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Sodium in PDB 4q92: 1.90 Angstrom Resolution Crystal Structure of Apo Betaine Aldehyde Dehydrogenase (Betb) G234S Mutant From Staphylococcus Aureus (IDP00699) with Bme-Modified CYS289

Enzymatic activity of 1.90 Angstrom Resolution Crystal Structure of Apo Betaine Aldehyde Dehydrogenase (Betb) G234S Mutant From Staphylococcus Aureus (IDP00699) with Bme-Modified CYS289

All present enzymatic activity of 1.90 Angstrom Resolution Crystal Structure of Apo Betaine Aldehyde Dehydrogenase (Betb) G234S Mutant From Staphylococcus Aureus (IDP00699) with Bme-Modified CYS289:
1.2.1.8;

Protein crystallography data

The structure of 1.90 Angstrom Resolution Crystal Structure of Apo Betaine Aldehyde Dehydrogenase (Betb) G234S Mutant From Staphylococcus Aureus (IDP00699) with Bme-Modified CYS289, PDB code: 4q92 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) 29.50 / 1.90
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 157.363, 156.438, 88.417, 90.00, 110.01, 90.00
R / Rfree (%) 19.4 / 22.3

Sodium Binding Sites:

The binding sites of Sodium atom in the 1.90 Angstrom Resolution Crystal Structure of Apo Betaine Aldehyde Dehydrogenase (Betb) G234S Mutant From Staphylococcus Aureus (IDP00699) with Bme-Modified CYS289 (pdb code 4q92). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 6 binding sites of Sodium where determined in the 1.90 Angstrom Resolution Crystal Structure of Apo Betaine Aldehyde Dehydrogenase (Betb) G234S Mutant From Staphylococcus Aureus (IDP00699) with Bme-Modified CYS289, PDB code: 4q92:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6;

Sodium binding site 1 out of 6 in 4q92

Go back to Sodium Binding Sites List in 4q92
Sodium binding site 1 out of 6 in the 1.90 Angstrom Resolution Crystal Structure of Apo Betaine Aldehyde Dehydrogenase (Betb) G234S Mutant From Staphylococcus Aureus (IDP00699) with 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 1.90 Angstrom Resolution Crystal Structure of Apo Betaine Aldehyde Dehydrogenase (Betb) G234S Mutant From Staphylococcus Aureus (IDP00699) with Bme-Modified CYS289 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na501

b:23.0
occ:1.00
O A:HOH956 2.3 29.6 1.0
O A:HOH785 2.4 27.7 1.0
O A:GLY286 2.5 16.0 1.0
O A:HOH644 2.6 18.5 1.0
O A:GLY393 2.6 15.9 1.0
N A:GLY393 3.3 19.0 1.0
C A:GLY286 3.4 17.2 1.0
CA A:GLY286 3.6 16.5 1.0
C A:GLY393 3.6 16.7 1.0
OE2 A:GLU390 3.6 19.5 0.5
CB A:ALA291 3.7 23.8 1.0
C A:PHE392 3.8 20.1 0.5
C A:PHE392 3.8 20.2 0.5
CA A:PHE392 3.8 20.7 0.5
CA A:PHE392 3.9 20.9 0.5
CA A:GLY393 4.0 18.1 1.0
N A:PHE392 4.2 20.7 0.5
N A:PHE392 4.2 20.6 0.5
O A:HOH784 4.2 34.4 1.0
O A:VAL395 4.2 16.6 1.0
CB A:SER293 4.2 17.5 1.0
O A:GLY281 4.5 15.7 1.0
N A:GLN287 4.6 16.6 1.0
CD A:GLU390 4.6 20.3 0.5
O A:PHE392 4.7 19.9 0.5
O A:PHE392 4.7 19.9 0.5
N A:VAL395 4.8 17.5 1.0
O A:HOH649 4.8 30.9 1.0
N A:PRO394 4.8 16.2 1.0
CA A:SER293 5.0 16.2 1.0
N A:GLY286 5.0 17.3 1.0

Sodium binding site 2 out of 6 in 4q92

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Sodium binding site 2 out of 6 in the 1.90 Angstrom Resolution Crystal Structure of Apo Betaine Aldehyde Dehydrogenase (Betb) G234S Mutant From Staphylococcus Aureus (IDP00699) with 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 1.90 Angstrom Resolution Crystal Structure of Apo Betaine Aldehyde Dehydrogenase (Betb) G234S Mutant From Staphylococcus Aureus (IDP00699) with Bme-Modified CYS289 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na502

b:17.6
occ:1.00
O B:HOH912 2.1 17.2 1.0
O A:LYS460 2.3 17.2 1.0
O B:VAL249 2.3 17.1 1.0
O A:HOH690 2.4 17.4 1.0
O A:GLY463 2.4 16.1 1.0
C A:LYS460 3.3 17.1 1.0
C B:VAL249 3.5 18.2 1.0
C A:GLY463 3.6 15.9 1.0
N A:LYS460 3.7 15.8 1.0
CA A:LYS460 3.8 17.6 1.0
CG1 A:ILE464 4.1 15.0 1.0
CG1 B:VAL249 4.2 18.1 1.0
CB B:VAL249 4.2 18.5 1.0
C A:TYR459 4.2 14.4 1.0
CA B:THR250 4.3 18.7 1.0
N B:THR250 4.4 18.4 1.0
OD1 B:ASN251 4.4 16.6 1.0
N A:GLY463 4.4 16.0 1.0
O B:HOH644 4.4 19.2 1.0
N B:ASN251 4.5 17.1 1.0
CA B:VAL249 4.5 19.1 1.0
N A:GLN461 4.5 16.8 1.0
O A:GLY458 4.5 14.1 1.0
CA A:GLY463 4.6 16.7 1.0
N A:ILE464 4.6 15.5 1.0
O B:HOH663 4.6 21.1 1.0
O B:ASN248 4.6 21.1 1.0
O A:TYR459 4.7 13.3 1.0
CA A:ILE464 4.7 15.0 1.0
C B:THR250 4.7 17.9 1.0
CG B:ASN251 4.8 15.9 1.0
O B:HOH623 4.9 18.8 1.0
CA A:GLN461 4.9 16.4 1.0
CA A:TYR459 5.0 13.9 1.0

Sodium binding site 3 out of 6 in 4q92

Go back to Sodium Binding Sites List in 4q92
Sodium binding site 3 out of 6 in the 1.90 Angstrom Resolution Crystal Structure of Apo Betaine Aldehyde Dehydrogenase (Betb) G234S Mutant From Staphylococcus Aureus (IDP00699) with 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 1.90 Angstrom Resolution Crystal Structure of Apo Betaine Aldehyde Dehydrogenase (Betb) G234S Mutant From Staphylococcus Aureus (IDP00699) with Bme-Modified CYS289 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na501

b:24.4
occ:1.00
O A:HOH978 2.2 18.8 1.0
O B:LYS460 2.3 22.5 1.0
O A:VAL249 2.3 18.7 1.0
O B:GLY463 2.5 18.8 1.0
O B:HOH699 2.5 18.4 1.0
C B:LYS460 3.3 21.2 1.0
C A:VAL249 3.5 18.7 1.0
C B:GLY463 3.7 19.1 1.0
N B:LYS460 3.7 20.1 1.0
CA B:LYS460 3.8 21.7 1.0
O A:HOH638 4.0 16.7 1.0
CG1 B:ILE464 4.1 18.4 1.0
CG1 A:VAL249 4.2 20.0 1.0
CB A:VAL249 4.2 20.0 1.0
C B:TYR459 4.3 20.0 1.0
CA A:THR250 4.3 17.5 1.0
O B:HOH626 4.3 21.9 1.0
OD1 A:ASN251 4.3 22.1 1.0
N A:THR250 4.4 18.1 1.0
N B:GLN461 4.5 21.8 1.0
N B:GLY463 4.5 20.8 1.0
N A:ASN251 4.5 15.8 1.0
CA A:VAL249 4.5 20.0 1.0
O A:ASN248 4.6 19.5 1.0
N B:ILE464 4.6 18.1 1.0
O B:GLY458 4.6 19.1 1.0
CA B:GLY463 4.6 20.2 1.0
O B:TYR459 4.7 19.7 1.0
C A:THR250 4.7 16.8 1.0
O A:HOH735 4.7 22.6 1.0
CA B:ILE464 4.8 17.1 1.0
CG A:ASN251 4.8 18.1 1.0
CA B:GLN461 4.8 21.1 1.0
CA B:TYR459 5.0 19.3 1.0

Sodium binding site 4 out of 6 in 4q92

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Sodium binding site 4 out of 6 in the 1.90 Angstrom Resolution Crystal Structure of Apo Betaine Aldehyde Dehydrogenase (Betb) G234S Mutant From Staphylococcus Aureus (IDP00699) with 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 1.90 Angstrom Resolution Crystal Structure of Apo Betaine Aldehyde Dehydrogenase (Betb) G234S Mutant From Staphylococcus Aureus (IDP00699) with Bme-Modified CYS289 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na501

b:14.5
occ:1.00
O D:HOH645 2.3 14.4 1.0
O C:HOH646 2.3 16.9 1.0
O D:VAL249 2.4 14.6 1.0
O C:GLY463 2.4 13.2 1.0
O C:LYS460 2.4 15.7 1.0
C C:LYS460 3.4 16.9 1.0
C D:VAL249 3.6 15.0 1.0
C C:GLY463 3.6 13.7 1.0
N C:LYS460 3.8 17.1 1.0
CA C:LYS460 3.9 17.7 1.0
CG1 C:ILE464 4.0 14.1 1.0
CG1 D:VAL249 4.2 16.0 1.0
CB D:VAL249 4.3 16.3 1.0
OD1 D:ASN251 4.3 17.7 1.0
C C:TYR459 4.3 16.9 1.0
CA D:THR250 4.4 14.0 1.0
O D:HOH636 4.4 17.1 1.0
N C:GLY463 4.4 14.9 1.0
N D:THR250 4.4 14.4 1.0
N C:ILE464 4.5 13.6 1.0
O D:HOH678 4.5 17.9 1.0
N D:ASN251 4.5 13.5 1.0
O C:GLY458 4.5 16.6 1.0
CA C:GLY463 4.5 14.5 1.0
CA D:VAL249 4.6 15.9 1.0
N C:GLN461 4.6 17.2 1.0
CA C:ILE464 4.6 13.5 1.0
O C:TYR459 4.7 16.7 1.0
O D:ASN248 4.7 19.7 1.0
C D:THR250 4.8 13.4 1.0
CG D:ASN251 4.8 13.5 1.0
ND2 D:ASN251 4.9 12.9 1.0
CA C:GLN461 4.9 17.1 1.0
O D:HOH621 4.9 14.1 1.0

Sodium binding site 5 out of 6 in 4q92

Go back to Sodium Binding Sites List in 4q92
Sodium binding site 5 out of 6 in the 1.90 Angstrom Resolution Crystal Structure of Apo Betaine Aldehyde Dehydrogenase (Betb) G234S Mutant From Staphylococcus Aureus (IDP00699) with Bme-Modified CYS289


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of 1.90 Angstrom Resolution Crystal Structure of Apo Betaine Aldehyde Dehydrogenase (Betb) G234S Mutant From Staphylococcus Aureus (IDP00699) with Bme-Modified CYS289 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na502

b:23.6
occ:1.00
O C:HOH1001 2.1 20.2 1.0
O C:HOH1030 2.3 23.9 1.0
O C:HOH651 2.3 19.6 1.0
O C:GLY393 2.4 25.1 1.0
O C:GLY286 2.5 23.4 1.0
OG C:SER293 3.0 21.3 0.5
C C:GLY286 3.3 22.8 1.0
N C:GLY393 3.3 25.3 1.0
CA C:GLY286 3.4 23.9 1.0
C C:GLY393 3.5 25.9 1.0
CB C:ALA291 3.7 22.3 1.0
C C:PHE392 3.9 25.1 1.0
CA C:GLY393 4.0 26.0 1.0
CA C:PHE392 4.0 24.6 1.0
OE2 C:GLU390 4.0 25.0 1.0
O C:VAL395 4.1 23.7 1.0
O C:GLY281 4.2 21.4 1.0
CB C:SER293 4.2 20.4 0.5
CB C:SER293 4.3 21.1 0.5
N C:PHE392 4.4 24.2 1.0
N C:GLN287 4.6 22.9 1.0
N C:VAL395 4.6 25.3 1.0
N C:PRO394 4.6 26.6 1.0
O C:PHE392 4.8 26.4 1.0
N C:GLY286 4.8 23.9 1.0
CA C:SER293 4.9 20.8 0.5
CA C:SER293 4.9 21.3 0.5
CA C:PRO394 4.9 26.6 1.0
O C:HOH695 5.0 22.8 1.0
CD C:GLU390 5.0 23.8 1.0

Sodium binding site 6 out of 6 in 4q92

Go back to Sodium Binding Sites List in 4q92
Sodium binding site 6 out of 6 in the 1.90 Angstrom Resolution Crystal Structure of Apo Betaine Aldehyde Dehydrogenase (Betb) G234S Mutant From Staphylococcus Aureus (IDP00699) with Bme-Modified CYS289


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of 1.90 Angstrom Resolution Crystal Structure of Apo Betaine Aldehyde Dehydrogenase (Betb) G234S Mutant From Staphylococcus Aureus (IDP00699) with Bme-Modified CYS289 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na501

b:14.3
occ:1.00
O C:HOH662 2.2 15.4 1.0
O C:VAL249 2.3 12.8 1.0
O D:LYS460 2.4 15.7 1.0
O D:GLY463 2.4 14.4 1.0
O D:HOH608 2.4 13.3 1.0
C D:LYS460 3.4 16.7 1.0
C C:VAL249 3.5 13.9 1.0
C D:GLY463 3.6 14.1 1.0
N D:LYS460 3.7 15.8 1.0
CA D:LYS460 3.9 17.7 1.0
CG1 D:ILE464 4.0 14.6 1.0
CG1 C:VAL249 4.2 14.0 1.0
CB C:VAL249 4.3 14.1 1.0
CA C:THR250 4.3 14.7 1.0
C D:TYR459 4.3 16.1 1.0
OD1 C:ASN251 4.3 18.5 1.0
N C:THR250 4.4 14.4 1.0
N C:ASN251 4.4 14.6 1.0
N D:GLY463 4.4 14.8 1.0
O C:HOH631 4.4 20.1 1.0
O C:HOH640 4.4 21.2 1.0
N D:ILE464 4.5 13.8 1.0
CA D:GLY463 4.5 14.6 1.0
CA C:VAL249 4.5 14.3 1.0
O D:GLY458 4.6 14.7 1.0
N D:GLN461 4.6 17.0 1.0
CA D:ILE464 4.6 13.8 1.0
C C:THR250 4.7 14.9 1.0
CG C:ASN251 4.7 14.0 1.0
O C:ASN248 4.7 14.2 1.0
O D:TYR459 4.7 15.3 1.0
ND2 C:ASN251 4.8 13.0 1.0
O C:HOH626 4.9 12.4 1.0
CA D:GLN461 4.9 17.2 1.0
O C:HOH751 4.9 17.9 1.0
CD1 D:ILE464 5.0 15.3 1.0
CB D:ILE464 5.0 14.1 1.0

Reference:

A.S.Halavaty, G.Minasov, C.Chen, J.C.Joo, A.F.Yakunin, W.F.Anderson. 1.90 Angstrom Resolution Crystal Structure of Apo Betaine Aldehyde Dehydrogenase (Betb) G234S Mutant From Staphylococcus Aureus (IDP00699) with Bme-Modified CYS289 To Be Published.
Page generated: Tue Dec 15 07:05:10 2020

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