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Sodium in PDB 4qto: 1.65 Angstrom Resolution Crystal Structure of Betaine Aldehyde Dehydrogenase (Betb) From Staphylococcus Aureus with Bme-Modified CYS289 and Peg Molecule in Active Site

Enzymatic activity of 1.65 Angstrom Resolution Crystal Structure of Betaine Aldehyde Dehydrogenase (Betb) From Staphylococcus Aureus with Bme-Modified CYS289 and Peg Molecule in Active Site

All present enzymatic activity of 1.65 Angstrom Resolution Crystal Structure of Betaine Aldehyde Dehydrogenase (Betb) From Staphylococcus Aureus with Bme-Modified CYS289 and Peg Molecule in Active Site:
1.2.1.8;

Protein crystallography data

The structure of 1.65 Angstrom Resolution Crystal Structure of Betaine Aldehyde Dehydrogenase (Betb) From Staphylococcus Aureus with Bme-Modified CYS289 and Peg Molecule in Active Site, PDB code: 4qto was solved by A.S.Halavaty, G.Minasov, I.Dubrovska, J.Winsor, L.Shuvalova, W.F.Anderson, Center For 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) 29.71 / 1.65
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 224.249, 102.474, 118.178, 90.00, 104.45, 90.00
R / Rfree (%) 13.6 / 15.6

Sodium Binding Sites:

The binding sites of Sodium atom in the 1.65 Angstrom Resolution Crystal Structure of Betaine Aldehyde Dehydrogenase (Betb) From Staphylococcus Aureus with Bme-Modified CYS289 and Peg Molecule in Active Site (pdb code 4qto). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the 1.65 Angstrom Resolution Crystal Structure of Betaine Aldehyde Dehydrogenase (Betb) From Staphylococcus Aureus with Bme-Modified CYS289 and Peg Molecule in Active Site, PDB code: 4qto:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 4qto

Go back to Sodium Binding Sites List in 4qto
Sodium binding site 1 out of 4 in the 1.65 Angstrom Resolution Crystal Structure of Betaine Aldehyde Dehydrogenase (Betb) From Staphylococcus Aureus with Bme-Modified CYS289 and Peg Molecule in Active Site


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of 1.65 Angstrom Resolution Crystal Structure of Betaine Aldehyde Dehydrogenase (Betb) From Staphylococcus Aureus with Bme-Modified CYS289 and Peg Molecule in Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na501

b:11.3
occ:1.00
 O A:LYS460 2.3 10.6 1.0
O A:GLY463 2.3 10.3 1.0
O B:VAL249 2.3 10.3 1.0
O A:HOH652 2.4 12.8 1.0
O B:HOH613 2.4 11.5 1.0
C A:LYS460 3.4 11.2 1.0
C A:GLY463 3.5 10.1 1.0
C B:VAL249 3.5 10.2 1.0
N A:LYS460 3.8 10.7 1.0
CA A:LYS460 3.9 11.7 1.0
CG1 A:ILE464 4.0 9.1 1.0
CG1 B:VAL249 4.2 12.6 1.0
CB B:VAL249 4.2 11.3 1.0
CA B:THR250 4.3 10.2 1.0
C A:TYR459 4.3 10.9 1.0
N A:GLY463 4.3 9.6 1.0
N B:ASN251 4.3 9.9 1.0
ND2 B:ASN251 4.4 11.1 1.0
N B:THR250 4.4 10.5 1.0
N A:ILE464 4.4 8.8 1.0
O B:HOH621 4.4 12.7 1.0
O B:HOH655 4.4 15.9 1.0
CA A:GLY463 4.5 10.3 1.0
O A:GLY458 4.5 13.9 1.0
N A:GLN461 4.5 10.9 1.0
CA B:VAL249 4.5 10.8 1.0
CA A:ILE464 4.6 8.4 1.0
C B:THR250 4.7 10.1 1.0
O B:ASN248 4.7 12.1 1.0
O A:TYR459 4.7 9.8 1.0
CG B:ASN251 4.7 10.2 1.0
CA A:GLN461 4.8 10.8 1.0
O B:HOH633 4.9 11.4 1.0
OD1 B:ASN251 4.9 10.0 1.0
CD1 A:ILE464 4.9 9.5 1.0
CB A:ILE464 5.0 8.6 1.0

Sodium binding site 2 out of 4 in 4qto

Go back to Sodium Binding Sites List in 4qto
Sodium binding site 2 out of 4 in the 1.65 Angstrom Resolution Crystal Structure of Betaine Aldehyde Dehydrogenase (Betb) From Staphylococcus Aureus with Bme-Modified CYS289 and Peg Molecule in Active Site


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of 1.65 Angstrom Resolution Crystal Structure of Betaine Aldehyde Dehydrogenase (Betb) From Staphylococcus Aureus with Bme-Modified CYS289 and Peg Molecule in Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na501

b:10.9
occ:1.00
 O A:VAL249 2.3 10.1 1.0
O B:LYS460 2.3 11.4 1.0
O A:HOH621 2.3 11.2 1.0
O B:HOH663 2.4 12.4 1.0
O B:GLY463 2.4 10.6 1.0
C B:LYS460 3.4 11.2 1.0
C A:VAL249 3.5 10.6 1.0
C B:GLY463 3.6 9.7 1.0
N B:LYS460 3.7 11.5 1.0
CA B:LYS460 3.8 12.0 1.0
CG1 B:ILE464 4.0 9.0 1.0
CG1 A:VAL249 4.2 12.3 1.0
CB A:VAL249 4.2 10.6 1.0
CA A:THR250 4.3 10.0 1.0
C B:TYR459 4.3 11.9 1.0
N A:THR250 4.3 9.9 1.0
N A:ASN251 4.4 9.6 1.0
N B:GLY463 4.4 10.2 1.0
ND2 A:ASN251 4.4 11.5 1.0
O A:HOH661 4.4 16.1 1.0
O A:HOH627 4.5 12.7 1.0
N B:ILE464 4.5 8.8 1.0
N B:GLN461 4.5 10.1 1.0
CA B:GLY463 4.5 10.5 1.0
O B:GLY458 4.5 12.8 1.0
CA A:VAL249 4.5 10.8 1.0
C A:THR250 4.6 9.7 1.0
CA B:ILE464 4.6 8.6 1.0
O A:ASN248 4.7 11.6 1.0
O B:TYR459 4.7 11.1 1.0
CG A:ASN251 4.8 9.8 1.0
CA B:GLN461 4.9 11.2 1.0
O A:HOH641 4.9 11.3 1.0
CD1 B:ILE464 4.9 10.2 1.0
OD1 A:ASN251 4.9 9.5 1.0
CB B:ILE464 5.0 8.8 1.0

Sodium binding site 3 out of 4 in 4qto

Go back to Sodium Binding Sites List in 4qto
Sodium binding site 3 out of 4 in the 1.65 Angstrom Resolution Crystal Structure of Betaine Aldehyde Dehydrogenase (Betb) From Staphylococcus Aureus with Bme-Modified CYS289 and Peg Molecule in Active Site


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of 1.65 Angstrom Resolution Crystal Structure of Betaine Aldehyde Dehydrogenase (Betb) From Staphylococcus Aureus with Bme-Modified CYS289 and Peg Molecule in Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na501

b:11.3
occ:1.00
 O D:VAL249 2.3 10.3 1.0
O C:LYS460 2.3 11.8 1.0
O C:GLY463 2.4 9.7 1.0
O D:HOH665 2.4 14.9 1.0
O C:HOH661 2.4 13.0 1.0
C C:LYS460 3.4 10.9 1.0
C D:VAL249 3.5 11.0 1.0
C C:GLY463 3.6 9.4 1.0
N C:LYS460 3.8 10.9 1.0
CA C:LYS460 3.9 11.3 1.0
CG1 C:ILE464 4.0 10.6 1.0
CG1 D:VAL249 4.2 10.4 1.0
CB D:VAL249 4.2 10.2 1.0
C C:TYR459 4.3 10.9 1.0
CA D:THR250 4.3 10.0 1.0
N C:GLY463 4.4 9.1 1.0
N D:THR250 4.4 10.3 1.0
O D:HOH648 4.4 15.6 1.0
ND2 D:ASN251 4.4 11.2 1.0
O D:HOH626 4.5 14.2 1.0
N D:ASN251 4.5 9.2 1.0
N C:ILE464 4.5 8.4 1.0
O C:GLY458 4.5 14.7 1.0
CA D:VAL249 4.5 9.9 1.0
CA C:GLY463 4.5 10.1 1.0
N C:GLN461 4.6 10.1 1.0
CA C:ILE464 4.6 8.5 1.0
O D:ASN248 4.7 10.6 1.0
C D:THR250 4.7 10.1 1.0
O C:TYR459 4.7 9.9 1.0
O D:HOH618 4.8 12.4 1.0
CG D:ASN251 4.8 10.7 1.0
CA C:GLN461 4.9 10.8 1.0
OD1 D:ASN251 5.0 10.6 1.0
O D:HOH784 5.0 23.6 1.0

Sodium binding site 4 out of 4 in 4qto

Go back to Sodium Binding Sites List in 4qto
Sodium binding site 4 out of 4 in the 1.65 Angstrom Resolution Crystal Structure of Betaine Aldehyde Dehydrogenase (Betb) From Staphylococcus Aureus with Bme-Modified CYS289 and Peg Molecule in Active Site


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of 1.65 Angstrom Resolution Crystal Structure of Betaine Aldehyde Dehydrogenase (Betb) From Staphylococcus Aureus with Bme-Modified CYS289 and Peg Molecule in Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na501

b:15.4
occ:1.00
 O D:LYS460 2.4 12.6 1.0
O D:GLY463 2.4 11.8 1.0
O C:VAL249 2.4 12.0 1.0
O D:HOH697 2.4 17.2 1.0
O C:HOH699 2.5 18.9 1.0
C D:LYS460 3.4 13.2 1.0
C D:GLY463 3.6 10.7 1.0
C C:VAL249 3.6 12.1 1.0
N D:LYS460 3.9 12.8 1.0
CA D:LYS460 4.0 13.5 1.0
CG1 D:ILE464 4.0 11.2 1.0
CG1 C:VAL249 4.2 15.2 1.0
CB C:VAL249 4.2 12.7 1.0
N D:GLY463 4.4 10.9 1.0
ND2 C:ASN251 4.4 15.0 1.0
C D:TYR459 4.4 12.9 1.0
CA C:THR250 4.4 11.1 1.0
N C:ASN251 4.4 11.3 1.0
N C:THR250 4.5 11.6 1.0
O C:HOH702 4.5 21.8 1.0
O C:HOH639 4.5 17.6 1.0
N D:ILE464 4.5 10.4 1.0
CA D:GLY463 4.5 11.4 1.0
N D:GLN461 4.6 11.8 1.0
O D:GLY458 4.6 16.2 1.0
CA C:VAL249 4.6 12.5 1.0
CA D:ILE464 4.6 9.7 1.0
C C:THR250 4.7 11.1 1.0
CG C:ASN251 4.8 13.2 1.0
O C:ASN248 4.8 14.0 1.0
O D:TYR459 4.8 11.7 1.0
CA D:GLN461 4.8 13.5 1.0
O C:HOH636 4.9 14.6 1.0
CD1 D:ILE464 4.9 12.2 1.0
OD1 C:ASN251 5.0 11.7 1.0
O C:HOH825 5.0 32.2 1.0

Reference:

A.S.Halavaty, G.Minasov, I.Dubrovska, J.Winsor, L.Shuvalova, W.F.Anderson. 1.65 Angstrom Resolution Crystal Structure of Betaine Aldehyde Dehydrogenase (Betb) From Staphylococcus Aureus with Bme-Modified CYS289 and Peg Molecule in Active Site To Be Published.
Page generated: Mon Oct 7 18:06:14 2024

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