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Sodium in PDB 4mpy: 1.85 Angstrom Resolution Crystal Structure of Betaine Aldehyde Dehydrogenase (Betb) From Staphylococcus Aureus (IDP00699) in Complex with Nad+

Enzymatic activity of 1.85 Angstrom Resolution Crystal Structure of Betaine Aldehyde Dehydrogenase (Betb) From Staphylococcus Aureus (IDP00699) in Complex with Nad+

All present enzymatic activity of 1.85 Angstrom Resolution Crystal Structure of Betaine Aldehyde Dehydrogenase (Betb) From Staphylococcus Aureus (IDP00699) in Complex with Nad+:
1.2.1.8;

Protein crystallography data

The structure of 1.85 Angstrom Resolution Crystal Structure of Betaine Aldehyde Dehydrogenase (Betb) From Staphylococcus Aureus (IDP00699) in Complex with Nad+, PDB code: 4mpy was solved by A.S.Halavaty, G.Minasov, L.Shuvalova, J.Winsor, S.N.Peterson, 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) 24.98 / 1.85
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 99.866, 159.146, 122.993, 90.00, 94.79, 90.00
R / Rfree (%) 12.6 / 16.7

Sodium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 19;

Binding sites:

The binding sites of Sodium atom in the 1.85 Angstrom Resolution Crystal Structure of Betaine Aldehyde Dehydrogenase (Betb) From Staphylococcus Aureus (IDP00699) in Complex with Nad+ (pdb code 4mpy). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 19 binding sites of Sodium where determined in the 1.85 Angstrom Resolution Crystal Structure of Betaine Aldehyde Dehydrogenase (Betb) From Staphylococcus Aureus (IDP00699) in Complex with Nad+, PDB code: 4mpy:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Sodium binding site 1 out of 19 in 4mpy

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Sodium binding site 1 out of 19 in the 1.85 Angstrom Resolution Crystal Structure of Betaine Aldehyde Dehydrogenase (Betb) From Staphylococcus Aureus (IDP00699) in Complex with Nad+


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 Betaine Aldehyde Dehydrogenase (Betb) From Staphylococcus Aureus (IDP00699) in Complex with Nad+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na502

b:17.1
occ:1.00
 O A:HOH648 2.2 19.6 1.0
O B:VAL249 2.3 16.6 1.0
O B:HOH726 2.3 18.9 1.0
O A:LYS460 2.3 17.4 1.0
O A:GLY463 2.3 16.3 1.0
C A:LYS460 3.4 16.7 1.0
C B:VAL249 3.5 16.3 1.0
C A:GLY463 3.5 14.1 1.0
N A:LYS460 3.8 17.0 1.0
CA A:LYS460 3.9 17.5 1.0
CG1 A:ILE464 4.1 16.1 1.0
CG1 B:VAL249 4.2 16.4 1.0
CB B:VAL249 4.3 16.2 1.0
C A:TYR459 4.3 18.0 1.0
N A:GLY463 4.3 14.6 1.0
ND2 B:ASN251 4.4 17.5 1.0
O B:HOH601 4.4 19.1 1.0
N B:THR250 4.4 15.3 1.0
CA A:GLY463 4.4 15.2 1.0
CA B:THR250 4.4 15.5 1.0
N A:ILE464 4.5 14.2 1.0
N A:GLN461 4.5 16.7 1.0
O B:HOH664 4.5 19.9 1.0
N B:ASN251 4.5 14.4 1.0
CA B:VAL249 4.6 16.2 1.0
O A:GLY458 4.6 18.2 1.0
O A:TYR459 4.7 15.9 1.0
CA A:ILE464 4.7 13.7 1.0
O B:ASN248 4.8 20.2 1.0
CG B:ASN251 4.8 17.7 1.0
CA A:GLN461 4.8 16.5 1.0
C B:THR250 4.8 15.7 1.0
O B:HOH630 5.0 14.8 1.0
OD1 B:ASN251 5.0 15.0 1.0

Sodium binding site 2 out of 19 in 4mpy

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Sodium binding site 2 out of 19 in the 1.85 Angstrom Resolution Crystal Structure of Betaine Aldehyde Dehydrogenase (Betb) From Staphylococcus Aureus (IDP00699) in Complex with Nad+


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 Betaine Aldehyde Dehydrogenase (Betb) From Staphylococcus Aureus (IDP00699) in Complex with Nad+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na503

b:19.4
occ:1.00
 O A:HOH843 2.2 30.6 1.0
OD1 A:ASP97 2.3 23.4 1.0
O A:ASP97 2.3 23.4 1.0
O A:ILE29 2.3 27.5 1.0
O A:ILE184 2.4 22.4 1.0
O A:HOH686 3.3 26.1 1.0
C A:ASP97 3.4 20.9 1.0
CG A:ASP97 3.4 22.4 1.0
C A:ILE29 3.6 26.6 1.0
C A:ILE184 3.7 20.6 1.0
CA A:ASP97 3.7 21.2 1.0
CG2 A:ILE28 3.8 21.0 1.0
CG2 A:THR185 4.0 20.9 1.0
CB A:ASP97 4.1 20.3 1.0
N A:ILE29 4.1 25.9 1.0
OD2 A:ASP97 4.3 22.2 1.0
CA A:ILE29 4.4 29.0 1.0
CA A:THR185 4.4 19.7 1.0
CD A:PRO31 4.5 23.6 1.0
N A:THR185 4.5 20.4 1.0
O A:HOH993 4.6 34.4 1.0
N A:THR98 4.6 19.8 1.0
N A:ASN30 4.6 24.7 1.0
CB A:THR185 4.8 19.8 1.0
CA A:ILE184 4.9 22.4 1.0
CB A:ILE29 4.9 36.1 1.0
CA A:ASN30 5.0 23.0 1.0
C A:ILE28 5.0 26.9 1.0

Sodium binding site 3 out of 19 in 4mpy

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Sodium binding site 3 out of 19 in the 1.85 Angstrom Resolution Crystal Structure of Betaine Aldehyde Dehydrogenase (Betb) From Staphylococcus Aureus (IDP00699) in Complex with Nad+


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 Betaine Aldehyde Dehydrogenase (Betb) From Staphylococcus Aureus (IDP00699) in Complex with Nad+ within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na502

b:13.2
occ:1.00
 O A:HOH627 2.3 13.5 1.0
O B:HOH674 2.3 15.7 1.0
O A:VAL249 2.3 14.4 1.0
O B:LYS460 2.3 15.5 1.0
O B:GLY463 2.3 11.8 1.0
C B:LYS460 3.4 13.9 1.0
C B:GLY463 3.5 12.1 1.0
C A:VAL249 3.5 14.3 1.0
N B:LYS460 3.8 14.3 1.0
CA B:LYS460 3.9 14.9 1.0
CG1 B:ILE464 4.1 13.4 1.0
CG1 A:VAL249 4.2 16.1 1.0
CB A:VAL249 4.2 15.4 1.0
ND2 A:ASN251 4.3 16.8 1.0
N B:GLY463 4.3 12.7 1.0
C B:TYR459 4.3 14.3 1.0
O A:HOH652 4.4 17.3 1.0
CA A:THR250 4.4 14.1 1.0
N A:THR250 4.4 13.5 1.0
CA B:GLY463 4.4 12.3 1.0
O A:HOH639 4.4 15.3 1.0
N A:ASN251 4.5 12.4 1.0
N B:ILE464 4.5 13.0 1.0
O B:GLY458 4.5 16.3 1.0
CA A:VAL249 4.5 14.7 1.0
N B:GLN461 4.5 14.0 1.0
CA B:ILE464 4.7 12.4 1.0
O A:ASN248 4.7 15.8 1.0
C A:THR250 4.7 13.4 1.0
CG A:ASN251 4.8 14.7 1.0
O B:TYR459 4.8 13.3 1.0
CA B:GLN461 4.9 14.2 1.0
CD1 B:ILE464 5.0 14.5 1.0
OD1 A:ASN251 5.0 15.2 1.0

Sodium binding site 4 out of 19 in 4mpy

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Sodium binding site 4 out of 19 in the 1.85 Angstrom Resolution Crystal Structure of Betaine Aldehyde Dehydrogenase (Betb) From Staphylococcus Aureus (IDP00699) in Complex with Nad+


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 Betaine Aldehyde Dehydrogenase (Betb) From Staphylococcus Aureus (IDP00699) in Complex with Nad+ within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na503

b:17.2
occ:1.00
 O B:HOH676 2.2 25.2 1.0
OD1 B:ASP97 2.3 19.2 1.0
O B:ASP97 2.3 18.2 1.0
O B:ILE29 2.4 19.8 1.0
O B:ILE184 2.4 18.3 1.0
C B:ASP97 3.3 16.2 1.0
O B:HOH685 3.4 20.1 1.0
CG B:ASP97 3.4 18.6 1.0
C B:ILE29 3.6 19.5 1.0
CA B:ASP97 3.7 16.6 1.0
C B:ILE184 3.7 15.0 1.0
CG2 B:ILE28 3.7 16.7 1.0
CG2 B:THR185 3.9 16.7 1.0
CB B:ASP97 4.1 16.3 1.0
N B:ILE29 4.1 18.6 1.0
CA B:THR185 4.3 16.3 1.0
OD2 B:ASP97 4.4 18.1 1.0
CA B:ILE29 4.4 20.3 1.0
O B:HOH940 4.5 24.4 1.0
N B:THR185 4.5 15.3 1.0
N B:THR98 4.6 15.8 1.0
CD B:PRO31 4.6 16.9 1.0
N B:ASN30 4.7 17.9 1.0
CB B:THR185 4.7 17.2 1.0
CA B:ILE184 4.9 15.6 1.0
O B:LEU96 5.0 15.9 1.0
CA B:ASN30 5.0 17.1 1.0

Sodium binding site 5 out of 19 in 4mpy

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Sodium binding site 5 out of 19 in the 1.85 Angstrom Resolution Crystal Structure of Betaine Aldehyde Dehydrogenase (Betb) From Staphylococcus Aureus (IDP00699) in Complex with Nad+


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 Betaine Aldehyde Dehydrogenase (Betb) From Staphylococcus Aureus (IDP00699) in Complex with Nad+ within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na502

b:11.1
occ:1.00
 O D:HOH667 2.3 12.1 1.0
O D:VAL249 2.3 11.7 1.0
O C:LYS460 2.3 11.4 1.0
O C:HOH641 2.3 14.3 1.0
O C:GLY463 2.3 9.4 1.0
C C:LYS460 3.3 11.0 1.0
C D:VAL249 3.5 11.0 1.0
C C:GLY463 3.6 9.9 1.0
N C:LYS460 3.7 11.2 1.0
CA C:LYS460 3.8 12.3 1.0
CG1 C:ILE464 4.1 11.0 1.0
CB D:VAL249 4.2 11.5 1.0
CG1 D:VAL249 4.2 11.6 1.0
C C:TYR459 4.3 12.4 1.0
N C:GLY463 4.3 8.9 1.0
CA D:THR250 4.4 10.9 1.0
N D:THR250 4.4 11.1 1.0
ND2 D:ASN251 4.4 14.0 1.0
O D:HOH693 4.4 16.3 1.0
O D:HOH632 4.4 13.6 1.0
O C:GLY458 4.5 11.9 1.0
CA D:VAL249 4.5 12.0 1.0
N C:GLN461 4.5 10.2 1.0
CA C:GLY463 4.5 10.1 1.0
N D:ASN251 4.5 10.9 1.0
N C:ILE464 4.6 9.2 1.0
O D:ASN248 4.6 13.3 1.0
O C:TYR459 4.7 11.0 1.0
CA C:ILE464 4.8 9.7 1.0
C D:THR250 4.8 10.9 1.0
CA C:GLN461 4.9 10.8 1.0
CG D:ASN251 4.9 12.7 1.0
CD1 C:ILE464 5.0 11.8 1.0

Sodium binding site 6 out of 19 in 4mpy

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Sodium binding site 6 out of 19 in the 1.85 Angstrom Resolution Crystal Structure of Betaine Aldehyde Dehydrogenase (Betb) From Staphylococcus Aureus (IDP00699) in Complex with Nad+


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 Betaine Aldehyde Dehydrogenase (Betb) From Staphylococcus Aureus (IDP00699) in Complex with Nad+ within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na503

b:16.6
occ:1.00
 O C:HOH871 2.3 23.9 1.0
OD1 C:ASP97 2.3 17.2 1.0
O C:ASP97 2.3 13.9 1.0
O C:ILE29 2.4 17.6 1.0
O C:ILE184 2.5 15.5 1.0
O C:HOH682 3.3 22.8 1.0
C C:ASP97 3.3 13.6 1.0
CG C:ASP97 3.4 14.8 1.0
CA C:ASP97 3.6 13.2 1.0
C C:ILE29 3.7 17.4 1.0
CG2 C:ILE28 3.7 16.4 1.0
C C:ILE184 3.8 13.8 1.0
CG2 C:THR185 3.9 14.1 1.0
CB C:ASP97 4.1 13.6 1.0
N C:ILE29 4.1 17.6 1.0
OD2 C:ASP97 4.4 15.0 1.0
O C:HOH757 4.4 20.2 1.0
CA C:THR185 4.4 13.2 1.0
CA C:ILE29 4.5 18.3 1.0
CD C:PRO31 4.6 14.8 1.0
N C:THR185 4.6 13.5 1.0
N C:THR98 4.6 13.5 1.0
CG1 C:ILE29 4.7 24.8 1.0
CB C:THR185 4.7 14.0 1.0
N C:ASN30 4.7 15.3 1.0
O C:LEU96 4.9 14.0 0.5
O C:LEU96 4.9 14.1 0.5
CA C:ILE184 5.0 15.1 1.0
C C:ILE28 5.0 17.1 1.0
N C:ASP97 5.0 13.3 1.0

Sodium binding site 7 out of 19 in 4mpy

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Sodium binding site 7 out of 19 in the 1.85 Angstrom Resolution Crystal Structure of Betaine Aldehyde Dehydrogenase (Betb) From Staphylococcus Aureus (IDP00699) in Complex with Nad+


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 Betaine Aldehyde Dehydrogenase (Betb) From Staphylococcus Aureus (IDP00699) in Complex with Nad+ within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na502

b:12.6
occ:1.00
 O D:HOH697 2.2 16.3 1.0
O D:LYS460 2.3 14.2 1.0
O C:VAL249 2.3 13.6 1.0
O C:HOH718 2.3 13.9 1.0
O D:GLY463 2.3 13.2 1.0
C D:LYS460 3.3 13.6 1.0
C D:GLY463 3.5 12.0 1.0
C C:VAL249 3.5 12.1 1.0
N D:LYS460 3.8 13.5 1.0
CA D:LYS460 3.8 15.3 1.0
CG1 D:ILE464 4.0 14.2 1.0
CG1 C:VAL249 4.2 13.0 1.0
CB C:VAL249 4.2 12.2 1.0
ND2 C:ASN251 4.3 16.5 1.0
N D:GLY463 4.3 11.5 1.0
C D:TYR459 4.3 14.7 1.0
O C:HOH617 4.4 15.6 1.0
N C:THR250 4.4 13.4 1.0
CA C:THR250 4.4 12.9 1.0
CA D:GLY463 4.4 13.6 1.0
N C:ASN251 4.4 11.9 1.0
N D:ILE464 4.5 11.6 1.0
N D:GLN461 4.5 13.1 1.0
CA C:VAL249 4.5 12.8 1.0
O D:GLY458 4.5 15.9 1.0
O C:HOH701 4.6 15.9 1.0
CG C:ASN251 4.7 15.7 1.0
C C:THR250 4.7 13.6 1.0
CA D:ILE464 4.7 12.0 1.0
O D:TYR459 4.7 12.3 1.0
O C:ASN248 4.8 16.1 1.0
CA D:GLN461 4.8 13.4 1.0
OD1 C:ASN251 4.8 13.6 1.0
CD1 D:ILE464 4.8 14.9 1.0
O D:HOH1071 5.0 42.4 1.0
O C:HOH631 5.0 12.6 1.0

Sodium binding site 8 out of 19 in 4mpy

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Sodium binding site 8 out of 19 in the 1.85 Angstrom Resolution Crystal Structure of Betaine Aldehyde Dehydrogenase (Betb) From Staphylococcus Aureus (IDP00699) in Complex with Nad+


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 Betaine Aldehyde Dehydrogenase (Betb) From Staphylococcus Aureus (IDP00699) in Complex with Nad+ within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na503

b:18.4
occ:1.00
 OD1 D:ASP97 2.2 18.3 1.0
O D:HOH832 2.2 27.8 1.0
O D:ASP97 2.3 16.9 1.0
O D:ILE29 2.3 23.4 1.0
O D:ILE184 2.5 17.4 1.0
C D:ASP97 3.3 15.7 1.0
O D:HOH737 3.3 21.8 1.0
CG D:ASP97 3.4 16.9 1.0
C D:ILE29 3.6 20.3 1.0
CA D:ASP97 3.6 15.6 1.0
CG2 D:ILE28 3.7 14.7 1.0
C D:ILE184 3.7 15.2 1.0
CG2 D:THR185 3.9 14.8 1.0
CB D:ASP97 4.1 16.7 1.0
N D:ILE29 4.1 18.0 1.0
OD2 D:ASP97 4.3 17.7 1.0
O D:HOH979 4.4 26.6 1.0
CA D:ILE29 4.4 21.7 1.0
CA D:THR185 4.4 13.9 1.0
N D:THR185 4.5 15.7 1.0
N D:THR98 4.6 15.2 1.0
CD D:PRO31 4.6 18.2 1.0
N D:ASN30 4.7 19.4 1.0
CB D:THR185 4.7 13.5 1.0
CA D:ILE184 4.9 17.1 1.0
CB D:ILE29 5.0 26.0 1.0
CA D:ASN30 5.0 18.7 1.0
N D:ASP97 5.0 14.5 1.0
C D:ILE28 5.0 18.1 1.0

Sodium binding site 9 out of 19 in 4mpy

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Sodium binding site 9 out of 19 in the 1.85 Angstrom Resolution Crystal Structure of Betaine Aldehyde Dehydrogenase (Betb) From Staphylococcus Aureus (IDP00699) in Complex with Nad+


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 9 of 1.85 Angstrom Resolution Crystal Structure of Betaine Aldehyde Dehydrogenase (Betb) From Staphylococcus Aureus (IDP00699) in Complex with Nad+ within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Na502

b:32.3
occ:1.00
 O F:HOH605 2.2 37.2 1.0
O F:HOH845 2.3 27.0 1.0
O F:HOH602 2.3 33.3 1.0
O E:HOH993 2.3 36.3 1.0
O E:HOH925 2.3 27.2 1.0
O F:HOH1032 2.3 37.3 1.0
NA E:NA503 3.2 31.5 1.0
O E:HOH797 3.8 24.6 1.0
O F:HOH858 3.9 30.7 1.0
O F:HOH953 4.0 25.7 1.0
O F:HOH657 4.1 15.5 1.0
OE1 E:GLU474 4.3 24.6 1.0
CB E:GLU474 4.4 14.1 1.0
O E:HOH698 4.5 17.8 1.0
O F:HOH990 4.5 31.3 1.0
OE1 F:GLU471 4.6 26.2 1.0
O E:HOH1050 4.6 36.8 1.0
OE1 F:GLU474 4.6 29.0 1.0
O E:HOH886 4.6 33.8 1.0
O E:HOH1227 4.8 30.4 1.0
O E:GLU474 4.8 11.4 1.0

Sodium binding site 10 out of 19 in 4mpy

Go back to Sodium Binding Sites List in 4mpy
Sodium binding site 10 out of 19 in the 1.85 Angstrom Resolution Crystal Structure of Betaine Aldehyde Dehydrogenase (Betb) From Staphylococcus Aureus (IDP00699) in Complex with Nad+


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 10 of 1.85 Angstrom Resolution Crystal Structure of Betaine Aldehyde Dehydrogenase (Betb) From Staphylococcus Aureus (IDP00699) in Complex with Nad+ within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Na503

b:31.5
occ:1.00
 O E:HOH1227 2.2 30.4 1.0
O E:HOH925 2.3 27.2 1.0
O F:HOH602 2.3 33.3 1.0
O E:HOH1050 2.3 36.8 1.0
O F:HOH845 2.3 27.0 1.0
O F:HOH936 3.0 33.4 1.0
NA E:NA502 3.2 32.3 1.0
O E:HOH873 3.9 27.6 1.0
O E:HOH698 4.0 17.8 1.0
O F:HOH849 4.0 12.9 0.5
O E:HOH886 4.0 33.8 1.0
O E:HOH1027 4.3 40.9 1.0
OE1 E:GLU471 4.3 23.7 1.0
OE1 F:GLU474 4.4 29.0 1.0
O F:HOH849 4.4 12.1 0.5
CB F:GLU474 4.5 15.1 1.0
OE1 E:GLU474 4.5 24.6 1.0
O F:HOH657 4.6 15.5 1.0
O F:HOH1032 4.8 37.3 1.0
CG E:GLU471 4.8 23.1 1.0
O F:HOH953 4.8 25.7 1.0
O E:HOH993 4.8 36.3 1.0
CD E:GLU471 4.9 21.1 1.0
O F:HOH605 4.9 37.2 1.0
O F:GLU474 4.9 10.6 1.0

Reference:

A.S.Halavaty, G.Minasov, L.Shuvalova, J.Winsor, S.N.Peterson, W.F.Anderson. 1.85 Angstrom Resolution Crystal Structure of Betaine Aldehyde Dehydrogenase (Betb) From Staphylococcus Aureus (IDP00699) in Complex with Nad+ To Be Published.
Page generated: Mon Oct 7 17:04:22 2024

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