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Sodium in PDB 4qf6: Structure of Aldehyde Dehydrogenase From Bacillus Cereus, E194S Mutant

Enzymatic activity of Structure of Aldehyde Dehydrogenase From Bacillus Cereus, E194S Mutant

All present enzymatic activity of Structure of Aldehyde Dehydrogenase From Bacillus Cereus, E194S Mutant:
1.2.1.3;

Protein crystallography data

The structure of Structure of Aldehyde Dehydrogenase From Bacillus Cereus, E194S Mutant, PDB code: 4qf6 was solved by H.P.T.Ngo, S.H.Hong, D.K.Oh, L.W.Kang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.56 / 1.90
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 145.558, 93.655, 247.854, 90.00, 95.55, 90.00
R / Rfree (%) 20.4 / 25.2

Sodium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 24;

Binding sites:

The binding sites of Sodium atom in the Structure of Aldehyde Dehydrogenase From Bacillus Cereus, E194S Mutant (pdb code 4qf6). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 24 binding sites of Sodium where determined in the Structure of Aldehyde Dehydrogenase From Bacillus Cereus, E194S Mutant, PDB code: 4qf6:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Sodium binding site 1 out of 24 in 4qf6

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Sodium binding site 1 out of 24 in the Structure of Aldehyde Dehydrogenase From Bacillus Cereus, E194S Mutant


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of Aldehyde Dehydrogenase From Bacillus Cereus, E194S Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na501

b:10.9
occ:1.00
 O A:HOH668 2.4 14.0 1.0
O A:GLN195 2.4 10.3 1.0
O A:HOH628 2.4 9.2 1.0
O A:TYR40 2.4 10.6 1.0
OD1 A:ASP108 2.4 8.8 1.0
OG1 A:THR39 2.5 10.2 1.0
O A:ASP108 2.5 7.7 1.0
C A:ASP108 3.4 7.7 1.0
CG A:ASP108 3.5 7.8 1.0
C A:TYR40 3.5 11.2 1.0
N A:TYR40 3.6 11.3 1.0
C A:GLN195 3.6 8.9 1.0
CA A:ASP108 3.7 7.8 1.0
CB A:THR39 3.9 9.2 1.0
CA A:TYR40 4.1 11.0 1.0
CB A:ASP108 4.2 7.8 1.0
C A:THR39 4.4 9.1 1.0
OD2 A:ASP108 4.5 7.5 1.0
CA A:GLN195 4.5 9.6 1.0
CA A:THR39 4.5 9.3 1.0
O A:HOH672 4.6 11.8 1.0
N A:ASN109 4.6 7.8 1.0
N A:THR196 4.6 8.8 1.0
CB A:TYR40 4.7 12.5 1.0
CG2 A:THR196 4.7 9.3 1.0
N A:ASN41 4.7 10.2 1.0
CA A:THR196 4.7 8.8 1.0
CD A:PRO42 4.8 7.6 1.0
CG2 A:THR39 4.8 10.5 1.0
CB A:GLN195 5.0 10.8 1.0

Sodium binding site 2 out of 24 in 4qf6

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Sodium binding site 2 out of 24 in the Structure of Aldehyde Dehydrogenase From Bacillus Cereus, E194S Mutant


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structure of Aldehyde Dehydrogenase From Bacillus Cereus, E194S Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na502

b:10.4
occ:1.00
 O A:GLY470 2.3 8.2 1.0
O A:LYS467 2.3 8.8 1.0
O A:HOH852 2.3 13.4 1.0
O C:HOH739 2.3 8.2 1.0
O C:ILE260 2.4 10.7 1.0
C A:LYS467 3.4 9.1 1.0
C A:GLY470 3.5 8.3 1.0
C C:ILE260 3.7 10.5 1.0
N A:LYS467 3.7 7.6 1.0
CA A:LYS467 3.8 9.0 1.0
CG1 A:ILE471 3.9 15.3 1.0
O C:HOH669 3.9 18.3 1.0
CG2 C:ILE260 3.9 14.6 1.0
O C:HOH603 4.0 6.2 1.0
C A:TYR466 4.2 7.1 1.0
CB C:ILE260 4.2 12.8 1.0
N A:ILE471 4.4 9.6 1.0
O A:GLY465 4.4 6.9 1.0
N A:GLY470 4.4 7.1 1.0
CA A:ILE471 4.5 10.6 1.0
N A:GLN468 4.5 9.7 1.0
CA A:GLY470 4.6 7.5 1.0
O A:TYR466 4.6 6.7 1.0
CA C:ILE260 4.6 12.2 1.0
OE1 C:GLU485 4.6 7.5 1.0
N C:LYS261 4.7 10.3 1.0
CA C:LYS261 4.8 10.2 1.0
O A:HOH818 4.8 15.5 1.0
CB A:ILE471 4.8 12.4 1.0
CA A:GLN468 4.9 9.7 1.0
O C:MET259 4.9 14.6 1.0
CA A:TYR466 4.9 6.3 1.0
CD1 A:ILE471 5.0 17.6 1.0

Sodium binding site 3 out of 24 in 4qf6

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Sodium binding site 3 out of 24 in the Structure of Aldehyde Dehydrogenase From Bacillus Cereus, E194S Mutant


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Structure of Aldehyde Dehydrogenase From Bacillus Cereus, E194S Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na501

b:17.3
occ:1.00
 O B:GLN195 2.3 16.8 1.0
O B:HOH709 2.3 18.6 1.0
O B:HOH662 2.3 15.3 1.0
O B:TYR40 2.4 15.0 1.0
O B:ASP108 2.4 17.2 1.0
OD1 B:ASP108 2.4 12.3 1.0
OG1 B:THR39 2.4 16.3 1.0
C B:ASP108 3.4 16.3 1.0
CG B:ASP108 3.4 15.0 1.0
C B:TYR40 3.5 15.5 1.0
C B:GLN195 3.5 15.3 1.0
N B:TYR40 3.5 16.2 1.0
CA B:ASP108 3.7 15.6 1.0
CB B:THR39 3.9 15.5 1.0
CA B:TYR40 4.1 16.8 1.0
CB B:ASP108 4.1 15.1 1.0
C B:THR39 4.3 14.5 1.0
OD2 B:ASP108 4.4 15.2 1.0
CA B:GLN195 4.4 16.6 1.0
CA B:THR39 4.4 14.9 1.0
N B:THR196 4.5 16.1 1.0
N B:ASN109 4.6 15.8 1.0
CD B:PRO42 4.6 12.6 1.0
N B:ASN41 4.7 14.6 1.0
CB B:TYR40 4.7 17.3 1.0
CA B:THR196 4.8 14.5 1.0
CG2 B:THR39 4.8 14.6 1.0
CG2 B:THR196 4.9 13.5 1.0
CD1 B:LEU48 4.9 15.0 1.0

Sodium binding site 4 out of 24 in 4qf6

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Sodium binding site 4 out of 24 in the Structure of Aldehyde Dehydrogenase From Bacillus Cereus, E194S Mutant


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Structure of Aldehyde Dehydrogenase From Bacillus Cereus, E194S Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na502

b:14.3
occ:1.00
 O B:GLY470 2.2 14.9 1.0
O I:HOH652 2.3 15.8 1.0
O B:LYS467 2.3 14.8 1.0
O B:HOH683 2.3 17.0 1.0
O I:ILE260 2.3 17.3 1.0
C B:LYS467 3.3 14.9 1.0
C B:GLY470 3.5 15.7 1.0
O I:HOH709 3.5 26.7 1.0
C I:ILE260 3.6 19.3 1.0
CG1 B:ILE471 3.8 24.5 1.0
N B:LYS467 3.9 15.0 1.0
CA B:LYS467 3.9 15.2 1.0
CG2 I:ILE260 4.0 20.5 1.0
O I:HOH604 4.1 14.5 1.0
CB I:ILE260 4.2 19.4 1.0
C B:TYR466 4.3 15.2 1.0
N B:ILE471 4.3 18.4 1.0
CA B:ILE471 4.4 17.5 1.0
O B:GLY465 4.4 13.6 1.0
N B:GLY470 4.4 15.1 1.0
CA B:GLY470 4.5 16.6 1.0
N B:GLN468 4.5 16.5 1.0
N I:LYS261 4.5 18.6 1.0
CA I:ILE260 4.6 19.1 1.0
O B:TYR466 4.6 14.3 1.0
CA I:LYS261 4.7 20.6 1.0
OE1 I:GLU485 4.7 15.8 1.0
CB B:ILE471 4.8 22.1 1.0
CA B:GLN468 4.9 16.2 1.0
CD1 B:ILE471 4.9 28.3 1.0
O I:MET259 4.9 24.6 1.0
N I:HIS262 5.0 14.5 1.0

Sodium binding site 5 out of 24 in 4qf6

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Sodium binding site 5 out of 24 in the Structure of Aldehyde Dehydrogenase From Bacillus Cereus, E194S Mutant


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Structure of Aldehyde Dehydrogenase From Bacillus Cereus, E194S Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na501

b:12.1
occ:1.00
 O C:HOH756 2.3 14.6 1.0
O C:GLN195 2.3 10.2 1.0
O C:HOH757 2.3 13.1 1.0
O C:TYR40 2.4 12.8 1.0
OD1 C:ASP108 2.4 10.4 1.0
OG1 C:THR39 2.5 12.2 1.0
O C:ASP108 2.5 11.1 1.0
C C:ASP108 3.4 9.8 1.0
CG C:ASP108 3.5 10.3 1.0
C C:TYR40 3.5 13.7 1.0
C C:GLN195 3.6 10.9 1.0
N C:TYR40 3.6 13.6 1.0
CA C:ASP108 3.7 11.4 1.0
CB C:THR39 3.9 11.0 1.0
CA C:TYR40 4.1 13.8 1.0
CB C:ASP108 4.2 10.5 1.0
C C:THR39 4.3 12.1 1.0
OD2 C:ASP108 4.4 10.2 1.0
CA C:GLN195 4.4 11.4 1.0
CA C:THR39 4.5 12.3 1.0
N C:THR196 4.5 9.7 1.0
CG2 C:THR39 4.6 11.3 1.0
CA C:THR196 4.6 9.4 1.0
N C:ASN109 4.6 10.6 1.0
O C:HOH686 4.7 16.2 1.0
N C:ASN41 4.7 12.3 1.0
CG2 C:THR196 4.8 8.6 1.0
CB C:TYR40 4.8 15.8 1.0
CD C:PRO42 4.9 11.9 1.0
CB C:GLN195 4.9 11.3 1.0

Sodium binding site 6 out of 24 in 4qf6

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Sodium binding site 6 out of 24 in the Structure of Aldehyde Dehydrogenase From Bacillus Cereus, E194S Mutant


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Structure of Aldehyde Dehydrogenase From Bacillus Cereus, E194S Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na502

b:9.9
occ:1.00
 O A:HOH703 2.3 8.7 1.0
O C:LYS467 2.3 12.4 1.0
O C:GLY470 2.3 7.4 1.0
O A:HOH642 2.4 9.3 1.0
O A:ILE260 2.4 11.7 1.0
C C:LYS467 3.4 12.2 1.0
C C:GLY470 3.5 8.1 1.0
C A:ILE260 3.7 12.0 1.0
N C:LYS467 3.7 10.5 1.0
O A:HOH631 3.8 18.9 1.0
CG1 C:ILE471 3.9 17.6 1.0
CG2 A:ILE260 4.0 15.3 1.0
CA C:LYS467 4.0 12.3 1.0
O A:HOH646 4.1 10.6 1.0
C C:TYR466 4.2 9.7 1.0
CB A:ILE260 4.2 14.6 1.0
N C:GLY470 4.4 8.0 1.0
N C:ILE471 4.4 9.6 1.0
O C:GLY465 4.4 7.0 1.0
O A:HOH712 4.4 12.1 1.0
CA C:ILE471 4.5 10.7 1.0
CA C:GLY470 4.5 8.4 1.0
OE1 A:GLU485 4.5 10.0 1.0
N C:GLN468 4.6 11.7 1.0
O C:TYR466 4.6 8.0 1.0
CA A:ILE260 4.6 13.5 1.0
N A:LYS261 4.7 11.5 1.0
CA A:LYS261 4.8 10.6 1.0
CA C:GLN468 4.9 11.1 1.0
CA C:TYR466 4.9 7.7 1.0
CB C:ILE471 4.9 13.5 1.0
CD1 C:ILE471 4.9 20.4 1.0
O A:MET259 4.9 16.9 1.0

Sodium binding site 7 out of 24 in 4qf6

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Sodium binding site 7 out of 24 in the Structure of Aldehyde Dehydrogenase From Bacillus Cereus, E194S Mutant


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of Structure of Aldehyde Dehydrogenase From Bacillus Cereus, E194S Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na501

b:11.1
occ:1.00
 O D:GLY470 2.2 10.5 1.0
O D:LYS467 2.3 12.7 1.0
O E:HOH667 2.3 12.4 1.0
O E:ILE260 2.3 15.4 1.0
O D:HOH632 2.4 11.4 1.0
C D:LYS467 3.4 11.5 1.0
C D:GLY470 3.5 11.1 1.0
C E:ILE260 3.6 13.2 1.0
N D:LYS467 3.7 9.8 1.0
CA D:LYS467 3.9 11.2 1.0
CG2 E:ILE260 3.9 13.7 1.0
O E:HOH676 3.9 18.2 1.0
CG1 D:ILE471 4.0 15.3 1.0
O E:HOH651 4.1 11.3 1.0
CB E:ILE260 4.2 13.5 1.0
C D:TYR466 4.2 8.7 1.0
N D:ILE471 4.3 10.8 1.0
N D:GLY470 4.3 11.2 1.0
CA D:ILE471 4.4 11.5 1.0
O E:HOH607 4.5 10.6 1.0
CA D:GLY470 4.5 11.0 1.0
N D:GLN468 4.5 11.4 1.0
CA E:ILE260 4.5 13.2 1.0
O D:GLY465 4.5 10.6 1.0
N E:LYS261 4.6 13.1 1.0
O D:TYR466 4.7 8.2 1.0
CA E:LYS261 4.7 12.9 1.0
OE1 E:GLU485 4.7 11.4 1.0
O E:MET259 4.8 15.6 1.0
CA D:GLN468 4.8 11.0 1.0
CB D:ILE471 4.9 13.0 1.0
O D:HOH700 4.9 15.8 1.0
CA D:TYR466 5.0 8.4 1.0

Sodium binding site 8 out of 24 in 4qf6

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Sodium binding site 8 out of 24 in the Structure of Aldehyde Dehydrogenase From Bacillus Cereus, E194S Mutant


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of Structure of Aldehyde Dehydrogenase From Bacillus Cereus, E194S Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na502

b:12.9
occ:1.00
 O D:GLN195 2.3 10.6 1.0
O D:TYR40 2.4 13.0 1.0
O D:HOH666 2.4 12.5 1.0
OD1 D:ASP108 2.4 13.6 1.0
O D:HOH641 2.4 14.1 1.0
O D:ASP108 2.4 9.6 1.0
OG1 D:THR39 2.5 13.3 1.0
C D:ASP108 3.4 9.3 1.0
CG D:ASP108 3.5 10.8 1.0
C D:GLN195 3.5 9.1 1.0
C D:TYR40 3.5 13.4 1.0
N D:TYR40 3.6 12.9 1.0
CA D:ASP108 3.8 10.1 1.0
CB D:THR39 3.9 12.0 1.0
CA D:TYR40 4.1 13.1 1.0
CB D:ASP108 4.2 10.2 1.0
CA D:GLN195 4.3 9.7 1.0
C D:THR39 4.3 12.2 1.0
OD2 D:ASP108 4.5 10.9 1.0
CA D:THR39 4.5 11.5 1.0
N D:THR196 4.5 8.4 1.0
CG2 D:THR196 4.6 8.1 1.0
N D:ASN109 4.6 8.5 1.0
O D:HOH674 4.6 14.0 1.0
CA D:THR196 4.7 8.1 1.0
N D:ASN41 4.7 13.4 1.0
CB D:TYR40 4.7 14.8 1.0
CB D:GLN195 4.8 10.3 1.0
CD D:PRO42 4.8 12.9 1.0
CG2 D:THR39 4.8 12.1 1.0

Sodium binding site 9 out of 24 in 4qf6

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Sodium binding site 9 out of 24 in the Structure of Aldehyde Dehydrogenase From Bacillus Cereus, E194S Mutant


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 9 of Structure of Aldehyde Dehydrogenase From Bacillus Cereus, E194S Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Na501

b:10.4
occ:1.00
 O E:GLN195 2.3 10.4 1.0
O E:HOH731 2.3 18.3 1.0
O E:HOH629 2.3 10.6 1.0
O E:TYR40 2.4 9.9 1.0
OD1 E:ASP108 2.4 8.7 1.0
OG1 E:THR39 2.5 10.6 1.0
O E:ASP108 2.5 8.5 1.0
C E:ASP108 3.4 7.5 1.0
N E:TYR40 3.5 10.4 1.0
CG E:ASP108 3.5 7.8 1.0
C E:GLN195 3.5 10.2 1.0
C E:TYR40 3.6 11.3 1.0
CA E:ASP108 3.7 8.1 1.0
CB E:THR39 3.9 11.0 1.0
CA E:TYR40 4.1 11.3 1.0
CB E:ASP108 4.2 7.7 1.0
C E:THR39 4.3 9.5 1.0
CA E:GLN195 4.3 9.8 1.0
CA E:THR39 4.4 10.2 1.0
OD2 E:ASP108 4.5 8.3 1.0
N E:THR196 4.5 8.9 1.0
N E:ASN109 4.6 7.9 1.0
O E:HOH746 4.7 18.8 1.0
CA E:THR196 4.7 8.2 1.0
CG2 E:THR39 4.7 11.4 1.0
CD E:PRO42 4.7 8.3 1.0
N E:ASN41 4.7 9.8 1.0
CG2 E:THR196 4.8 7.1 1.0
CB E:GLN195 4.8 10.2 1.0
CB E:TYR40 4.9 13.5 1.0
CD2 E:LEU48 5.0 10.1 1.0

Sodium binding site 10 out of 24 in 4qf6

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Sodium binding site 10 out of 24 in the Structure of Aldehyde Dehydrogenase From Bacillus Cereus, E194S Mutant


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 10 of Structure of Aldehyde Dehydrogenase From Bacillus Cereus, E194S Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Na502

b:12.9
occ:1.00
 O D:HOH762 2.2 9.4 1.0
O E:GLY470 2.3 11.2 1.0
O E:LYS467 2.3 13.4 1.0
O D:HOH609 2.3 9.1 1.0
O D:ILE260 2.4 11.4 1.0
C E:LYS467 3.4 11.3 1.0
C E:GLY470 3.5 11.7 1.0
C D:ILE260 3.6 11.0 1.0
N E:LYS467 3.7 8.8 1.0
CA E:LYS467 3.9 10.4 1.0
CG2 D:ILE260 3.9 11.5 1.0
CG1 E:ILE471 4.0 19.4 1.0
O D:HOH650 4.1 10.2 1.0
C E:TYR466 4.2 8.4 1.0
CB D:ILE260 4.3 11.5 1.0
N E:ILE471 4.4 11.7 1.0
N E:GLY470 4.4 10.0 1.0
O D:HOH811 4.4 10.0 1.0
CA E:ILE471 4.5 13.1 1.0
N E:GLN468 4.5 12.7 1.0
CA D:ILE260 4.6 12.0 1.0
CA E:GLY470 4.6 11.1 1.0
O E:GLY465 4.6 6.2 1.0
N D:LYS261 4.6 12.0 1.0
O E:TYR466 4.7 8.9 1.0
OE1 D:GLU485 4.7 11.2 1.0
CA D:LYS261 4.7 12.5 1.0
O D:MET259 4.8 12.4 1.0
CB E:ILE471 4.8 15.5 1.0
CA E:GLN468 4.9 13.0 1.0
CA E:TYR466 5.0 7.6 1.0

Reference:

H.P.T.Ngo, S.H.Hong, D.K.Oh, L.W.Kang. Structural and Kinetic Analysis For Cofactor-Binding Residues in Mammalian-Like Aldehyde Dehydrogenase From Bacillus Cereus Involved in Oxidation and Reduction Activity For All-Trans-Retinal To Be Published.
Page generated: Mon Oct 7 17:58:36 2024

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