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Sodium in PDB 5ez4: 2.11 Angstrom Resolution Crystal Structure of Betaine Aldehyde Dehydrogenase (Betb) P449M/Y450L Double Mutant From Staphylococcus Aureus in Complex with Nad+ and Bme-Modified CYS289

Enzymatic activity of 2.11 Angstrom Resolution Crystal Structure of Betaine Aldehyde Dehydrogenase (Betb) P449M/Y450L Double Mutant From Staphylococcus Aureus in Complex with Nad+ and Bme-Modified CYS289

All present enzymatic activity of 2.11 Angstrom Resolution Crystal Structure of Betaine Aldehyde Dehydrogenase (Betb) P449M/Y450L Double Mutant From Staphylococcus Aureus in Complex with Nad+ and Bme-Modified CYS289:
1.2.1.8;

Protein crystallography data

The structure of 2.11 Angstrom Resolution Crystal Structure of Betaine Aldehyde Dehydrogenase (Betb) P449M/Y450L Double Mutant From Staphylococcus Aureus in Complex with Nad+ and Bme-Modified CYS289, PDB code: 5ez4 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) 29.69 / 2.11
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 225.026, 102.158, 118.330, 90.00, 104.85, 90.00
R / Rfree (%) 14.1 / 17.5

Sodium Binding Sites:

The binding sites of Sodium atom in the 2.11 Angstrom Resolution Crystal Structure of Betaine Aldehyde Dehydrogenase (Betb) P449M/Y450L Double Mutant From Staphylococcus Aureus in Complex with Nad+ and Bme-Modified CYS289 (pdb code 5ez4). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the 2.11 Angstrom Resolution Crystal Structure of Betaine Aldehyde Dehydrogenase (Betb) P449M/Y450L Double Mutant From Staphylococcus Aureus in Complex with Nad+ and Bme-Modified CYS289, PDB code: 5ez4:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 5ez4

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Sodium binding site 1 out of 4 in the 2.11 Angstrom Resolution Crystal Structure of Betaine Aldehyde Dehydrogenase (Betb) P449M/Y450L Double 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 2.11 Angstrom Resolution Crystal Structure of Betaine Aldehyde Dehydrogenase (Betb) P449M/Y450L Double 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:15.5
occ:1.00
 O A:LYS460 2.3 15.6 1.0
O A:GLY463 2.3 12.4 1.0
O B:VAL249 2.4 17.4 1.0
O B:HOH984 2.4 14.5 1.0
O A:HOH866 2.4 16.4 1.0
C A:LYS460 3.3 18.5 1.0
C A:GLY463 3.5 13.1 1.0
C B:VAL249 3.6 15.3 1.0
CG1 B:VAL249 3.6 15.5 1.0
N A:LYS460 3.7 20.6 1.0
CA A:LYS460 3.8 19.0 1.0
CG1 A:ILE464 3.9 13.6 1.0
ND2 B:ASN251 4.2 16.9 1.0
N B:ASN251 4.3 14.8 1.0
CB B:VAL249 4.3 15.3 1.0
N A:GLY463 4.3 14.4 1.0
CA B:THR250 4.3 14.7 1.0
C A:TYR459 4.3 18.2 1.0
O A:GLY458 4.3 18.4 1.0
N B:THR250 4.4 15.1 1.0
N A:ILE464 4.4 12.1 1.0
CA A:GLY463 4.5 13.8 1.0
N A:GLN461 4.5 15.8 1.0
O B:HOH777 4.5 13.6 1.0
O B:HOH836 4.5 20.7 1.0
CA A:ILE464 4.6 12.3 1.0
CA B:VAL249 4.6 15.9 1.0
CG B:ASN251 4.6 16.9 1.0
C B:THR250 4.6 14.6 1.0
O A:TYR459 4.7 16.7 1.0
O B:ASN248 4.8 19.5 1.0
O B:HOH687 4.8 13.8 1.0
OD1 B:ASN251 4.8 15.3 1.0
CA A:GLN461 4.8 15.6 1.0
CD1 A:ILE464 4.9 14.9 1.0
CB A:ILE464 4.9 13.7 1.0

Sodium binding site 2 out of 4 in 5ez4

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Sodium binding site 2 out of 4 in the 2.11 Angstrom Resolution Crystal Structure of Betaine Aldehyde Dehydrogenase (Betb) P449M/Y450L Double 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 2.11 Angstrom Resolution Crystal Structure of Betaine Aldehyde Dehydrogenase (Betb) P449M/Y450L Double 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:15.2
occ:1.00
 O A:HOH996 2.2 10.6 1.0
O B:LYS460 2.2 13.1 1.0
O A:VAL249 2.3 12.4 1.0
O B:HOH906 2.4 14.6 1.0
O B:GLY463 2.4 11.4 1.0
C B:LYS460 3.2 14.8 1.0
C A:VAL249 3.5 14.3 1.0
C B:GLY463 3.6 12.8 1.0
N B:LYS460 3.6 16.1 1.0
CG1 A:VAL249 3.6 15.8 1.0
CA B:LYS460 3.7 15.3 1.0
CG1 B:ILE464 4.0 13.0 1.0
C B:TYR459 4.2 16.5 1.0
CA A:THR250 4.3 13.3 1.0
CB A:VAL249 4.3 15.3 1.0
O B:GLY458 4.3 14.6 1.0
ND2 A:ASN251 4.3 17.9 1.0
N B:GLY463 4.3 13.4 1.0
N A:THR250 4.4 13.1 1.0
N A:ASN251 4.4 14.3 1.0
N B:GLN461 4.4 15.9 1.0
O A:HOH775 4.5 14.4 1.0
CA B:GLY463 4.5 12.9 1.0
O A:HOH717 4.5 11.9 1.0
N B:ILE464 4.5 11.5 1.0
CA A:VAL249 4.6 15.0 1.0
O B:TYR459 4.6 15.6 1.0
C A:THR250 4.7 12.9 1.0
O A:ASN248 4.7 18.0 1.0
CA B:ILE464 4.7 11.8 1.0
CG A:ASN251 4.7 16.8 1.0
CA B:GLN461 4.8 16.2 1.0
OD1 A:ASN251 4.9 18.3 1.0
O A:HOH899 5.0 32.6 1.0
CD1 B:ILE464 5.0 14.3 1.0

Sodium binding site 3 out of 4 in 5ez4

Go back to Sodium Binding Sites List in 5ez4
Sodium binding site 3 out of 4 in the 2.11 Angstrom Resolution Crystal Structure of Betaine Aldehyde Dehydrogenase (Betb) P449M/Y450L Double 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 2.11 Angstrom Resolution Crystal Structure of Betaine Aldehyde Dehydrogenase (Betb) P449M/Y450L Double Mutant From Staphylococcus Aureus in Complex with Nad+ and Bme-Modified CYS289 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na502

b:15.5
occ:1.00
 O C:LYS460 2.3 15.2 1.0
O C:GLY463 2.4 13.6 1.0
O D:VAL249 2.4 12.4 1.0
O D:HOH1005 2.4 17.6 1.0
O C:HOH818 2.5 13.0 1.0
C C:LYS460 3.4 14.2 1.0
C D:VAL249 3.6 13.9 1.0
C C:GLY463 3.6 14.1 1.0
N C:LYS460 3.7 14.2 1.0
CA C:LYS460 3.8 14.6 1.0
CG1 C:ILE464 4.0 10.2 1.0
C C:TYR459 4.3 14.9 1.0
CG1 D:VAL249 4.3 12.6 1.0
CB D:VAL249 4.3 12.8 1.0
ND2 D:ASN251 4.3 15.4 1.0
O C:GLY458 4.3 18.4 1.0
N C:GLY463 4.4 13.8 1.0
CA D:THR250 4.4 13.4 1.0
N D:ASN251 4.4 12.9 1.0
N D:THR250 4.4 15.3 1.0
O D:HOH799 4.5 15.0 1.0
O D:HOH809 4.5 13.1 1.0
N C:GLN461 4.5 14.4 1.0
N C:ILE464 4.5 11.4 1.0
CA C:GLY463 4.5 14.9 1.0
CA D:VAL249 4.6 13.1 1.0
CA C:ILE464 4.6 10.3 1.0
O C:TYR459 4.7 13.6 1.0
O D:HOH655 4.7 14.6 1.0
CG D:ASN251 4.7 15.3 1.0
C D:THR250 4.7 14.0 1.0
O D:ASN248 4.7 16.8 1.0
CA C:GLN461 4.8 14.4 1.0
OD1 D:ASN251 4.9 16.3 1.0
O D:HOH824 4.9 40.5 1.0
CD1 C:ILE464 5.0 9.6 1.0
CB C:ILE464 5.0 9.9 1.0

Sodium binding site 4 out of 4 in 5ez4

Go back to Sodium Binding Sites List in 5ez4
Sodium binding site 4 out of 4 in the 2.11 Angstrom Resolution Crystal Structure of Betaine Aldehyde Dehydrogenase (Betb) P449M/Y450L Double 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 4 of 2.11 Angstrom Resolution Crystal Structure of Betaine Aldehyde Dehydrogenase (Betb) P449M/Y450L Double Mutant From Staphylococcus Aureus in Complex with Nad+ and Bme-Modified CYS289 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na502

b:14.0
occ:1.00
 O D:LYS460 2.3 14.4 1.0
O C:VAL249 2.4 14.5 1.0
O D:GLY463 2.4 11.5 1.0
O C:HOH1017 2.5 20.2 1.0
O D:HOH884 2.5 12.5 1.0
C D:LYS460 3.4 15.7 1.0
CG1 C:VAL249 3.5 15.1 1.0
C C:VAL249 3.6 14.9 1.0
C D:GLY463 3.6 12.1 1.0
N D:LYS460 3.8 15.9 1.0
CA D:LYS460 3.9 15.0 1.0
CG1 D:ILE464 3.9 14.8 1.0
CB C:VAL249 4.2 15.1 1.0
ND2 C:ASN251 4.3 14.2 1.0
CA C:THR250 4.4 13.7 1.0
N C:ASN251 4.4 12.4 1.0
C D:TYR459 4.4 15.2 1.0
N D:GLY463 4.4 13.7 1.0
N C:THR250 4.4 13.7 1.0
O D:GLY458 4.4 15.4 1.0
N D:GLN461 4.5 14.9 1.0
N D:ILE464 4.5 12.2 1.0
CA D:GLY463 4.5 13.3 1.0
O C:HOH796 4.5 14.5 1.0
CA C:VAL249 4.6 15.0 1.0
O C:HOH835 4.6 19.4 1.0
CA D:ILE464 4.6 11.9 1.0
C C:THR250 4.7 12.3 1.0
CG C:ASN251 4.7 12.5 1.0
O C:ASN248 4.7 18.8 1.0
O D:TYR459 4.8 14.6 1.0
CA D:GLN461 4.8 16.5 1.0
O C:HOH788 4.9 18.3 1.0
OD1 C:ASN251 4.9 12.0 1.0
CD1 D:ILE464 4.9 15.2 1.0
CB D:ILE464 4.9 13.9 1.0
O C:HOH913 5.0 34.7 1.0

Reference:

A.S.Halavaty, G.Minasov, C.Chen, J.C.Joo, A.F.Yakunin, W.F.Anderson. 2.11 Angstrom Resolution Crystal Structure of Betaine Aldehyde Dehydrogenase (Betb) P449M/Y450L Double Mutant From Staphylococcus Aureus in Complex with Nad+ and Bme-Modified CYS289 To Be Published.
Page generated: Mon Oct 7 20:55:08 2024

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