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Sodium in PDB 5dib: 2.25 Angstrom Resolution Crystal Structure of Betaine Aldehyde Dehydrogenase (Betb) Y450L Point Mutant From Staphylococcus Aureus in Complex with Nad+ and Bme-Modified CYS289

Enzymatic activity of 2.25 Angstrom Resolution Crystal Structure of Betaine Aldehyde Dehydrogenase (Betb) Y450L Point Mutant From Staphylococcus Aureus in Complex with Nad+ and Bme-Modified CYS289

All present enzymatic activity of 2.25 Angstrom Resolution Crystal Structure of Betaine Aldehyde Dehydrogenase (Betb) Y450L Point Mutant From Staphylococcus Aureus in Complex with Nad+ and Bme-Modified CYS289:
1.2.1.8;

Protein crystallography data

The structure of 2.25 Angstrom Resolution Crystal Structure of Betaine Aldehyde Dehydrogenase (Betb) Y450L Point Mutant From Staphylococcus Aureus in Complex with Nad+ and Bme-Modified CYS289, PDB code: 5dib was solved by A.S.Halavaty, G.Minasov, C.Chen, J.C.Joo, A.F.Yakunin, W.F.Anderson, Centerfor Structural Genomics Of Infectious Diseases (Csgid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.72 / 2.25
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 224.866, 102.633, 118.243, 90.00, 104.83, 90.00
R / Rfree (%) 21.6 / 25.5

Sodium Binding Sites:

The binding sites of Sodium atom in the 2.25 Angstrom Resolution Crystal Structure of Betaine Aldehyde Dehydrogenase (Betb) Y450L Point Mutant From Staphylococcus Aureus in Complex with Nad+ and Bme-Modified CYS289 (pdb code 5dib). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the 2.25 Angstrom Resolution Crystal Structure of Betaine Aldehyde Dehydrogenase (Betb) Y450L Point Mutant From Staphylococcus Aureus in Complex with Nad+ and Bme-Modified CYS289, PDB code: 5dib:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in 5dib

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Sodium binding site 1 out of 3 in the 2.25 Angstrom Resolution Crystal Structure of Betaine Aldehyde Dehydrogenase (Betb) Y450L Point Mutant From Staphylococcus Aureus in Complex with Nad+ and Bme-Modified CYS289


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of 2.25 Angstrom Resolution Crystal Structure of Betaine Aldehyde Dehydrogenase (Betb) Y450L Point Mutant From Staphylococcus Aureus in Complex with Nad+ and Bme-Modified CYS289 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na502

b:45.5
occ:1.00
 O A:HOH779 2.3 50.7 1.0
O A:ILE184 2.5 27.4 1.0
O A:ASP97 2.5 21.1 1.0
OD1 A:ASP97 2.5 26.7 1.0
O A:ILE29 2.6 34.2 1.0
O A:HOH649 3.2 31.2 1.0
C A:ASP97 3.5 23.9 1.0
CG A:ASP97 3.6 27.6 1.0
CG2 A:THR185 3.6 24.0 1.0
C A:ILE184 3.7 28.0 1.0
C A:ILE29 3.8 40.2 1.0
CA A:ASP97 4.0 24.4 1.0
CG2 A:ILE28 4.1 29.5 1.0
CD A:PRO31 4.2 26.5 1.0
N A:ILE29 4.2 39.1 1.0
CA A:THR185 4.3 26.1 1.0
CB A:ASP97 4.4 26.0 1.0
OD2 A:ASP97 4.5 23.6 1.0
N A:THR185 4.5 25.5 1.0
CB A:THR185 4.5 25.1 1.0
CA A:ILE29 4.5 36.8 1.0
CD1 A:ILE332 4.7 26.9 1.0
N A:THR98 4.7 19.6 1.0
CB A:ILE184 4.7 30.1 1.0
CA A:ILE184 4.8 26.5 1.0
N A:ASN30 4.9 30.7 1.0
CB A:ILE29 5.0 45.9 1.0

Sodium binding site 2 out of 3 in 5dib

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Sodium binding site 2 out of 3 in the 2.25 Angstrom Resolution Crystal Structure of Betaine Aldehyde Dehydrogenase (Betb) Y450L Point Mutant From Staphylococcus Aureus in Complex with Nad+ and Bme-Modified CYS289


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of 2.25 Angstrom Resolution Crystal Structure of Betaine Aldehyde Dehydrogenase (Betb) Y450L Point Mutant From Staphylococcus Aureus in Complex with Nad+ and Bme-Modified CYS289 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na505

b:29.4
occ:1.00
 O A:HOH796 2.2 22.7 1.0
O A:VAL249 2.3 25.2 1.0
O B:LYS460 2.3 24.2 1.0
O B:HOH738 2.4 16.5 1.0
O B:GLY463 2.5 21.7 1.0
C B:LYS460 3.3 22.6 1.0
C A:VAL249 3.5 23.2 1.0
C B:GLY463 3.7 19.9 1.0
CA B:LYS460 3.7 21.6 1.0
N B:LYS460 3.8 22.5 1.0
CG1 B:ILE464 4.0 20.5 1.0
CG1 A:VAL249 4.2 26.7 1.0
CA A:THR250 4.2 22.5 1.0
CB A:VAL249 4.3 24.9 1.0
N A:THR250 4.3 23.3 1.0
C B:TYR459 4.3 21.1 1.0
ND2 A:ASN251 4.3 20.4 1.0
N A:ASN251 4.3 18.6 1.0
N B:GLN461 4.4 23.7 1.0
O A:HOH668 4.4 17.5 1.0
O A:HOH738 4.4 23.7 1.0
CA A:VAL249 4.5 23.3 1.0
O B:GLY458 4.5 21.4 1.0
O A:ASN248 4.6 30.7 1.0
N B:GLY463 4.6 22.2 1.0
C A:THR250 4.6 20.5 1.0
N B:ILE464 4.6 18.4 1.0
O B:TYR459 4.6 18.6 1.0
CG A:ASN251 4.6 20.2 1.0
CA B:ILE464 4.6 18.2 1.0
CA B:GLY463 4.7 21.1 1.0
CA B:GLN461 4.8 22.4 1.0
OD1 A:ASN251 4.8 21.6 1.0

Sodium binding site 3 out of 3 in 5dib

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Sodium binding site 3 out of 3 in the 2.25 Angstrom Resolution Crystal Structure of Betaine Aldehyde Dehydrogenase (Betb) Y450L Point Mutant From Staphylococcus Aureus in Complex with Nad+ and Bme-Modified CYS289


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of 2.25 Angstrom Resolution Crystal Structure of Betaine Aldehyde Dehydrogenase (Betb) Y450L Point Mutant From Staphylococcus Aureus in Complex with Nad+ and Bme-Modified CYS289 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na502

b:39.3
occ:1.00
 OD1 B:ASP97 2.3 42.7 1.0
O B:HOH791 2.3 36.3 1.0
O B:ILE29 2.4 37.2 1.0
O B:ILE184 2.6 30.9 1.0
O B:ASP97 2.6 27.5 1.0
O B:HOH649 3.1 42.5 1.0
CG B:ASP97 3.4 35.2 1.0
C B:ASP97 3.5 26.6 1.0
C B:ILE29 3.6 38.0 1.0
CG2 B:ILE28 3.7 30.5 1.0
C B:ILE184 3.8 29.8 1.0
CA B:ASP97 3.8 30.1 1.0
CG2 B:THR185 3.8 32.8 1.0
N B:ILE29 4.0 36.9 1.0
CB B:ASP97 4.2 33.7 1.0
CD B:PRO31 4.3 29.4 1.0
CA B:ILE29 4.3 42.2 1.0
OD2 B:ASP97 4.3 35.6 1.0
CA B:THR185 4.4 28.8 1.0
N B:THR185 4.6 28.8 1.0
N B:ASN30 4.6 35.5 1.0
CB B:THR185 4.7 33.8 1.0
N B:THR98 4.8 24.2 1.0
CB B:ILE29 4.9 47.7 1.0
CA B:ILE184 4.9 28.7 1.0
CB B:ILE184 4.9 27.8 1.0
C B:ILE28 4.9 33.7 1.0
CA B:ASN30 4.9 33.1 1.0

Reference:

A.S.Halavaty, G.Minasov, C.Chen, J.C.Joo, A.F.Yakunin, W.F.Anderson, Center For Structural Genomics Of Infectious Diseases(Csgid). 2.25 Angstrom Resolution Crystal Structure of Betaine Aldehyde Dehydrogenase (Betb) Y450L Point Mutant From Staphylococcus Aureus in Complex with Nad+ and Bme-Modified CYS289 To Be Published.
Page generated: Tue Dec 15 10:48:57 2020

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