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Sodium in PDB 4qje: 1.85 Angstrom Resolution Crystal Structure of Apo Betaine Aldehyde Dehydrogenase (Betb) G234S Mutant From Staphylococcus Aureus (IDP00699) with Bme-Free Sulfinic Acid Form of CYS289

Enzymatic activity of 1.85 Angstrom Resolution Crystal Structure of Apo Betaine Aldehyde Dehydrogenase (Betb) G234S Mutant From Staphylococcus Aureus (IDP00699) with Bme-Free Sulfinic Acid Form of CYS289

All present enzymatic activity of 1.85 Angstrom Resolution Crystal Structure of Apo Betaine Aldehyde Dehydrogenase (Betb) G234S Mutant From Staphylococcus Aureus (IDP00699) with Bme-Free Sulfinic Acid Form of CYS289:
1.2.1.8;

Protein crystallography data

The structure of 1.85 Angstrom Resolution Crystal Structure of Apo Betaine Aldehyde Dehydrogenase (Betb) G234S Mutant From Staphylococcus Aureus (IDP00699) with Bme-Free Sulfinic Acid Form of CYS289, PDB code: 4qje 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) 29.83 / 1.85
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 218.665, 102.929, 118.074, 90.00, 101.42, 90.00
R / Rfree (%) 15 / 17.5

Sodium Binding Sites:

The binding sites of Sodium atom in the 1.85 Angstrom Resolution Crystal Structure of Apo Betaine Aldehyde Dehydrogenase (Betb) G234S Mutant From Staphylococcus Aureus (IDP00699) with Bme-Free Sulfinic Acid Form of CYS289 (pdb code 4qje). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 8 binding sites of Sodium where determined in the 1.85 Angstrom Resolution Crystal Structure of Apo Betaine Aldehyde Dehydrogenase (Betb) G234S Mutant From Staphylococcus Aureus (IDP00699) with Bme-Free Sulfinic Acid Form of CYS289, PDB code: 4qje:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Sodium binding site 1 out of 8 in 4qje

Go back to Sodium Binding Sites List in 4qje
Sodium binding site 1 out of 8 in the 1.85 Angstrom Resolution Crystal Structure of Apo Betaine Aldehyde Dehydrogenase (Betb) G234S Mutant From Staphylococcus Aureus (IDP00699) with Bme-Free Sulfinic Acid Form of CYS289


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of 1.85 Angstrom Resolution Crystal Structure of Apo Betaine Aldehyde Dehydrogenase (Betb) G234S Mutant From Staphylococcus Aureus (IDP00699) with Bme-Free Sulfinic Acid Form of CYS289 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na501

b:21.9
occ:1.00
 OD1 A:ASP97 2.3 18.0 1.0
O A:HOH856 2.4 25.7 1.0
O A:ILE29 2.5 21.1 1.0
O A:ASP97 2.5 19.9 1.0
O A:ILE184 2.8 18.7 1.0
O A:HOH691 3.4 20.4 1.0
CG A:ASP97 3.4 18.4 1.0
C A:ASP97 3.4 18.4 1.0
CA A:ASP97 3.6 18.5 1.0
C A:ILE29 3.7 21.8 1.0
CG2 A:ILE28 3.7 19.9 1.0
CG2 A:THR185 3.9 18.0 1.0
C A:ILE184 4.0 18.3 1.0
CB A:ASP97 4.1 18.1 1.0
N A:ILE29 4.1 21.4 1.0
OD2 A:ASP97 4.4 17.1 1.0
CA A:THR185 4.4 17.5 1.0
CA A:ILE29 4.4 23.1 1.0
O A:HOH829 4.5 26.2 1.0
CD A:PRO31 4.6 19.2 1.0
N A:THR98 4.6 17.3 1.0
N A:THR185 4.7 17.8 1.0
N A:ASN30 4.7 21.5 1.0
CB A:THR185 4.7 17.4 1.0
CD1 A:ILE37 4.9 24.0 1.0
CA A:ASN30 4.9 21.0 1.0
C A:ILE28 4.9 21.8 1.0
N A:ASP97 5.0 18.3 1.0
CB A:ILE29 5.0 24.8 1.0
O A:LEU96 5.0 19.4 1.0

Sodium binding site 2 out of 8 in 4qje

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Sodium binding site 2 out of 8 in the 1.85 Angstrom Resolution Crystal Structure of Apo Betaine Aldehyde Dehydrogenase (Betb) G234S Mutant From Staphylococcus Aureus (IDP00699) with Bme-Free Sulfinic Acid Form of CYS289


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of 1.85 Angstrom Resolution Crystal Structure of Apo Betaine Aldehyde Dehydrogenase (Betb) G234S Mutant From Staphylococcus Aureus (IDP00699) with Bme-Free Sulfinic Acid Form of CYS289 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na502

b:15.4
occ:1.00
 O A:LYS460 2.3 15.3 1.0
O B:HOH728 2.4 16.2 1.0
O B:VAL249 2.4 12.7 1.0
O A:HOH612 2.4 12.4 1.0
O A:GLY463 2.4 13.6 1.0
C A:LYS460 3.3 14.4 1.0
C B:VAL249 3.6 13.2 1.0
C A:GLY463 3.6 12.7 1.0
N A:LYS460 3.8 13.4 1.0
CA A:LYS460 3.8 14.2 1.0
CG1 A:ILE464 4.1 14.0 1.0
CG1 B:VAL249 4.2 13.7 1.0
CB B:VAL249 4.3 13.8 1.0
C A:TYR459 4.3 12.9 1.0
O B:HOH692 4.3 20.3 1.0
OD1 B:ASN251 4.3 16.4 1.0
N A:GLY463 4.4 12.5 1.0
CA B:THR250 4.4 12.4 1.0
O B:HOH616 4.4 16.4 1.0
N B:THR250 4.5 12.1 1.0
N A:GLN461 4.5 14.3 1.0
N B:ASN251 4.5 11.7 1.0
O A:GLY458 4.5 15.9 1.0
CA A:GLY463 4.5 12.8 1.0
N A:ILE464 4.6 12.6 1.0
CA B:VAL249 4.6 13.5 1.0
O A:TYR459 4.7 12.6 1.0
CA A:ILE464 4.7 12.2 1.0
O B:ASN248 4.7 15.0 1.0
C B:THR250 4.8 12.1 1.0
CG B:ASN251 4.8 13.1 1.0
CA A:GLN461 4.8 15.0 1.0
O B:HOH723 4.9 26.4 1.0
ND2 B:ASN251 5.0 12.5 1.0

Sodium binding site 3 out of 8 in 4qje

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Sodium binding site 3 out of 8 in the 1.85 Angstrom Resolution Crystal Structure of Apo Betaine Aldehyde Dehydrogenase (Betb) G234S Mutant From Staphylococcus Aureus (IDP00699) with Bme-Free Sulfinic Acid Form of CYS289


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of 1.85 Angstrom Resolution Crystal Structure of Apo Betaine Aldehyde Dehydrogenase (Betb) G234S Mutant From Staphylococcus Aureus (IDP00699) with Bme-Free Sulfinic Acid Form of CYS289 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na501

b:21.8
occ:1.00
 OD1 B:ASP97 2.3 17.8 1.0
O B:HOH777 2.3 24.4 1.0
O B:ASP97 2.4 18.6 1.0
O B:ILE29 2.5 21.5 1.0
O B:ILE184 2.8 17.4 1.0
O B:HOH679 3.1 22.2 1.0
C B:ASP97 3.3 18.2 1.0
CG B:ASP97 3.4 17.9 1.0
CA B:ASP97 3.6 18.5 1.0
C B:ILE29 3.7 22.9 1.0
CG2 B:ILE28 3.8 19.1 1.0
CG2 B:THR185 3.9 16.9 1.0
C B:ILE184 4.0 17.5 1.0
CB B:ASP97 4.1 17.9 1.0
N B:ILE29 4.1 21.2 1.0
OD2 B:ASP97 4.4 16.7 1.0
CA B:THR185 4.4 16.7 1.0
CA B:ILE29 4.4 23.1 1.0
O B:HOH772 4.4 27.1 1.0
CD B:PRO31 4.5 22.2 1.0
N B:THR98 4.6 18.3 1.0
N B:THR185 4.6 16.3 1.0
CB B:THR185 4.7 16.2 1.0
N B:ASN30 4.7 23.2 1.0
CB B:ILE29 4.9 24.4 1.0
CA B:ASN30 5.0 23.1 1.0
C B:ILE28 5.0 20.5 1.0
N B:ASP97 5.0 18.8 1.0

Sodium binding site 4 out of 8 in 4qje

Go back to Sodium Binding Sites List in 4qje
Sodium binding site 4 out of 8 in the 1.85 Angstrom Resolution Crystal Structure of Apo Betaine Aldehyde Dehydrogenase (Betb) G234S Mutant From Staphylococcus Aureus (IDP00699) with Bme-Free Sulfinic Acid Form of CYS289


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of 1.85 Angstrom Resolution Crystal Structure of Apo Betaine Aldehyde Dehydrogenase (Betb) G234S Mutant From Staphylococcus Aureus (IDP00699) with Bme-Free Sulfinic Acid Form of CYS289 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na502

b:15.3
occ:1.00
 O A:HOH657 2.2 15.7 1.0
O B:LYS460 2.4 14.1 1.0
O A:VAL249 2.4 14.5 1.0
O B:GLY463 2.4 13.1 1.0
O B:HOH621 2.4 13.9 1.0
C B:LYS460 3.4 15.6 1.0
C A:VAL249 3.6 15.0 1.0
C B:GLY463 3.6 12.0 1.0
N B:LYS460 3.8 15.1 1.0
CA B:LYS460 3.9 16.0 1.0
CG1 B:ILE464 4.1 12.5 1.0
CG1 A:VAL249 4.2 15.2 1.0
CB A:VAL249 4.3 14.9 1.0
CA A:THR250 4.3 14.3 1.0
OD1 A:ASN251 4.3 17.8 1.0
C B:TYR459 4.4 14.8 1.0
O A:HOH675 4.4 18.5 1.0
N A:ASN251 4.4 12.9 1.0
O A:HOH656 4.4 20.4 1.0
N A:THR250 4.4 14.5 1.0
N B:GLY463 4.4 12.2 1.0
O B:GLY458 4.5 16.3 1.0
CA B:GLY463 4.5 12.1 1.0
N B:ILE464 4.5 11.8 1.0
N B:GLN461 4.6 15.2 1.0
CA A:VAL249 4.6 15.0 1.0
CA B:ILE464 4.7 11.6 1.0
C A:THR250 4.7 13.4 1.0
O A:ASN248 4.7 14.4 1.0
CG A:ASN251 4.7 14.6 1.0
O B:TYR459 4.8 14.2 1.0
CA B:GLN461 4.9 15.8 1.0
ND2 A:ASN251 4.9 13.3 1.0
O A:HOH661 4.9 13.6 1.0

Sodium binding site 5 out of 8 in 4qje

Go back to Sodium Binding Sites List in 4qje
Sodium binding site 5 out of 8 in the 1.85 Angstrom Resolution Crystal Structure of Apo Betaine Aldehyde Dehydrogenase (Betb) G234S Mutant From Staphylococcus Aureus (IDP00699) with Bme-Free Sulfinic Acid Form of CYS289


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of 1.85 Angstrom Resolution Crystal Structure of Apo Betaine Aldehyde Dehydrogenase (Betb) G234S Mutant From Staphylococcus Aureus (IDP00699) with Bme-Free Sulfinic Acid Form of CYS289 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na501

b:19.3
occ:1.00
 OD1 C:ASP97 2.3 18.0 1.0
O C:HOH763 2.4 22.9 1.0
O C:ILE29 2.4 21.2 0.5
O C:ILE29 2.4 21.4 0.5
O C:ASP97 2.4 16.7 1.0
O C:ILE184 2.9 17.5 1.0
C C:ASP97 3.4 17.5 1.0
O C:HOH707 3.4 20.6 1.0
CG C:ASP97 3.4 17.4 1.0
C C:ILE29 3.6 21.7 0.5
C C:ILE29 3.6 22.0 0.5
CA C:ASP97 3.7 17.9 1.0
CG2 C:ILE28 3.7 18.1 1.0
CG2 C:THR185 4.0 16.8 1.0
C C:ILE184 4.0 17.2 1.0
N C:ILE29 4.1 21.5 0.5
N C:ILE29 4.1 21.3 0.5
CB C:ASP97 4.1 17.4 1.0
CA C:ILE29 4.4 22.9 0.5
CA C:ILE29 4.4 22.4 0.5
OD2 C:ASP97 4.4 16.2 1.0
CD C:PRO31 4.5 19.2 1.0
CA C:THR185 4.5 16.2 1.0
O C:HOH721 4.5 27.5 1.0
N C:THR98 4.6 17.3 1.0
N C:ASN30 4.6 22.1 1.0
N C:THR185 4.7 16.7 1.0
CB C:THR185 4.8 16.3 1.0
CA C:ASN30 4.9 21.1 1.0
CD1 C:ILE37 4.9 25.6 1.0
CB C:ILE29 4.9 24.1 0.5
O C:LEU96 4.9 19.5 1.0
CB C:ILE29 5.0 23.3 0.5
C C:ILE28 5.0 21.3 1.0
N C:ASP97 5.0 17.8 1.0

Sodium binding site 6 out of 8 in 4qje

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Sodium binding site 6 out of 8 in the 1.85 Angstrom Resolution Crystal Structure of Apo Betaine Aldehyde Dehydrogenase (Betb) G234S Mutant From Staphylococcus Aureus (IDP00699) with Bme-Free Sulfinic Acid Form of CYS289


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of 1.85 Angstrom Resolution Crystal Structure of Apo Betaine Aldehyde Dehydrogenase (Betb) G234S Mutant From Staphylococcus Aureus (IDP00699) with Bme-Free Sulfinic Acid Form of CYS289 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na502

b:12.1
occ:1.00
 O D:HOH662 2.3 12.3 1.0
O C:LYS460 2.3 12.4 1.0
O C:HOH618 2.4 10.6 1.0
O D:VAL249 2.4 10.7 1.0
O C:GLY463 2.4 10.9 1.0
C C:LYS460 3.4 12.7 1.0
C D:VAL249 3.6 11.2 1.0
C C:GLY463 3.6 10.7 1.0
N C:LYS460 3.7 12.9 1.0
CA C:LYS460 3.8 12.8 1.0
CG1 C:ILE464 4.1 10.9 1.0
C C:TYR459 4.3 11.8 1.0
CA D:THR250 4.3 11.7 1.0
CG1 D:VAL249 4.3 11.8 1.0
CB D:VAL249 4.3 11.5 1.0
N D:ASN251 4.3 10.6 1.0
OD1 D:ASN251 4.3 14.7 1.0
N D:THR250 4.4 11.2 1.0
N C:GLY463 4.4 11.2 1.0
O D:HOH627 4.4 10.5 1.0
O D:HOH631 4.4 14.6 1.0
O C:GLY458 4.5 12.2 1.0
N C:GLN461 4.5 12.2 1.0
N C:ILE464 4.5 10.5 1.0
CA C:GLY463 4.6 11.3 1.0
CA D:VAL249 4.6 11.9 1.0
C D:THR250 4.6 11.4 1.0
CA C:ILE464 4.7 10.2 1.0
O D:ASN248 4.7 12.2 1.0
O C:TYR459 4.7 11.3 1.0
CG D:ASN251 4.7 11.5 1.0
CA C:GLN461 4.9 13.5 1.0
ND2 D:ASN251 4.9 10.1 1.0
O D:HOH619 4.9 10.3 1.0

Sodium binding site 7 out of 8 in 4qje

Go back to Sodium Binding Sites List in 4qje
Sodium binding site 7 out of 8 in the 1.85 Angstrom Resolution Crystal Structure of Apo Betaine Aldehyde Dehydrogenase (Betb) G234S Mutant From Staphylococcus Aureus (IDP00699) with Bme-Free Sulfinic Acid Form of CYS289


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of 1.85 Angstrom Resolution Crystal Structure of Apo Betaine Aldehyde Dehydrogenase (Betb) G234S Mutant From Staphylococcus Aureus (IDP00699) with Bme-Free Sulfinic Acid Form of CYS289 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na501

b:19.1
occ:1.00
 OD1 D:ASP97 2.3 17.6 1.0
O D:ASP97 2.4 15.7 1.0
O D:ILE29 2.5 18.7 1.0
O D:HOH800 2.5 25.3 1.0
O D:ILE184 2.9 16.3 1.0
O D:HOH723 3.3 19.9 1.0
C D:ASP97 3.3 15.1 1.0
CG D:ASP97 3.4 15.9 1.0
CA D:ASP97 3.6 15.7 1.0
C D:ILE29 3.6 19.7 1.0
CG2 D:ILE28 3.7 15.6 1.0
CG2 D:THR185 4.0 16.4 1.0
CB D:ASP97 4.0 15.1 1.0
C D:ILE184 4.1 15.7 1.0
N D:ILE29 4.1 18.3 1.0
OD2 D:ASP97 4.4 14.4 1.0
CA D:ILE29 4.5 20.6 1.0
CD D:PRO31 4.5 16.8 1.0
CA D:THR185 4.5 15.9 1.0
N D:THR98 4.5 14.5 1.0
O D:HOH790 4.5 23.6 1.0
N D:ASN30 4.7 18.9 1.0
N D:THR185 4.7 15.7 1.0
CB D:THR185 4.8 16.1 1.0
CA D:ASN30 4.9 17.9 1.0
CD1 D:ILE37 4.9 20.0 1.0
O D:LEU96 4.9 14.5 1.0
N D:ASP97 4.9 14.4 1.0
C D:ILE28 5.0 17.6 1.0

Sodium binding site 8 out of 8 in 4qje

Go back to Sodium Binding Sites List in 4qje
Sodium binding site 8 out of 8 in the 1.85 Angstrom Resolution Crystal Structure of Apo Betaine Aldehyde Dehydrogenase (Betb) G234S Mutant From Staphylococcus Aureus (IDP00699) with Bme-Free Sulfinic Acid Form of CYS289


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of 1.85 Angstrom Resolution Crystal Structure of Apo Betaine Aldehyde Dehydrogenase (Betb) G234S Mutant From Staphylococcus Aureus (IDP00699) with Bme-Free Sulfinic Acid Form of CYS289 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na502

b:13.2
occ:1.00
 O D:LYS460 2.3 12.8 1.0
O C:HOH657 2.3 11.8 1.0
O C:VAL249 2.4 11.9 1.0
O D:GLY463 2.4 10.5 1.0
O D:HOH632 2.4 12.1 1.0
C D:LYS460 3.4 13.3 1.0
C C:VAL249 3.6 12.8 1.0
C D:GLY463 3.6 10.8 1.0
N D:LYS460 3.8 13.5 1.0
CA D:LYS460 3.9 14.0 1.0
CG1 D:ILE464 4.0 12.1 1.0
CG1 C:VAL249 4.2 13.6 1.0
OD1 C:ASN251 4.3 13.6 1.0
CB C:VAL249 4.3 13.7 1.0
CA C:THR250 4.3 11.8 1.0
N C:ASN251 4.3 11.6 1.0
N D:GLY463 4.3 11.5 1.0
C D:TYR459 4.4 12.4 1.0
N C:THR250 4.4 12.5 1.0
O C:HOH628 4.4 13.8 1.0
CA D:GLY463 4.5 11.6 1.0
N D:ILE464 4.5 10.3 1.0
N D:GLN461 4.5 12.9 1.0
O C:HOH647 4.5 16.4 1.0
O D:GLY458 4.5 13.2 1.0
CA C:VAL249 4.6 13.3 1.0
CA D:ILE464 4.6 10.3 1.0
C C:THR250 4.6 11.8 1.0
CG C:ASN251 4.7 11.0 1.0
O D:TYR459 4.7 11.4 1.0
O C:ASN248 4.8 13.8 1.0
CA D:GLN461 4.8 13.6 1.0
ND2 C:ASN251 4.9 10.1 1.0
O C:HOH656 5.0 12.4 1.0
CB D:ILE464 5.0 10.8 1.0
CD1 D:ILE464 5.0 12.6 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). 1.85 Angstrom Resolution Crystal Structure of Apo Betaine Aldehyde Dehydrogenase (Betb) G234S Mutant From Staphylococcus Aureus (IDP00699) with Bme-Free Sulfinic Acid Form of CYS289 To Be Published.
Page generated: Mon Oct 7 18:00:11 2024

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