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Sodium in PDB 5eyu: 1.72 Angstrom Resolution Crystal Structure of Betaine Aldehyde Dehydrogenase (Betb) P449M Point Mutant From Staphylococcus Aureus in Complex with Nad+ and Bme-Modified CYS289

Enzymatic activity of 1.72 Angstrom Resolution Crystal Structure of Betaine Aldehyde Dehydrogenase (Betb) P449M Point Mutant From Staphylococcus Aureus in Complex with Nad+ and Bme-Modified CYS289

All present enzymatic activity of 1.72 Angstrom Resolution Crystal Structure of Betaine Aldehyde Dehydrogenase (Betb) P449M Point Mutant From Staphylococcus Aureus in Complex with Nad+ and Bme-Modified CYS289:
1.2.1.8;

Protein crystallography data

The structure of 1.72 Angstrom Resolution Crystal Structure of Betaine Aldehyde Dehydrogenase (Betb) P449M Point Mutant From Staphylococcus Aureus in Complex with Nad+ and Bme-Modified CYS289, PDB code: 5eyu 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) 29.66 / 1.72
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 224.271, 102.721, 117.810, 90.00, 104.75, 90.00
R / Rfree (%) 16.4 / 18.3

Sodium Binding Sites:

The binding sites of Sodium atom in the 1.72 Angstrom Resolution Crystal Structure of Betaine Aldehyde Dehydrogenase (Betb) P449M Point Mutant From Staphylococcus Aureus in Complex with Nad+ and Bme-Modified CYS289 (pdb code 5eyu). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 8 binding sites of Sodium where determined in the 1.72 Angstrom Resolution Crystal Structure of Betaine Aldehyde Dehydrogenase (Betb) P449M Point Mutant From Staphylococcus Aureus in Complex with Nad+ and Bme-Modified CYS289, PDB code: 5eyu:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Sodium binding site 1 out of 8 in 5eyu

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Sodium binding site 1 out of 8 in the 1.72 Angstrom Resolution Crystal Structure of Betaine Aldehyde Dehydrogenase (Betb) P449M Point 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 1.72 Angstrom Resolution Crystal Structure of Betaine Aldehyde Dehydrogenase (Betb) P449M Point 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:12.4
occ:1.00
 O B:VAL249 2.3 9.6 1.0
O A:LYS460 2.3 12.5 1.0
O A:GLY463 2.4 9.7 1.0
O B:HOH1052 2.4 11.3 1.0
O A:HOH961 2.4 11.9 1.0
C A:LYS460 3.4 12.9 1.0
C B:VAL249 3.5 10.7 1.0
C A:GLY463 3.6 9.6 1.0
N A:LYS460 3.7 12.2 1.0
CA A:LYS460 3.8 13.6 1.0
CG1 A:ILE464 3.9 10.8 1.0
CG1 B:VAL249 4.2 11.6 1.0
CB B:VAL249 4.2 11.2 1.0
CA B:THR250 4.3 10.4 1.0
N B:ASN251 4.3 9.5 1.0
C A:TYR459 4.3 11.1 1.0
N A:GLY463 4.3 9.4 1.0
ND2 B:ASN251 4.3 10.5 1.0
N B:THR250 4.4 10.3 1.0
O A:GLY458 4.4 10.8 1.0
O B:HOH866 4.5 15.5 1.0
N A:ILE464 4.5 9.5 1.0
CA A:GLY463 4.5 9.7 1.0
CA B:VAL249 4.5 11.2 1.0
N A:GLN461 4.5 12.8 1.0
O B:HOH785 4.5 11.6 1.0
O B:ASN248 4.6 12.4 1.0
C B:THR250 4.6 10.1 1.0
CA A:ILE464 4.7 9.6 1.0
CG B:ASN251 4.7 10.2 1.0
O A:TYR459 4.7 10.8 1.0
CA A:GLN461 4.8 13.1 1.0
OD1 B:ASN251 4.9 9.7 1.0
CD1 A:ILE464 4.9 11.7 1.0
O B:HOH754 5.0 11.7 1.0
CB A:ILE464 5.0 10.1 1.0

Sodium binding site 2 out of 8 in 5eyu

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Sodium binding site 2 out of 8 in the 1.72 Angstrom Resolution Crystal Structure of Betaine Aldehyde Dehydrogenase (Betb) P449M Point 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 1.72 Angstrom Resolution Crystal Structure of Betaine Aldehyde Dehydrogenase (Betb) P449M Point Mutant From Staphylococcus Aureus in Complex with Nad+ and Bme-Modified CYS289 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na503

b:17.8
occ:1.00
 OD1 A:ASP97 2.3 15.5 1.0
O A:HOH1049 2.3 23.1 1.0
O A:ASP97 2.4 13.3 1.0
O A:ILE29 2.5 17.1 1.0
O A:ILE184 2.8 14.0 1.0
O A:HOH727 3.3 18.9 1.0
C A:ASP97 3.3 13.8 1.0
CG A:ASP97 3.4 14.2 1.0
CA A:ASP97 3.6 13.8 1.0
C A:ILE29 3.7 18.5 1.0
CG2 A:ILE28 3.7 14.0 1.0
CG2 A:THR185 3.9 12.7 1.0
C A:ILE184 3.9 13.6 1.0
CB A:ASP97 4.1 14.0 1.0
N A:ILE29 4.1 17.3 1.0
O A:HOH1090 4.3 25.6 1.0
CA A:THR185 4.4 12.7 1.0
OD2 A:ASP97 4.4 14.7 1.0
CA A:ILE29 4.5 19.6 1.0
CD A:PRO31 4.5 14.8 1.0
N A:THR98 4.6 13.2 1.0
N A:THR185 4.6 13.0 1.0
CB A:THR185 4.7 12.7 1.0
N A:ASN30 4.7 17.1 1.0
CD1 A:ILE37 4.9 17.7 1.0
CA A:ASN30 4.9 16.1 1.0
N A:ASP97 5.0 13.8 1.0

Sodium binding site 3 out of 8 in 5eyu

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Sodium binding site 3 out of 8 in the 1.72 Angstrom Resolution Crystal Structure of Betaine Aldehyde Dehydrogenase (Betb) P449M Point 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 1.72 Angstrom Resolution Crystal Structure of Betaine Aldehyde Dehydrogenase (Betb) P449M Point 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:11.8
occ:1.00
 O A:HOH1047 2.3 9.6 1.0
O B:HOH939 2.3 9.9 1.0
O B:LYS460 2.3 11.7 1.0
O A:VAL249 2.4 10.3 1.0
O B:GLY463 2.4 9.2 1.0
C B:LYS460 3.4 12.2 1.0
C A:VAL249 3.6 10.8 1.0
C B:GLY463 3.6 9.2 1.0
N B:LYS460 3.7 11.6 1.0
CA B:LYS460 3.8 12.2 1.0
CG1 B:ILE464 4.0 9.6 1.0
C B:TYR459 4.2 11.1 1.0
CB A:VAL249 4.3 11.0 1.0
CA A:THR250 4.3 10.1 1.0
CG1 A:VAL249 4.3 11.4 1.0
N A:ASN251 4.3 9.8 1.0
N B:GLY463 4.3 9.6 1.0
O B:GLY458 4.4 11.7 1.0
N A:THR250 4.4 10.4 1.0
ND2 A:ASN251 4.4 11.2 1.0
O A:HOH828 4.5 11.7 1.0
O A:HOH840 4.5 15.0 1.0
N B:ILE464 4.5 9.3 1.0
CA B:GLY463 4.5 9.4 1.0
N B:GLN461 4.5 11.9 1.0
CA A:VAL249 4.6 11.3 1.0
O A:ASN248 4.6 12.8 1.0
C A:THR250 4.6 10.2 1.0
CA B:ILE464 4.7 8.9 1.0
O B:TYR459 4.7 10.9 1.0
CG A:ASN251 4.7 10.8 1.0
OD1 A:ASN251 4.8 10.1 1.0
CA B:GLN461 4.9 12.5 1.0
CD1 B:ILE464 4.9 10.5 1.0
O A:HOH770 4.9 10.6 1.0
CA B:TYR459 5.0 10.9 1.0

Sodium binding site 4 out of 8 in 5eyu

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Sodium binding site 4 out of 8 in the 1.72 Angstrom Resolution Crystal Structure of Betaine Aldehyde Dehydrogenase (Betb) P449M Point 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 1.72 Angstrom Resolution Crystal Structure of Betaine Aldehyde Dehydrogenase (Betb) P449M Point Mutant From Staphylococcus Aureus in Complex with Nad+ and Bme-Modified CYS289 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na503

b:21.2
occ:1.00
 O B:HOH1044 2.3 25.3 1.0
OD1 B:ASP97 2.4 16.0 1.0
O B:ILE29 2.4 19.1 1.0
O B:ASP97 2.5 17.1 1.0
O B:ILE184 2.7 15.2 1.0
O B:HOH686 3.4 19.2 1.0
C B:ASP97 3.4 16.5 1.0
CG B:ASP97 3.5 16.9 1.0
C B:ILE29 3.6 21.2 1.0
CA B:ASP97 3.7 17.0 1.0
CG2 B:ILE28 3.7 19.7 1.0
CG2 B:THR185 3.9 15.7 1.0
C B:ILE184 3.9 15.5 1.0
N B:ILE29 4.1 21.1 1.0
CB B:ASP97 4.2 16.7 1.0
O B:HOH1101 4.4 26.4 1.0
CA B:THR185 4.4 15.2 1.0
CA B:ILE29 4.4 22.6 1.0
OD2 B:ASP97 4.4 16.0 1.0
CD B:PRO31 4.5 17.8 1.0
N B:THR185 4.6 15.0 1.0
N B:THR98 4.6 16.4 1.0
N B:ASN30 4.7 20.4 1.0
CB B:THR185 4.7 15.1 1.0
CD1 B:ILE37 4.9 22.0 1.0
CA B:ASN30 4.9 19.9 1.0
CB B:ILE29 5.0 25.6 1.0
C B:ILE28 5.0 21.1 1.0

Sodium binding site 5 out of 8 in 5eyu

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Sodium binding site 5 out of 8 in the 1.72 Angstrom Resolution Crystal Structure of Betaine Aldehyde Dehydrogenase (Betb) P449M Point 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 5 of 1.72 Angstrom Resolution Crystal Structure of Betaine Aldehyde Dehydrogenase (Betb) P449M Point 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:10.3
occ:1.00
 O D:VAL249 2.3 9.8 1.0
O C:GLY463 2.3 9.5 1.0
O C:LYS460 2.4 11.3 1.0
O D:HOH1043 2.4 11.9 1.0
O C:HOH901 2.5 11.2 1.0
C C:LYS460 3.4 11.6 1.0
C D:VAL249 3.5 10.7 1.0
C C:GLY463 3.6 9.2 1.0
N C:LYS460 3.8 11.2 1.0
CA C:LYS460 3.9 12.2 1.0
CG1 C:ILE464 4.0 9.3 1.0
CG1 D:VAL249 4.2 11.3 1.0
CB D:VAL249 4.2 10.6 1.0
CA D:THR250 4.3 10.2 1.0
N C:GLY463 4.3 9.3 1.0
C C:TYR459 4.3 10.7 1.0
N D:THR250 4.4 10.4 1.0
N D:ASN251 4.4 9.8 1.0
O D:HOH860 4.4 13.6 1.0
ND2 D:ASN251 4.4 11.5 1.0
O C:GLY458 4.4 11.8 1.0
O D:HOH790 4.5 11.2 1.0
CA D:VAL249 4.5 10.6 1.0
CA C:GLY463 4.5 9.3 1.0
N C:ILE464 4.5 8.9 1.0
N C:GLN461 4.6 11.2 1.0
O D:ASN248 4.6 12.1 1.0
C D:THR250 4.6 10.1 1.0
CA C:ILE464 4.7 8.6 1.0
CG D:ASN251 4.7 10.7 1.0
O C:TYR459 4.7 11.2 1.0
O D:HOH798 4.8 13.3 1.0
CA C:GLN461 4.9 11.7 1.0
OD1 D:ASN251 4.9 10.9 1.0
CD1 C:ILE464 4.9 9.8 1.0

Sodium binding site 6 out of 8 in 5eyu

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Sodium binding site 6 out of 8 in the 1.72 Angstrom Resolution Crystal Structure of Betaine Aldehyde Dehydrogenase (Betb) P449M Point 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 6 of 1.72 Angstrom Resolution Crystal Structure of Betaine Aldehyde Dehydrogenase (Betb) P449M Point Mutant From Staphylococcus Aureus in Complex with Nad+ and Bme-Modified CYS289 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na503

b:16.7
occ:1.00
 O C:HOH1030 2.3 19.2 1.0
O C:ASP97 2.4 13.1 1.0
OD1 C:ASP97 2.4 13.1 1.0
O C:ILE29 2.5 15.6 1.0
O C:ILE184 2.8 12.9 1.0
C C:ASP97 3.4 13.5 1.0
O C:HOH746 3.4 15.1 1.0
CG C:ASP97 3.5 13.1 1.0
C C:ILE29 3.7 16.1 1.0
CA C:ASP97 3.7 13.7 1.0
CG2 C:ILE28 3.8 14.5 1.0
CG2 C:THR185 3.9 12.9 1.0
C C:ILE184 3.9 12.8 1.0
N C:ILE29 4.1 15.6 1.0
CB C:ASP97 4.2 13.3 1.0
O C:HOH1097 4.3 21.2 1.0
CA C:ILE29 4.4 16.8 1.0
CA C:THR185 4.4 12.5 1.0
CD C:PRO31 4.5 13.8 1.0
OD2 C:ASP97 4.5 12.8 1.0
N C:THR98 4.6 13.4 1.0
N C:THR185 4.6 12.2 1.0
CB C:THR185 4.7 12.6 1.0
N C:ASN30 4.7 15.2 1.0
CD1 C:ILE37 4.9 17.2 1.0
CA C:ASN30 4.9 14.7 1.0
CB C:ILE29 5.0 18.7 1.0
C C:ILE28 5.0 15.1 1.0
CA C:ILE184 5.0 12.4 1.0

Sodium binding site 7 out of 8 in 5eyu

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Sodium binding site 7 out of 8 in the 1.72 Angstrom Resolution Crystal Structure of Betaine Aldehyde Dehydrogenase (Betb) P449M Point 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 7 of 1.72 Angstrom Resolution Crystal Structure of Betaine Aldehyde Dehydrogenase (Betb) P449M Point 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:12.8
occ:1.00
 O C:HOH1050 2.3 15.7 1.0
O C:VAL249 2.3 10.5 1.0
O D:HOH942 2.4 14.8 1.0
O D:GLY463 2.4 10.2 1.0
O D:LYS460 2.4 13.2 1.0
C D:LYS460 3.5 13.0 1.0
C C:VAL249 3.5 11.3 1.0
C D:GLY463 3.6 10.0 1.0
N D:LYS460 3.9 12.3 1.0
CA D:LYS460 4.0 13.3 1.0
CG1 D:ILE464 4.0 11.2 1.0
CG1 C:VAL249 4.3 12.9 1.0
CB C:VAL249 4.3 12.8 1.0
N C:ASN251 4.3 10.7 1.0
CA C:THR250 4.3 10.9 1.0
ND2 C:ASN251 4.3 12.7 1.0
N C:THR250 4.4 11.1 1.0
N D:GLY463 4.4 10.2 1.0
C D:TYR459 4.4 12.1 1.0
O C:HOH847 4.4 15.2 1.0
O C:HOH832 4.5 14.5 1.0
O D:GLY458 4.5 13.1 1.0
N D:ILE464 4.5 9.7 1.0
CA D:GLY463 4.5 10.2 1.0
CA C:VAL249 4.6 12.3 1.0
N D:GLN461 4.6 13.0 1.0
C C:THR250 4.6 11.1 1.0
CG C:ASN251 4.7 11.6 1.0
CA D:ILE464 4.7 9.7 1.0
O C:ASN248 4.7 13.7 1.0
OD1 C:ASN251 4.8 11.8 1.0
O D:TYR459 4.8 11.2 1.0
O C:HOH826 4.8 12.5 1.0
CD1 D:ILE464 4.9 12.4 1.0
CA D:GLN461 4.9 13.3 1.0
CB D:ILE464 5.0 10.4 1.0

Sodium binding site 8 out of 8 in 5eyu

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Sodium binding site 8 out of 8 in the 1.72 Angstrom Resolution Crystal Structure of Betaine Aldehyde Dehydrogenase (Betb) P449M Point 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 8 of 1.72 Angstrom Resolution Crystal Structure of Betaine Aldehyde Dehydrogenase (Betb) P449M Point Mutant From Staphylococcus Aureus in Complex with Nad+ and Bme-Modified CYS289 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na503

b:18.9
occ:1.00
 O D:HOH1038 2.2 22.4 1.0
O D:ASP97 2.4 16.1 1.0
OD1 D:ASP97 2.4 17.5 1.0
O D:ILE29 2.4 17.1 1.0
O D:ILE184 2.8 13.8 1.0
C D:ASP97 3.3 16.4 1.0
CG D:ASP97 3.5 16.2 1.0
O D:HOH781 3.5 16.5 1.0
CA D:ASP97 3.7 16.5 1.0
C D:ILE29 3.7 18.6 1.0
CG2 D:THR185 3.8 13.1 1.0
CG2 D:ILE28 3.9 16.0 1.0
C D:ILE184 3.9 13.7 1.0
CB D:ASP97 4.1 16.3 1.0
N D:ILE29 4.2 18.6 1.0
O D:HOH1109 4.4 23.4 1.0
CA D:THR185 4.4 13.3 1.0
CD D:PRO31 4.4 16.0 1.0
CA D:ILE29 4.5 19.5 1.0
OD2 D:ASP97 4.5 17.0 1.0
N D:THR98 4.6 15.2 1.0
N D:THR185 4.6 12.9 1.0
N D:ASN30 4.7 18.6 1.0
CB D:THR185 4.7 12.8 1.0
CA D:ASN30 4.9 17.7 1.0
CD1 D:ILE37 4.9 23.4 1.0
O D:LEU96 5.0 16.9 1.0
N D:ASP97 5.0 16.2 1.0

Reference:

A.S.Halavaty, G.Minasov, C.Chen, J.C.Joo, A.F.Yakunin, W.F.Anderson. 1.72 Angstrom Resolution Crystal Structure of Betaine Aldehyde Dehydrogenase (Betb) P449M Point Mutant From Staphylococcus Aureus in Complex with Nad+ and Bme-Modified CYS289 To Be Published.
Page generated: Mon Oct 7 20:54:55 2024

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