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Sodium in PDB 9d03: Co-Crystal Structure of Circularly Permuted Human Taspase-1 Bound to Ligand SMDC1014689 1-(Ethenesulfonyl)-4-{[3-Fluoro-4- (Trifluoromethoxy)Phenyl]Methyl}Piperazine

Protein crystallography data

The structure of Co-Crystal Structure of Circularly Permuted Human Taspase-1 Bound to Ligand SMDC1014689 1-(Ethenesulfonyl)-4-{[3-Fluoro-4- (Trifluoromethoxy)Phenyl]Methyl}Piperazine, PDB code: 9d03 was solved by S.L.Delker, T.E.Edwards, J.Abendroth, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.83 / 2.45
Space group P 65
Cell size a, b, c (Å), α, β, γ (°) 60.33, 60.33, 316.67, 90, 90, 120
R / Rfree (%) 15.9 / 20.1

Other elements in 9d03:

The structure of Co-Crystal Structure of Circularly Permuted Human Taspase-1 Bound to Ligand SMDC1014689 1-(Ethenesulfonyl)-4-{[3-Fluoro-4- (Trifluoromethoxy)Phenyl]Methyl}Piperazine also contains other interesting chemical elements:

Fluorine (F) 8 atoms
Chlorine (Cl) 3 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Co-Crystal Structure of Circularly Permuted Human Taspase-1 Bound to Ligand SMDC1014689 1-(Ethenesulfonyl)-4-{[3-Fluoro-4- (Trifluoromethoxy)Phenyl]Methyl}Piperazine (pdb code 9d03). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Co-Crystal Structure of Circularly Permuted Human Taspase-1 Bound to Ligand SMDC1014689 1-(Ethenesulfonyl)-4-{[3-Fluoro-4- (Trifluoromethoxy)Phenyl]Methyl}Piperazine, PDB code: 9d03:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 9d03

Go back to Sodium Binding Sites List in 9d03
Sodium binding site 1 out of 2 in the Co-Crystal Structure of Circularly Permuted Human Taspase-1 Bound to Ligand SMDC1014689 1-(Ethenesulfonyl)-4-{[3-Fluoro-4- (Trifluoromethoxy)Phenyl]Methyl}Piperazine


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Co-Crystal Structure of Circularly Permuted Human Taspase-1 Bound to Ligand SMDC1014689 1-(Ethenesulfonyl)-4-{[3-Fluoro-4- (Trifluoromethoxy)Phenyl]Methyl}Piperazine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na401

b:30.6
occ:0.64
O A:SER244 2.2 53.7 1.0
O A:ALA249 2.3 50.3 1.0
O A:MET251 2.3 51.6 1.0
O A:GLU242 2.4 46.7 1.0
OG1 A:THR247 2.4 40.4 1.0
O A:THR247 2.6 41.7 1.0
C A:SER244 3.4 47.5 1.0
C A:MET251 3.4 49.4 1.0
C A:GLU242 3.5 46.6 1.0
C A:ALA249 3.5 36.9 1.0
C A:THR247 3.5 44.3 1.0
CB A:THR247 3.7 42.2 1.0
N A:THR247 3.8 47.3 1.0
CA A:THR247 3.9 46.8 1.0
N A:MET251 3.9 41.9 1.0
N A:ALA249 4.0 37.0 1.0
O A:LEU241 4.0 44.2 1.0
N A:SER244 4.1 45.5 1.0
CA A:GLU242 4.1 38.0 1.0
CA A:MET251 4.2 51.2 1.0
C A:GLY250 4.2 40.0 1.0
CA A:SER244 4.3 47.2 1.0
N A:PRO245 4.3 49.8 1.0
CA A:ALA249 4.3 35.6 1.0
CA A:PRO245 4.3 50.2 1.0
C A:PRO245 4.4 55.0 1.0
C A:ASP243 4.4 46.2 1.0
N A:GLY252 4.5 51.8 1.0
N A:GLY250 4.5 38.4 1.0
N A:ASP243 4.5 41.9 1.0
CB A:MET251 4.6 56.4 1.0
CA A:GLY250 4.6 38.0 1.0
CA A:GLY252 4.6 51.2 1.0
N A:ASN248 4.7 39.8 1.0
N A:PHE246 4.7 53.9 1.0
O A:GLY250 4.7 42.7 1.0
CG2 A:THR247 4.7 41.5 1.0
CB A:SER244 4.8 46.5 1.0
C A:GLY252 4.8 50.5 1.0
O A:PRO245 4.8 58.9 1.0
CA A:ASP243 4.8 44.5 1.0
CB A:ALA249 4.9 34.4 1.0
O A:ASP243 4.9 48.4 1.0
C A:PHE246 4.9 47.4 1.0
N A:SER253 4.9 47.7 1.0
C A:LEU241 5.0 46.5 1.0

Sodium binding site 2 out of 2 in 9d03

Go back to Sodium Binding Sites List in 9d03
Sodium binding site 2 out of 2 in the Co-Crystal Structure of Circularly Permuted Human Taspase-1 Bound to Ligand SMDC1014689 1-(Ethenesulfonyl)-4-{[3-Fluoro-4- (Trifluoromethoxy)Phenyl]Methyl}Piperazine


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Co-Crystal Structure of Circularly Permuted Human Taspase-1 Bound to Ligand SMDC1014689 1-(Ethenesulfonyl)-4-{[3-Fluoro-4- (Trifluoromethoxy)Phenyl]Methyl}Piperazine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na401

b:52.2
occ:1.00
O B:ALA249 2.2 59.0 1.0
O B:MET251 2.2 52.6 1.0
O B:SER244 2.4 63.2 1.0
OG1 B:THR247 2.5 41.0 1.0
O B:THR247 2.5 41.5 1.0
O B:GLU242 2.5 48.6 1.0
C B:ALA249 3.3 44.5 1.0
C B:THR247 3.4 49.7 1.0
C B:MET251 3.4 49.4 1.0
C B:SER244 3.5 63.9 1.0
C B:GLU242 3.6 41.6 1.0
CB B:THR247 3.7 47.7 1.0
N B:ALA249 3.7 44.4 1.0
N B:THR247 3.8 46.8 1.0
CA B:THR247 3.8 51.7 1.0
N B:MET251 4.0 45.2 1.0
CA B:ALA249 4.0 43.9 1.0
O B:LEU241 4.1 50.6 1.0
CA B:GLU242 4.2 37.9 1.0
C B:GLY250 4.2 46.6 1.0
CA B:MET251 4.2 44.1 1.0
N B:SER244 4.3 55.3 1.0
CA B:PRO245 4.3 57.5 1.0
N B:PRO245 4.4 62.8 1.0
N B:GLY252 4.4 49.8 1.0
N B:GLY250 4.4 37.1 1.0
C B:PRO245 4.4 60.5 1.0
CA B:SER244 4.5 56.3 1.0
CA B:GLY252 4.5 50.1 1.0
N B:ASN248 4.5 43.2 1.0
O B:GLY250 4.5 48.5 1.0
CB B:ALA249 4.6 39.3 1.0
C B:GLY252 4.6 53.1 1.0
C B:ASP243 4.6 59.5 1.0
CA B:GLY250 4.6 44.5 1.0
N B:ASP243 4.7 45.6 1.0
O B:PRO245 4.8 63.0 1.0
C B:ASN248 4.8 39.8 1.0
CB B:MET251 4.8 47.2 1.0
CG2 B:THR247 4.8 46.1 1.0
N B:SER253 4.8 40.7 1.0
N B:PHE246 4.8 63.0 1.0
CB B:SER244 4.9 50.4 1.0
CA B:ASN248 5.0 39.4 1.0
C B:PHE246 5.0 59.9 1.0

Reference:

S.L.Delker, T.E.Edwards, J.Abendroth. Co-Crystal Structure of Circularly Permuted Human Taspase-1 Bound to Ligand SMDC1014689 1-(Ethenesulfonyl)-4-{[3-Fluoro-4-(Trifluoromethoxy) Phenyl]Methyl}Piperazine To Be Published.
Page generated: Mon Aug 18 16:39:59 2025

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