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Sodium in PDB 6ooi: Crystal Structure of Triosephosphate Isomerase From Schistosoma Mansoni in Complex with 2PG

Enzymatic activity of Crystal Structure of Triosephosphate Isomerase From Schistosoma Mansoni in Complex with 2PG

All present enzymatic activity of Crystal Structure of Triosephosphate Isomerase From Schistosoma Mansoni in Complex with 2PG:
5.3.1.1;

Protein crystallography data

The structure of Crystal Structure of Triosephosphate Isomerase From Schistosoma Mansoni in Complex with 2PG, PDB code: 6ooi was solved by P.Jimenez-Sandoval, L.Brieba, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 58.61 / 2.14
Space group P 43
Cell size a, b, c (Å), α, β, γ (°) 108.050, 108.050, 182.720, 90.00, 90.00, 90.00
R / Rfree (%) 18.1 / 22.9

Other elements in 6ooi:

The structure of Crystal Structure of Triosephosphate Isomerase From Schistosoma Mansoni in Complex with 2PG also contains other interesting chemical elements:

Chlorine (Cl) 6 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Triosephosphate Isomerase From Schistosoma Mansoni in Complex with 2PG (pdb code 6ooi). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 8 binding sites of Sodium where determined in the Crystal Structure of Triosephosphate Isomerase From Schistosoma Mansoni in Complex with 2PG, PDB code: 6ooi:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Sodium binding site 1 out of 8 in 6ooi

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Sodium binding site 1 out of 8 in the Crystal Structure of Triosephosphate Isomerase From Schistosoma Mansoni in Complex with 2PG


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 Triosephosphate Isomerase From Schistosoma Mansoni in Complex with 2PG within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na303

b:17.0
occ:1.00
 OD1 A:ASN202 2.8 30.4 1.0
O A:ALA200 2.9 17.7 1.0
O A:LYS197 3.1 22.9 1.0
N A:ASN202 3.7 25.3 1.0
CA A:ASN202 3.9 22.5 1.0
CG A:ASN202 3.9 34.3 1.0
C A:PRO201 4.0 26.6 1.0
C A:ALA200 4.1 24.7 1.0
O A:HOH421 4.2 21.8 1.0
C A:LYS197 4.3 26.6 1.0
O A:THR198 4.4 27.8 1.0
CA A:PRO201 4.4 21.9 1.0
O A:PRO201 4.5 23.2 1.0
O A:HOH446 4.5 18.2 1.0
CB A:ASN202 4.6 29.8 1.0
C A:THR198 4.6 24.2 1.0
O A:PHE196 4.7 21.5 1.0
N A:PRO201 4.8 22.0 1.0
N A:ALA200 4.9 23.5 1.0

Sodium binding site 2 out of 8 in 6ooi

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Sodium binding site 2 out of 8 in the Crystal Structure of Triosephosphate Isomerase From Schistosoma Mansoni in Complex with 2PG


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 Triosephosphate Isomerase From Schistosoma Mansoni in Complex with 2PG within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na304

b:9.1
occ:1.00
 O A:LYS54 2.8 29.4 1.0
O A:LEU56 2.9 22.0 1.0
O A:ARG53 3.1 25.5 1.0
C A:LYS54 3.6 26.1 1.0
C A:LEU56 4.0 18.8 1.0
CA A:LYS54 4.2 26.3 1.0
C A:ARG53 4.2 23.1 1.0
N A:LEU56 4.4 24.8 1.0
C A:SER55 4.5 27.8 1.0
N A:SER55 4.5 22.1 1.0
NH2 A:ARG53 4.5 22.0 1.0
NE A:ARG53 4.6 20.2 1.0
N A:LYS54 4.7 19.8 1.0
N A:LYS58 4.8 26.6 1.0
O A:SER55 4.8 32.2 1.0
N A:LYS57 4.8 20.9 1.0
CA A:LEU56 4.8 25.8 1.0
CA A:LYS57 4.8 27.4 1.0
CA A:SER55 4.9 26.0 1.0
C A:LYS57 4.9 25.8 1.0

Sodium binding site 3 out of 8 in 6ooi

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Sodium binding site 3 out of 8 in the Crystal Structure of Triosephosphate Isomerase From Schistosoma Mansoni in Complex with 2PG


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 Triosephosphate Isomerase From Schistosoma Mansoni in Complex with 2PG within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na303

b:18.2
occ:1.00
 O B:ALA200 2.8 25.4 1.0
O B:LYS197 3.0 26.9 1.0
OD1 B:ASN202 3.0 34.1 1.0
O B:HOH525 3.3 28.9 1.0
O B:HOH532 3.8 25.2 1.0
N B:ASN202 4.0 25.2 1.0
C B:ALA200 4.0 21.7 1.0
O B:HOH531 4.0 32.6 1.0
O B:HOH520 4.1 26.4 1.0
C B:PRO201 4.1 27.1 1.0
C B:LYS197 4.1 29.6 1.0
CG B:ASN202 4.1 42.7 1.0
O B:THR198 4.1 31.5 1.0
CA B:ASN202 4.2 24.2 1.0
C B:THR198 4.3 29.7 1.0
O B:HOH469 4.4 23.3 1.0
CA B:PRO201 4.4 21.8 1.0
O B:PRO201 4.5 21.2 1.0
CA B:THR198 4.5 24.1 1.0
N B:PRO201 4.7 24.0 1.0
O B:HOH510 4.7 29.8 1.0
N B:THR198 4.8 23.9 1.0
N B:ALA200 4.8 23.5 1.0
CB B:ASN202 4.8 30.6 1.0
N B:ASN199 5.0 25.1 1.0
O B:PHE196 5.0 25.9 1.0

Sodium binding site 4 out of 8 in 6ooi

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Sodium binding site 4 out of 8 in the Crystal Structure of Triosephosphate Isomerase From Schistosoma Mansoni in Complex with 2PG


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 Triosephosphate Isomerase From Schistosoma Mansoni in Complex with 2PG within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na304

b:13.1
occ:1.00
 O C:LYS54 3.0 28.7 1.0
O C:LEU56 3.0 29.4 1.0
O C:ARG53 3.1 22.0 1.0
C C:LYS54 3.6 24.2 1.0
O C:HOH532 3.9 33.6 1.0
C C:LEU56 4.0 28.2 1.0
O C:HOH505 4.0 29.0 1.0
CA C:LYS54 4.1 24.7 1.0
C C:ARG53 4.2 26.5 1.0
N C:LEU56 4.5 27.0 1.0
N C:SER55 4.6 23.5 1.0
N C:LYS58 4.6 26.8 1.0
N C:LYS54 4.6 24.2 1.0
C C:SER55 4.7 31.1 1.0
NE C:ARG53 4.7 21.3 1.0
NH2 C:ARG53 4.8 25.0 1.0
C C:LYS57 4.8 30.8 1.0
N C:LYS57 4.8 28.8 1.0
CA C:LYS57 4.8 27.0 1.0
CA C:LEU56 4.9 29.1 1.0
CA C:SER55 5.0 32.6 1.0

Sodium binding site 5 out of 8 in 6ooi

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Sodium binding site 5 out of 8 in the Crystal Structure of Triosephosphate Isomerase From Schistosoma Mansoni in Complex with 2PG


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 Triosephosphate Isomerase From Schistosoma Mansoni in Complex with 2PG within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na305

b:25.2
occ:1.00
 NH2 C:ARG251 2.5 36.5 1.0
O C:GLN227 2.9 30.1 1.0
O C:VAL230 3.2 26.3 1.0
CZ C:ARG251 3.3 37.0 1.0
O C:ALA225 3.4 32.3 1.0
O C:HIS228 3.6 24.7 1.0
NE C:ARG251 3.7 33.9 1.0
C C:GLN227 4.0 29.9 1.0
C C:HIS228 4.1 32.9 1.0
NH1 C:ARG251 4.2 34.0 1.0
C C:VAL230 4.3 29.4 1.0
CA C:HIS228 4.3 30.6 1.0
C C:ALA225 4.5 28.7 1.0
N C:VAL230 4.6 27.6 1.0
N C:HIS228 4.6 28.8 1.0
C C:GLN226 4.8 30.6 1.0
O C:GLN226 4.9 37.6 1.0
N C:ASP229 4.9 27.4 1.0
CA C:VAL230 5.0 23.6 1.0
N C:GLN227 5.0 27.2 1.0
CD C:ARG251 5.0 34.0 1.0

Sodium binding site 6 out of 8 in 6ooi

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Sodium binding site 6 out of 8 in the Crystal Structure of Triosephosphate Isomerase From Schistosoma Mansoni in Complex with 2PG


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 Triosephosphate Isomerase From Schistosoma Mansoni in Complex with 2PG within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Na302

b:25.1
occ:1.00
 O E:GLN227 2.8 35.8 1.0
O E:ALA225 3.1 35.1 1.0
O E:VAL230 3.2 29.1 1.0
O E:HIS228 3.6 33.9 1.0
C E:GLN227 3.9 37.1 1.0
O E:GLN226 4.0 42.9 1.0
C E:HIS228 4.0 34.6 1.0
CA E:HIS228 4.2 34.7 1.0
C E:GLN226 4.3 40.1 1.0
C E:ALA225 4.3 41.1 1.0
C E:VAL230 4.3 27.6 1.0
N E:HIS228 4.5 32.8 1.0
N E:VAL230 4.6 32.0 1.0
N E:GLN227 4.7 34.9 1.0
CA E:GLN226 4.7 36.8 1.0
N E:ASP229 4.9 31.5 1.0
CA E:VAL230 5.0 29.1 1.0
CA E:GLN227 5.0 37.6 1.0
N E:GLN226 5.0 33.8 1.0

Sodium binding site 7 out of 8 in 6ooi

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Sodium binding site 7 out of 8 in the Crystal Structure of Triosephosphate Isomerase From Schistosoma Mansoni in Complex with 2PG


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 Triosephosphate Isomerase From Schistosoma Mansoni in Complex with 2PG within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Na303

b:21.8
occ:1.00
 O E:LEU56 2.7 39.9 1.0
O E:LYS54 3.1 36.7 1.0
O E:ARG53 3.1 26.8 1.0
C E:LYS54 3.8 31.6 1.0
C E:LEU56 3.8 37.0 1.0
CA E:LYS54 4.3 31.2 1.0
C E:ARG53 4.3 30.4 1.0
N E:LEU56 4.3 31.5 1.0
N E:LYS58 4.5 31.9 1.0
N E:SER55 4.5 34.0 1.0
NH2 E:ARG53 4.6 35.2 1.0
C E:SER55 4.6 35.3 1.0
NE E:ARG53 4.7 27.7 1.0
N E:LYS57 4.7 31.2 1.0
CA E:LYS57 4.7 36.6 1.0
CA E:LEU56 4.7 36.3 1.0
C E:LYS57 4.7 34.2 1.0
N E:LYS54 4.8 28.2 1.0
CA E:SER55 5.0 37.3 1.0

Sodium binding site 8 out of 8 in 6ooi

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Sodium binding site 8 out of 8 in the Crystal Structure of Triosephosphate Isomerase From Schistosoma Mansoni in Complex with 2PG


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 Triosephosphate Isomerase From Schistosoma Mansoni in Complex with 2PG within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Na303

b:10.4
occ:1.00
 O H:LEU56 2.9 24.6 1.0
O H:LYS54 3.0 25.9 1.0
O H:ARG53 3.1 21.1 1.0
C H:LYS54 3.7 25.1 1.0
C H:LEU56 3.9 21.2 1.0
O H:HOH504 4.0 24.3 1.0
CA H:LYS54 4.3 22.1 1.0
C H:ARG53 4.3 23.1 1.0
N H:LEU56 4.4 27.5 1.0
C H:SER55 4.5 30.0 1.0
N H:LYS58 4.6 21.1 1.0
N H:SER55 4.6 20.5 1.0
NE H:ARG53 4.6 21.6 1.0
CA H:LYS57 4.7 24.5 1.0
N H:LYS57 4.7 23.7 1.0
C H:LYS57 4.7 23.3 1.0
NH2 H:ARG53 4.8 20.2 1.0
O H:SER55 4.8 26.6 1.0
CA H:LEU56 4.8 27.7 1.0
N H:LYS54 4.8 18.9 1.0
CA H:SER55 4.9 27.5 1.0

Reference:

P.Jimenez-Sandoval, L.Brieba. Crystal Structures of Triosephosphate Isomerases From Taenia Solium and Schistosoma Mansoni Provide Insights For Rationale Vaccine and Drug Design Against Helminth Parasites To Be Published.
Page generated: Tue Oct 8 12:34:16 2024

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