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Sodium in PDB 3c17: Hexagonal Crystal Structure of Precursor E. Coli Isoaspartyl Peptidase/L-Asparaginase (Ecaiii) with Active-Site T179A Mutation

Enzymatic activity of Hexagonal Crystal Structure of Precursor E. Coli Isoaspartyl Peptidase/L-Asparaginase (Ecaiii) with Active-Site T179A Mutation

All present enzymatic activity of Hexagonal Crystal Structure of Precursor E. Coli Isoaspartyl Peptidase/L-Asparaginase (Ecaiii) with Active-Site T179A Mutation:
3.4.19.5; 3.5.1.1;

Protein crystallography data

The structure of Hexagonal Crystal Structure of Precursor E. Coli Isoaspartyl Peptidase/L-Asparaginase (Ecaiii) with Active-Site T179A Mutation, PDB code: 3c17 was solved by K.Michalska, A.Hernandez-Santoyo, M.Jaskolski, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 44.51 / 1.95
Space group P 61 2 2
Cell size a, b, c (Å), α, β, γ (°) 149.470, 149.470, 214.350, 90.00, 90.00, 120.00
R / Rfree (%) 18.4 / 20.3

Other elements in 3c17:

The structure of Hexagonal Crystal Structure of Precursor E. Coli Isoaspartyl Peptidase/L-Asparaginase (Ecaiii) with Active-Site T179A Mutation also contains other interesting chemical elements:

Chlorine (Cl) 17 atoms

Sodium Binding Sites:

Pages:

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

Binding sites:

The binding sites of Sodium atom in the Hexagonal Crystal Structure of Precursor E. Coli Isoaspartyl Peptidase/L-Asparaginase (Ecaiii) with Active-Site T179A Mutation (pdb code 3c17). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 11 binding sites of Sodium where determined in the Hexagonal Crystal Structure of Precursor E. Coli Isoaspartyl Peptidase/L-Asparaginase (Ecaiii) with Active-Site T179A Mutation, PDB code: 3c17:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Sodium binding site 1 out of 11 in 3c17

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Sodium binding site 1 out of 11 in the Hexagonal Crystal Structure of Precursor E. Coli Isoaspartyl Peptidase/L-Asparaginase (Ecaiii) with Active-Site T179A Mutation


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Hexagonal Crystal Structure of Precursor E. Coli Isoaspartyl Peptidase/L-Asparaginase (Ecaiii) with Active-Site T179A Mutation within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1

b:25.1
occ:1.00
 O A:ILE70 2.2 34.0 1.0
O A:ALA68 2.2 33.4 1.0
O A:CYS63 2.3 34.1 1.0
O A:GLU61 2.5 34.7 1.0
O A:PHE66 2.6 34.6 1.0
O A:LEU60 2.9 34.8 1.0
C A:GLU61 3.2 34.0 1.0
C A:ILE70 3.3 33.9 1.0
C A:CYS63 3.4 35.2 1.0
C A:ALA68 3.5 34.2 1.0
CA A:GLU61 3.6 34.8 1.0
C A:PHE66 3.7 35.1 1.0
N A:CYS63 3.9 35.6 1.0
C A:LEU60 3.9 34.3 1.0
N A:ALA68 3.9 35.2 1.0
N A:ILE70 4.0 34.0 1.0
N A:PHE66 4.2 34.4 1.0
CA A:ILE70 4.2 34.1 1.0
C A:GLY69 4.2 32.9 1.0
CA A:CYS63 4.2 35.9 1.0
N A:GLU61 4.2 34.5 1.0
CA A:PRO64 4.2 35.0 1.0
N A:PRO64 4.2 35.1 1.0
N A:GLU62 4.3 34.5 1.0
CA A:PHE66 4.3 34.4 1.0
CA A:ALA68 4.3 34.6 1.0
C A:GLU62 4.3 35.4 1.0
N A:GLY71 4.3 32.6 1.0
CB A:PHE66 4.4 35.0 1.0
CA A:GLY71 4.5 32.6 1.0
N A:GLY69 4.5 33.7 1.0
C A:PRO64 4.5 34.9 1.0
CA A:GLY69 4.6 33.9 1.0
CB A:ILE70 4.6 35.5 1.0
O A:GLY69 4.6 33.4 1.0
CB A:ALA68 4.7 34.7 1.0
CA A:GLU62 4.8 35.3 1.0
N A:ASN67 4.8 35.2 1.0
CB A:CYS63 4.8 35.9 1.0
O A:GLU62 4.8 35.9 1.0
O A:PRO64 4.9 35.1 1.0
C A:GLY71 4.9 32.5 1.0
CB A:GLU61 4.9 34.3 1.0
N A:LEU65 4.9 34.3 1.0
C A:ASN67 5.0 35.5 1.0

Sodium binding site 2 out of 11 in 3c17

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Sodium binding site 2 out of 11 in the Hexagonal Crystal Structure of Precursor E. Coli Isoaspartyl Peptidase/L-Asparaginase (Ecaiii) with Active-Site T179A Mutation


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Hexagonal Crystal Structure of Precursor E. Coli Isoaspartyl Peptidase/L-Asparaginase (Ecaiii) with Active-Site T179A Mutation within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na322

b:38.0
occ:1.00
 O A:HOH529 2.2 43.9 1.0
O A:HOH528 2.3 39.0 1.0
O A:PHE290 2.5 31.4 1.0
O A:THR292 2.5 32.5 1.0
O A:HOH459 2.5 37.4 1.0
CD2 A:PHE290 3.4 30.6 1.0
C A:PHE290 3.6 31.5 1.0
CE2 A:PHE290 3.7 32.8 1.0
C A:THR292 3.7 31.9 1.0
C A:ASN291 3.9 31.7 1.0
O A:HOH428 4.0 41.0 1.0
N A:THR292 4.1 32.3 1.0
CA A:ASN291 4.1 31.6 1.0
CG A:PHE290 4.2 32.5 1.0
N A:ASN291 4.2 31.8 1.0
O A:HOH530 4.3 30.7 1.0
O A:ASN291 4.3 31.4 1.0
O A:HOH518 4.5 36.4 1.0
CA A:THR292 4.5 31.9 1.0
O A:GLU293 4.6 34.5 1.0
CZ A:PHE290 4.6 31.5 1.0
CA A:PHE290 4.6 32.3 1.0
N A:GLU293 4.6 32.4 1.0
CA A:GLU293 4.6 32.4 1.0
C A:GLU293 4.7 33.1 1.0
CB A:PHE290 4.7 32.4 1.0
O A:HOH444 4.9 46.3 1.0
CE A:MET265 5.0 38.3 1.0
N A:PHE290 5.0 32.8 1.0

Sodium binding site 3 out of 11 in 3c17

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Sodium binding site 3 out of 11 in the Hexagonal Crystal Structure of Precursor E. Coli Isoaspartyl Peptidase/L-Asparaginase (Ecaiii) with Active-Site T179A Mutation


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Hexagonal Crystal Structure of Precursor E. Coli Isoaspartyl Peptidase/L-Asparaginase (Ecaiii) with Active-Site T179A Mutation within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na323

b:28.6
occ:1.00
 O A:HIS119 2.3 31.9 1.0
O A:HOH426 2.4 32.7 1.0
O A:SER117 2.4 34.7 1.0
O A:HOH412 2.5 34.7 1.0
O A:VAL113 2.7 33.6 1.0
O A:MET114 2.7 34.2 1.0
C A:MET114 3.3 36.0 1.0
N A:HIS119 3.3 32.7 1.0
C A:HIS119 3.3 32.9 1.0
CA A:MET114 3.4 35.6 1.0
C A:SER117 3.5 34.5 1.0
C A:VAL113 3.6 34.1 1.0
C A:PRO118 3.7 34.1 1.0
OG A:SER117 3.7 34.9 1.0
O A:HOH460 3.8 44.5 1.0
CA A:HIS119 3.9 32.8 1.0
N A:MET114 4.0 34.8 1.0
CA A:PRO118 4.1 34.7 1.0
N A:PRO118 4.2 34.9 1.0
CE A:LYS93 4.3 40.0 1.0
O A:PRO118 4.3 34.4 1.0
CA A:SER117 4.4 34.9 1.0
NZ A:LYS93 4.4 40.5 1.0
CL B:CL333 4.4 45.6 1.0
N A:SER117 4.4 35.1 1.0
N A:GLU115 4.5 36.8 1.0
O A:ALA94 4.5 33.9 1.0
N A:VAL120 4.5 33.0 1.0
CB A:MET114 4.7 36.0 1.0
CB A:SER117 4.7 34.9 1.0
O A:HOH354 4.9 38.7 1.0
CA A:VAL120 4.9 33.1 1.0
CG1 A:VAL113 4.9 31.2 1.0
CG A:MET114 5.0 39.2 1.0
CA A:VAL113 5.0 33.6 1.0

Sodium binding site 4 out of 11 in 3c17

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Sodium binding site 4 out of 11 in the Hexagonal Crystal Structure of Precursor E. Coli Isoaspartyl Peptidase/L-Asparaginase (Ecaiii) with Active-Site T179A Mutation


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Hexagonal Crystal Structure of Precursor E. Coli Isoaspartyl Peptidase/L-Asparaginase (Ecaiii) with Active-Site T179A Mutation within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na324

b:26.7
occ:1.00
 O A:HOH375 2.3 23.5 1.0
O A:LYS176 2.3 35.2 1.0
O A:HOH374 2.3 27.1 1.0
O A:GLY231 2.4 37.5 1.0
CL A:CL330 2.7 31.7 1.0
C A:LYS176 3.5 35.0 1.0
C A:GLY231 3.5 36.3 1.0
N A:GLY231 3.8 35.7 1.0
O A:HOH363 3.8 27.6 1.0
O A:GLY178 4.0 35.7 1.0
OD1 A:ASP210 4.0 35.7 1.0
CA A:GLY231 4.2 36.3 1.0
CA A:MET177 4.3 35.8 1.0
N A:MET177 4.3 35.2 1.0
CA A:LYS176 4.4 35.6 1.0
CB A:LYS176 4.4 35.3 1.0
N A:GLY233 4.5 38.5 1.0
C A:MET177 4.5 36.2 1.0
O A:HOH366 4.6 24.2 1.0
N A:THR232 4.6 36.5 1.0
CB A:ALA179 4.7 33.3 1.0
O A:GLY199 4.7 37.4 1.0
N A:GLY178 4.8 35.8 1.0
OG A:SER211 4.8 37.6 1.0
C A:GLY178 4.8 34.7 1.0
CA A:GLY233 4.9 37.4 1.0
CA A:THR232 4.9 37.1 1.0
C A:THR230 4.9 35.4 1.0
OG1 A:THR230 5.0 38.0 1.0
OG1 A:THR197 5.0 33.5 1.0
O A:MET177 5.0 36.2 1.0

Sodium binding site 5 out of 11 in 3c17

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Sodium binding site 5 out of 11 in the Hexagonal Crystal Structure of Precursor E. Coli Isoaspartyl Peptidase/L-Asparaginase (Ecaiii) with Active-Site T179A Mutation


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Hexagonal Crystal Structure of Precursor E. Coli Isoaspartyl Peptidase/L-Asparaginase (Ecaiii) with Active-Site T179A Mutation within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na325

b:54.5
occ:1.00
 O A:HOH538 2.2 55.4 1.0
O A:HOH537 2.3 38.4 1.0
O A:HOH536 2.4 48.5 1.0
O A:HOH535 2.7 44.9 1.0
O B:HOH512 2.7 37.7 1.0
O B:HOH442 2.8 37.9 1.0
OD2 A:ASP250 4.0 43.0 1.0
ND2 A:ASN221 4.0 31.9 1.0
O A:HOH423 4.2 41.2 1.0
O A:HOH524 4.2 37.8 1.0
O A:HOH483 4.5 40.1 1.0
OD1 A:ASN221 4.6 33.7 1.0
CB A:ALA223 4.6 33.3 1.0
O A:HOH445 4.7 37.9 1.0
O A:HOH462 4.7 44.3 1.0
NZ B:LYS267 4.7 36.1 1.0
CG A:ASN221 4.7 33.2 1.0
CG A:ASP250 4.9 39.5 1.0
CL B:CL334 4.9 43.9 1.0
CE B:LYS267 5.0 39.0 1.0

Sodium binding site 6 out of 11 in 3c17

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Sodium binding site 6 out of 11 in the Hexagonal Crystal Structure of Precursor E. Coli Isoaspartyl Peptidase/L-Asparaginase (Ecaiii) with Active-Site T179A Mutation


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Hexagonal Crystal Structure of Precursor E. Coli Isoaspartyl Peptidase/L-Asparaginase (Ecaiii) with Active-Site T179A Mutation within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na322

b:29.8
occ:1.00
 O B:ILE70 2.2 34.4 1.0
O B:ALA68 2.3 33.4 1.0
O B:CYS63 2.3 34.7 1.0
O B:PHE66 2.6 33.3 1.0
O B:GLU61 2.6 36.6 1.0
O B:LEU60 2.8 35.1 1.0
C B:GLU61 3.3 35.5 1.0
C B:CYS63 3.3 36.3 1.0
C B:ILE70 3.4 34.0 1.0
C B:ALA68 3.5 34.3 1.0
CA B:GLU61 3.6 35.2 1.0
C B:PHE66 3.7 34.0 1.0
N B:ALA68 3.9 34.2 1.0
C B:LEU60 3.9 34.5 1.0
N B:CYS63 3.9 36.7 1.0
N B:ILE70 4.0 34.5 1.0
N B:PHE66 4.1 34.1 1.0
N B:PRO64 4.2 36.2 1.0
CA B:CYS63 4.2 36.9 1.0
CA B:PRO64 4.2 36.1 1.0
CA B:ILE70 4.2 34.4 1.0
N B:GLU61 4.2 35.0 1.0
CA B:ALA68 4.2 33.6 1.0
C B:GLY69 4.3 34.5 1.0
CA B:PHE66 4.3 34.4 1.0
C B:GLU62 4.3 36.3 1.0
N B:GLU62 4.3 35.3 1.0
N B:GLY71 4.3 33.4 1.0
CA B:GLY71 4.5 33.3 1.0
CB B:PHE66 4.5 35.2 1.0
N B:GLY69 4.5 34.1 1.0
C B:PRO64 4.5 35.7 1.0
CA B:GLY69 4.7 34.4 1.0
CB B:ALA68 4.7 33.0 1.0
CB B:ILE70 4.7 34.8 1.0
O B:GLY69 4.7 35.1 1.0
N B:ASN67 4.7 33.8 1.0
CB B:CYS63 4.8 37.6 1.0
O B:GLU62 4.8 35.6 1.0
CA B:GLU62 4.8 36.2 1.0
C B:GLY71 4.9 32.8 1.0
N B:LEU65 4.9 34.5 1.0
O B:PRO64 4.9 35.2 1.0
C B:ASN67 4.9 32.8 1.0
CB B:GLU61 4.9 35.8 1.0

Sodium binding site 7 out of 11 in 3c17

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Sodium binding site 7 out of 11 in the Hexagonal Crystal Structure of Precursor E. Coli Isoaspartyl Peptidase/L-Asparaginase (Ecaiii) with Active-Site T179A Mutation


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of Hexagonal Crystal Structure of Precursor E. Coli Isoaspartyl Peptidase/L-Asparaginase (Ecaiii) with Active-Site T179A Mutation within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na323

b:48.0
occ:1.00
 O B:HOH390 2.4 35.1 1.0
O B:HOH493 2.4 44.3 1.0
O B:HOH389 2.4 34.5 1.0
O B:HOH491 2.5 35.9 1.0
O A:HOH448 2.6 38.9 1.0
O B:HOH388 2.6 42.6 1.0
OD2 B:ASP250 3.9 38.3 1.0
O B:HOH495 4.2 54.5 1.0
ND2 B:ASN221 4.3 36.6 1.0
CL A:CL326 4.3 44.8 1.0
O B:HOH454 4.4 34.6 1.0
O B:HOH451 4.4 41.7 1.0
O B:HOH494 4.7 48.9 1.0
CE A:LYS267 4.7 40.8 1.0
CB B:ALA223 4.7 34.1 1.0
NZ A:LYS267 4.7 38.8 1.0
O B:HOH393 4.7 36.5 1.0
O B:HOH366 4.8 38.1 1.0
OD1 B:ASN221 4.9 35.0 1.0
CL A:CL333 5.0 35.8 1.0
CG B:ASP250 5.0 38.0 1.0

Sodium binding site 8 out of 11 in 3c17

Go back to Sodium Binding Sites List in 3c17
Sodium binding site 8 out of 11 in the Hexagonal Crystal Structure of Precursor E. Coli Isoaspartyl Peptidase/L-Asparaginase (Ecaiii) with Active-Site T179A Mutation


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of Hexagonal Crystal Structure of Precursor E. Coli Isoaspartyl Peptidase/L-Asparaginase (Ecaiii) with Active-Site T179A Mutation within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na324

b:31.9
occ:1.00
 O B:SER117 2.3 34.6 1.0
O B:HOH443 2.3 37.9 1.0
O B:HIS119 2.4 33.5 1.0
O B:VAL113 2.6 34.7 1.0
O B:MET114 2.6 33.4 1.0
O B:HOH383 2.8 33.0 1.0
C B:MET114 3.3 34.7 1.0
N B:HIS119 3.3 34.5 1.0
C B:SER117 3.3 35.0 1.0
CA B:MET114 3.4 34.1 1.0
C B:HIS119 3.4 33.8 1.0
OG B:SER117 3.6 33.7 1.0
C B:VAL113 3.6 33.2 1.0
O B:HOH357 3.6 44.1 1.0
C B:PRO118 3.7 34.9 1.0
CA B:HIS119 3.9 34.5 1.0
N B:MET114 4.0 33.5 1.0
CA B:PRO118 4.0 34.7 1.0
N B:PRO118 4.1 34.7 1.0
CA B:SER117 4.3 35.4 1.0
N B:SER117 4.3 36.0 1.0
O B:PRO118 4.4 34.7 1.0
N B:GLU115 4.4 35.2 1.0
CE B:LYS93 4.5 35.8 1.0
CB B:SER117 4.5 35.2 1.0
CL A:CL331 4.5 46.8 1.0
N B:VAL120 4.6 33.0 1.0
O B:ALA94 4.6 33.0 1.0
CB B:MET114 4.7 34.7 1.0
NZ B:LYS93 4.8 32.6 1.0
CA B:VAL113 4.9 32.8 1.0
CA B:VAL120 4.9 32.3 1.0
O B:HOH488 5.0 45.0 1.0
CG1 B:VAL113 5.0 32.7 1.0
CG B:MET114 5.0 37.3 1.0

Sodium binding site 9 out of 11 in 3c17

Go back to Sodium Binding Sites List in 3c17
Sodium binding site 9 out of 11 in the Hexagonal Crystal Structure of Precursor E. Coli Isoaspartyl Peptidase/L-Asparaginase (Ecaiii) with Active-Site T179A Mutation


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 9 of Hexagonal Crystal Structure of Precursor E. Coli Isoaspartyl Peptidase/L-Asparaginase (Ecaiii) with Active-Site T179A Mutation within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na325

b:28.5
occ:1.00
 O B:LYS176 2.1 36.8 1.0
O B:GLY231 2.3 35.1 1.0
O B:HOH378 2.3 30.0 1.0
O B:HOH370 2.5 26.4 1.0
CL B:CL332 2.6 31.5 1.0
C B:LYS176 3.3 37.0 1.0
C B:GLY231 3.4 35.0 1.0
N B:GLY231 3.8 33.5 1.0
O B:HOH379 3.9 33.9 1.0
CA B:MET177 4.1 36.4 1.0
OD1 B:ASP210 4.1 35.7 1.0
CA B:GLY231 4.2 34.7 1.0
N B:MET177 4.2 36.4 1.0
CA B:LYS176 4.2 38.4 1.0
CB B:LYS176 4.2 38.1 1.0
O B:GLY178 4.2 36.7 1.0
N B:GLY233 4.2 37.0 1.0
C B:MET177 4.4 36.4 1.0
N B:THR232 4.5 34.8 1.0
N B:GLY178 4.7 36.1 1.0
O B:GLY199 4.7 35.5 1.0
CA B:THR232 4.7 35.8 1.0
CA B:GLY233 4.8 36.7 1.0
C B:GLY178 4.9 36.3 1.0
O B:MET177 4.9 36.0 1.0
C B:THR232 4.9 37.1 1.0
C B:THR230 5.0 34.2 1.0

Sodium binding site 10 out of 11 in 3c17

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Sodium binding site 10 out of 11 in the Hexagonal Crystal Structure of Precursor E. Coli Isoaspartyl Peptidase/L-Asparaginase (Ecaiii) with Active-Site T179A Mutation


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 10 of Hexagonal Crystal Structure of Precursor E. Coli Isoaspartyl Peptidase/L-Asparaginase (Ecaiii) with Active-Site T179A Mutation within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na326

b:51.9
occ:1.00
 O B:HOH520 2.4 61.4 1.0
O B:LYS158 2.5 43.6 1.0
O B:GLY160 2.5 49.4 1.0
O B:ALA155 2.7 32.8 1.0
C B:LYS158 3.5 43.2 1.0
O B:ALA156 3.6 36.1 1.0
C B:GLY160 3.7 49.3 1.0
C B:ALA155 3.8 33.1 1.0
C B:ALA156 4.0 35.7 1.0
N B:GLY160 4.1 47.7 1.0
CA B:ALA156 4.1 34.7 1.0
N B:LYS158 4.2 40.4 1.0
CA B:LYS158 4.2 42.1 1.0
N B:ALA156 4.4 34.0 1.0
CB B:LYS158 4.4 42.4 1.0
N B:GLU159 4.5 44.8 1.0
O B:HOH470 4.5 54.2 1.0
CA B:GLY160 4.5 48.6 1.0
N B:ALA161 4.7 50.1 1.0
C B:ALA161 4.7 50.5 1.0
C B:GLU159 4.7 46.6 1.0
CA B:GLU159 4.7 45.8 1.0
N B:ARG157 4.8 36.7 1.0
CA B:ALA161 4.8 50.4 1.0
C B:ARG157 4.8 39.0 1.0
CA B:ALA155 4.9 33.2 1.0

Reference:

K.Michalska, A.Hernandez-Santoyo, M.Jaskolski. The Mechanism of Autocatalytic Activation of Plant-Type L-Asparaginases J.Biol.Chem. V. 283 13388 2008.
ISSN: ISSN 0021-9258
PubMed: 18334484
DOI: 10.1074/JBC.M800746200
Page generated: Mon Oct 7 06:07:33 2024

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