Atomistry » Sodium » PDB 5en3-5f00 » 5ez4
Atomistry »
  Sodium »
    PDB 5en3-5f00 »
      5ez4 »

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

Go back to Sodium Binding Sites List in 5ez4
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

Go back to Sodium Binding Sites List in 5ez4
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: Tue Dec 15 10:58:11 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy