0
N B:GLY25 3.8 26.9 1.0
C B:TYR24 3.8 30.4 1.0
O B:TYR24 4.1 29.2 1.0
CA B:GLY25 4.2 26.6 1.0
CA B:PHE23 4.2 31.0 1.0
N B:TYR24 4.2 25.6 1.0
CA B:TYR24 4.4 24.3 1.0
CG B:TYR110 4.4 41.9 1.0
N B:CYS26 4.5 29.2 1.0
CD2 B:TYR110 4.6 42.6 1.0
N B:PRO111 4.6 36.2 1.0
CB B:PHE23 4.6 34.1 1.0
C B:PHE109 4.7 43.8 1.0
CA B:CYS26 4.8 31.2 1.0
O B:HOH306 4.9 46.3 1.0
O B:HOH380 4.9 47.2 1.0
N B:ASP112 5.0 32.5 1.0
O B:TYR107 5.0 31.7 1.0

Sodium binding site 5 out of 12 in 6tmy

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Sodium binding site 5 out of 12 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 Sodium with other atoms in the Na 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
C:Na201

b:36.5
occ:1.00
 O C:TYR27 2.3 30.5 1.0
O C:GLY31 2.3 41.7 1.0
OD2 C:ASP48 2.4 54.0 1.0
O C:GLY29 2.4 41.2 1.0
OD1 C:ASP48 2.5 52.0 1.0
CG C:ASP48 2.8 48.6 1.0
C C:GLY31 3.4 44.4 1.0
C C:TYR27 3.4 30.3 1.0
C C:GLY29 3.6 40.6 1.0
N C:GLY31 3.7 41.7 1.0
O C:HOH317 3.8 54.8 1.0
C C:TRP30 4.1 43.2 1.0
CA C:GLY31 4.1 41.3 1.0
CA C:TYR27 4.1 29.7 1.0
N C:GLY29 4.2 31.8 1.0
O C:HOH361 4.2 46.6 1.0
O1 C:PG4202 4.3 42.2 1.0
CB C:ASP48 4.3 32.6 1.0
C C:CYS28 4.4 34.5 1.0
CA C:TRP30 4.4 38.9 1.0
N C:TRP30 4.4 38.5 1.0
CB C:TYR27 4.5 30.0 1.0
N C:GLY32 4.5 42.1 1.0
N C:CYS28 4.5 27.6 1.0
O C:HOH352 4.5 52.9 1.0
CA C:GLY29 4.5 33.0 1.0
O C:CYS44 4.6 28.9 1.0
O C:TRP30 4.6 43.0 1.0
CA C:CYS28 4.6 28.4 1.0
CD1 C:TYR27 4.7 35.2 1.0
CA C:GLY32 4.8 42.0 1.0
O C:CYS28 4.9 34.8 1.0

Sodium binding site 6 out of 12 in 6tmy

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Sodium binding site 6 out of 12 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 Sodium with other atoms in the Na 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
C:Na206

b:74.7
occ:1.00
 O C:TYR110 2.4 61.1 1.0
O C:HOH340 2.4 53.7 1.0
O C:PHE23 2.7 37.8 1.0
O C:GLY25 2.8 37.7 1.0
O C:HOH306 3.0 36.1 1.0
C C:TYR110 3.3 60.9 1.0
CB C:TYR110 3.5 54.0 1.0
N C:TYR110 3.5 52.9 1.0
CA C:TYR110 3.6 53.8 1.0
C C:PHE23 3.6 38.8 1.0
C C:GLY25 4.0 38.5 1.0
CA C:PHE23 4.3 39.1 1.0
C C:TYR24 4.4 31.7 1.0
N C:GLY25 4.4 31.3 1.0
OD1 C:ASP112 4.5 81.5 1.0
N C:PRO111 4.5 59.9 1.0
C C:PHE109 4.6 54.8 1.0
N C:TYR24 4.6 30.3 1.0
CB C:PHE23 4.6 42.0 1.0
O C:TYR24 4.6 30.9 1.0
CG C:TYR110 4.6 54.1 1.0
CA C:GLY25 4.7 32.9 1.0
CD2 C:TYR110 4.8 54.4 1.0
CA C:TYR24 4.8 29.0 1.0

Sodium binding site 7 out of 12 in 6tmy

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Sodium binding site 7 out of 12 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 Sodium with other atoms in the Na 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
D:Na201

b:42.2
occ:1.00
 O D:GLY31 2.2 60.3 1.0
O D:TYR27 2.2 32.9 1.0
O D:GLY29 2.4 51.7 1.0
OD2 D:ASP48 2.5 55.0 1.0
O1 D:PG4202 2.5 60.3 1.0
OD1 D:ASP48 2.7 46.5 1.0
CG D:ASP48 2.9 46.9 1.0
O D:HOH313 3.0 50.3 1.0
C D:GLY31 3.3 60.2 1.0
C D:TYR27 3.4 32.3 1.0
C1 D:PG4202 3.6 58.5 1.0
N D:GLY31 3.6 58.9 1.0
C D:GLY29 3.7 52.5 1.0
C D:TRP30 4.0 63.3 1.0
CA D:TYR27 4.0 31.5 1.0
CA D:GLY31 4.0 58.2 1.0
CA D:TRP30 4.2 60.4 1.0
C D:CYS28 4.4 36.6 1.0
N D:GLY29 4.4 37.2 1.0
N D:GLY32 4.4 53.8 1.0
CB D:TYR27 4.4 33.4 1.0
CB D:ASP48 4.4 30.9 1.0
N D:TRP30 4.4 57.3 1.0
N D:CYS28 4.4 28.4 1.0
O D:TRP30 4.5 62.7 1.0
O D:CYS44 4.6 26.4 1.0
CA D:CYS28 4.6 29.4 1.0
O D:CYS28 4.6 34.5 1.0
CA D:GLY32 4.6 52.7 1.0
CD1 D:TYR27 4.7 39.2 1.0
CA D:GLY29 4.7 40.5 1.0
C2 D:PG4202 4.8 56.0 1.0

Sodium binding site 8 out of 12 in 6tmy

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Sodium binding site 8 out of 12 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 Sodium with other atoms in the Na binding site number 8 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:Na204

b:73.6
occ:1.00
 O D:HOH302 2.5 43.7 1.0
O D:HOH322 2.6 40.7 1.0
O D:GLY25 2.8 32.7 1.0
OD1 D:ASP112 3.3 69.4 1.0
O D:HOH340 3.5 51.2 1.0
O D:TYR110 3.9 34.4 1.0
C D:GLY25 4.0 33.4 1.0
CA D:CYS26 4.2 35.4 1.0
O D:CYS26 4.2 34.5 1.0
O D:PHE23 4.3 31.0 1.0
C D:CYS26 4.3 36.2 1.0
N D:CYS26 4.5 33.0 1.0
CG D:ASP112 4.6 69.6 1.0
SG D:CYS115 4.6 45.9 1.0
O D:HOH316 4.7 38.3 1.0
C D:TYR110 4.8 36.6 1.0
C D:PHE23 4.9 31.2 1.0
CB D:TYR110 4.9 34.7 1.0
O D:TYR24 4.9 28.7 1.0
CA D:ASP112 4.9 47.6 1.0
N D:ASP112 5.0 43.9 1.0

Sodium binding site 9 out of 12 in 6tmy

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Sodium binding site 9 out of 12 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 Sodium with other atoms in the Na binding site number 9 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:Na202

b:32.2
occ:1.00
 O E:TYR27 2.2 31.7 1.0
O E:GLY31 2.3 44.3 1.0
OD2 E:ASP48 2.4 46.0 1.0
O E:GLY29 2.5 35.8 1.0
OD1 E:ASP48 2.5 40.5 1.0
CG E:ASP48 2.8 39.6 1.0
C E:TYR27 3.4 31.5 1.0
O E:HOH344 3.4 52.8 1.0
C E:GLY31 3.4 46.3 1.0
C E:GLY29 3.6 36.6 1.0
N E:GLY31 3.7 43.3 1.0
C E:TRP30 4.0 45.4 1.0
CA E:TYR27 4.0 30.1 1.0
CA E:GLY31 4.1 43.6 1.0
N E:GLY29 4.2 27.1 1.0
O1 E:PG4203 4.3 44.3 1.0
C E:CYS28 4.3 30.7 1.0
CB E:ASP48 4.3 30.2 1.0
N E:CYS28 4.4 27.2 1.0
CA E:TRP30 4.4 41.4 1.0
CB E:TYR27 4.4 30.6 1.0
N E:TRP30 4.5 36.7 1.0
N E:GLY32 4.5 42.4 1.0
O E:CYS44 4.5 29.4 1.0
CA E:CYS28 4.5 27.3 1.0
O E:TRP30 4.6 44.7 1.0
CA E:GLY29 4.6 28.3 1.0
O E:HOH302 4.7 42.3 1.0
O E:CYS28 4.7 29.6 1.0
CD1 E:TYR27 4.7 35.0 1.0
CA E:GLY32 4.8 42.5 1.0
O E:HOH404 4.8 67.0 1.0

Sodium binding site 10 out of 12 in 6tmy

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Sodium binding site 10 out of 12 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 Sodium with other atoms in the Na binding site number 10 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:Na205

b:52.4
occ:1.00
 O E:HOH301 2.2 34.5 1.0
O E:HOH304 2.2 41.2 1.0
O E:HOH324 2.2 48.2 1.0
O E:GLY25 2.3 32.8 1.0
O E:HOH396 3.1 61.3 1.0
O E:PHE23 3.2 29.6 1.0
O E:TYR110 3.3 37.6 1.0
C E:GLY25 3.5 33.4 1.0
C E:PHE23 3.9 28.8 1.0
O E:HOH359 4.0 47.1 1.0
O E:TYR24 4.1 27.6 1.0
CB E:TYR110 4.2 33.2 1.0
OD1 E:ASP112 4.2 61.9 1.0
C E:TYR24 4.2 27.9 1.0
C E:TYR110 4.3 36.2 1.0
CA E:CYS26 4.3 35.5 1.0
N E:CYS26 4.3 33.7 1.0
N E:GLY25 4.4 28.2 1.0
C E:CYS26 4.4 35.5 1.0
CA E:GLY25 4.5 28.4 1.0
CA E:PHE23 4.5 22.5 1.0
O E:HOH333 4.5 39.7 1.0
O E:CYS26 4.6 34.1 1.0
CA E:TYR110 4.6 31.5 1.0
N E:TYR24 4.6 23.7 1.0
N E:TYR110 4.7 30.9 1.0
O E:CYS28 4.7 29.6 1.0
CA E:TYR24 5.0 23.3 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: Tue Oct 8 13:59:49 2024

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