Atomistry » Sodium » PDB 4q3d-4qom » 4qet
Atomistry »
  Sodium »
    PDB 4q3d-4qom »
      4qet »

Sodium in PDB 4qet: Structure of Aldehyde Dehydrogenase From Bacillus Cereus, G224D Mutant

Enzymatic activity of Structure of Aldehyde Dehydrogenase From Bacillus Cereus, G224D Mutant

All present enzymatic activity of Structure of Aldehyde Dehydrogenase From Bacillus Cereus, G224D Mutant:
1.2.1.3;

Protein crystallography data

The structure of Structure of Aldehyde Dehydrogenase From Bacillus Cereus, G224D Mutant, PDB code: 4qet 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) 19.64 / 2.60
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 83.139, 93.099, 145.085, 90.00, 97.87, 90.00
R / Rfree (%) 17.1 / 22.7

Sodium Binding Sites:

The binding sites of Sodium atom in the Structure of Aldehyde Dehydrogenase From Bacillus Cereus, G224D Mutant (pdb code 4qet). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 8 binding sites of Sodium where determined in the Structure of Aldehyde Dehydrogenase From Bacillus Cereus, G224D Mutant, PDB code: 4qet:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Sodium binding site 1 out of 8 in 4qet

Go back to Sodium Binding Sites List in 4qet
Sodium binding site 1 out of 8 in the Structure of Aldehyde Dehydrogenase From Bacillus Cereus, G224D 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, G224D Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na501

b:24.4
occ:1.00
 O A:GLN195 2.3 23.8 1.0
OD1 A:ASP108 2.4 23.6 1.0
OG1 A:THR39 2.6 23.0 1.0
O A:HOH634 2.6 20.9 1.0
O A:TYR40 2.6 21.9 1.0
O A:ASP108 2.7 20.6 1.0
CG A:ASP108 3.4 22.4 1.0
N A:TYR40 3.5 20.7 1.0
C A:GLN195 3.5 21.8 1.0
C A:ASP108 3.6 21.6 1.0
C A:TYR40 3.6 21.8 1.0
CA A:ASP108 3.8 20.1 1.0
CB A:THR39 4.0 20.9 1.0
CA A:TYR40 4.1 22.2 1.0
CB A:ASP108 4.2 21.0 1.0
C A:THR39 4.3 19.7 1.0
CA A:GLN195 4.3 22.5 1.0
OD2 A:ASP108 4.3 23.4 1.0
N A:THR196 4.4 20.2 1.0
CA A:THR39 4.5 20.6 1.0
CA A:THR196 4.6 20.1 1.0
CG2 A:THR39 4.6 20.2 1.0
CG2 A:THR196 4.6 19.7 1.0
CB A:GLN195 4.8 23.5 1.0
CB A:TYR40 4.8 24.0 1.0
N A:ASN41 4.8 23.8 1.0
N A:ASN109 4.8 22.1 1.0
CD A:PRO42 5.0 21.4 1.0

Sodium binding site 2 out of 8 in 4qet

Go back to Sodium Binding Sites List in 4qet
Sodium binding site 2 out of 8 in the Structure of Aldehyde Dehydrogenase From Bacillus Cereus, G224D 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, G224D Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na502

b:37.2
occ:1.00
 O A:GLY470 2.2 22.0 1.0
O A:LYS467 2.3 28.6 1.0
O C:HOH620 2.5 18.5 1.0
O C:ILE260 2.5 32.9 1.0
C A:GLY470 3.4 24.2 1.0
C A:LYS467 3.4 25.9 1.0
N A:LYS467 3.7 24.8 1.0
C C:ILE260 3.7 30.1 1.0
CG2 C:ILE260 3.8 24.2 1.0
CA A:LYS467 3.8 25.4 1.0
CG1 A:ILE471 3.8 23.7 1.0
C A:TYR466 4.2 22.4 1.0
O C:HOH615 4.2 14.6 1.0
N A:ILE471 4.2 22.4 1.0
CB C:ILE260 4.3 25.9 1.0
N A:GLY470 4.3 25.1 1.0
CA A:GLY470 4.4 24.4 1.0
CA A:ILE471 4.4 22.8 1.0
O A:GLY465 4.5 18.9 1.0
N A:GLN468 4.5 25.4 1.0
O A:TYR466 4.6 25.0 1.0
N C:LYS261 4.7 28.6 1.0
CA C:ILE260 4.7 28.2 1.0
CA C:LYS261 4.7 29.6 1.0
N C:HIS262 4.8 25.8 1.0
CB A:ILE471 4.8 22.4 1.0
CD1 A:ILE471 4.8 22.1 1.0
CA A:GLN468 4.9 26.9 1.0
CA A:TYR466 4.9 20.7 1.0

Sodium binding site 3 out of 8 in 4qet

Go back to Sodium Binding Sites List in 4qet
Sodium binding site 3 out of 8 in the Structure of Aldehyde Dehydrogenase From Bacillus Cereus, G224D 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, G224D Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na501

b:32.2
occ:1.00
 O B:GLN195 2.3 25.6 1.0
O B:TYR40 2.4 23.0 1.0
O B:ASP108 2.5 21.1 1.0
OD1 B:ASP108 2.5 19.5 1.0
O B:HOH615 2.6 21.3 1.0
OG1 B:THR39 2.8 17.4 1.0
C B:ASP108 3.4 20.6 1.0
C B:TYR40 3.5 24.4 1.0
C B:GLN195 3.5 24.2 1.0
CG B:ASP108 3.6 18.4 1.0
N B:TYR40 3.6 24.2 1.0
CA B:ASP108 3.7 18.8 1.0
CA B:TYR40 4.1 23.9 1.0
CB B:THR39 4.2 20.0 1.0
CB B:ASP108 4.2 18.3 1.0
C B:THR39 4.3 22.8 1.0
CA B:GLN195 4.4 22.3 1.0
OD2 B:ASP108 4.5 17.5 1.0
CD B:PRO42 4.5 20.5 1.0
N B:THR196 4.5 22.1 1.0
CA B:THR196 4.6 20.4 1.0
N B:ASN109 4.6 20.7 1.0
CA B:THR39 4.7 21.9 1.0
N B:ASN41 4.7 25.8 1.0
CG2 B:THR196 4.7 20.1 1.0
CB B:TYR40 4.8 25.4 1.0
O B:LEU107 4.8 18.3 1.0
CB B:GLN195 4.9 20.9 1.0
CG2 B:THR39 4.9 20.2 1.0

Sodium binding site 4 out of 8 in 4qet

Go back to Sodium Binding Sites List in 4qet
Sodium binding site 4 out of 8 in the Structure of Aldehyde Dehydrogenase From Bacillus Cereus, G224D 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, G224D Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na502

b:34.1
occ:1.00
 O D:HOH627 2.3 24.1 1.0
O B:GLY470 2.4 28.4 1.0
O B:LYS467 3.3 25.2 1.0
O B:GLY465 3.3 22.6 1.0
C B:GLY470 3.5 27.8 1.0
N B:LYS467 3.6 20.4 1.0
OE1 D:GLU485 3.7 25.0 1.0
C B:TYR466 3.8 20.0 1.0
O D:ILE260 3.9 24.7 1.0
CA B:TYR466 4.0 19.6 1.0
CA B:ILE471 4.1 26.4 1.0
C B:LYS467 4.2 23.6 1.0
N B:ILE471 4.2 28.8 1.0
OE2 D:GLU485 4.2 24.8 1.0
C B:GLY465 4.2 20.6 1.0
CA B:LYS467 4.2 21.7 1.0
CD D:GLU485 4.3 25.5 1.0
CG1 B:ILE471 4.5 28.5 1.0
O B:TYR466 4.5 22.2 1.0
N B:TYR466 4.6 20.3 1.0
CA B:GLY470 4.7 28.1 1.0
N B:GLY470 4.7 27.7 1.0
CB B:ILE471 4.9 29.2 1.0

Sodium binding site 5 out of 8 in 4qet

Go back to Sodium Binding Sites List in 4qet
Sodium binding site 5 out of 8 in the Structure of Aldehyde Dehydrogenase From Bacillus Cereus, G224D 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, G224D Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na501

b:34.6
occ:1.00
 O C:GLN195 2.4 21.6 1.0
O C:TYR40 2.5 23.0 1.0
OD1 C:ASP108 2.6 17.6 1.0
OG1 C:THR39 2.6 19.6 1.0
O C:ASP108 2.6 17.9 1.0
N C:TYR40 3.2 21.2 1.0
C C:TYR40 3.5 22.5 1.0
C C:GLN195 3.6 23.3 1.0
C C:ASP108 3.6 17.5 1.0
CG C:ASP108 3.6 17.4 1.0
CA C:TYR40 3.9 22.0 1.0
CA C:ASP108 3.9 17.1 1.0
CB C:THR39 4.0 19.6 1.0
C C:THR39 4.1 20.3 1.0
CA C:GLN195 4.3 21.9 1.0
CB C:ASP108 4.4 17.5 1.0
CA C:THR39 4.4 20.8 1.0
CB C:TYR40 4.5 22.7 1.0
CD C:PRO42 4.5 18.0 1.0
OD2 C:ASP108 4.5 17.3 1.0
N C:THR196 4.6 22.0 1.0
N C:ASN41 4.7 24.7 1.0
CB C:GLN195 4.7 20.9 1.0
CG2 C:THR39 4.8 19.8 1.0
N C:ASN109 4.8 17.1 1.0
CA C:THR196 4.9 19.4 1.0
CG2 C:THR196 4.9 18.2 1.0

Sodium binding site 6 out of 8 in 4qet

Go back to Sodium Binding Sites List in 4qet
Sodium binding site 6 out of 8 in the Structure of Aldehyde Dehydrogenase From Bacillus Cereus, G224D 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, G224D Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na502

b:30.4
occ:1.00
 O A:ILE260 2.4 31.0 1.0
O C:LYS467 2.4 27.3 1.0
O C:GLY470 3.0 24.0 1.0
C C:LYS467 3.4 24.5 1.0
C A:ILE260 3.6 32.2 1.0
N C:LYS467 3.7 21.5 1.0
CA C:LYS467 3.7 22.0 1.0
CG2 A:ILE260 4.2 29.1 1.0
C C:GLY470 4.2 24.3 1.0
C C:TYR466 4.2 21.6 1.0
CG1 C:ILE471 4.3 25.6 1.0
OE1 A:GLU485 4.4 20.8 1.0
CB A:ILE260 4.5 29.4 1.0
N A:LYS261 4.5 29.2 1.0
N A:HIS262 4.6 27.9 1.0
N C:GLN468 4.6 22.8 1.0
CA A:LYS261 4.6 28.8 1.0
CA A:ILE260 4.7 30.8 1.0
O C:TYR466 4.7 24.7 1.0
O C:GLY465 4.7 23.5 1.0
O A:MET259 4.9 28.8 1.0
C A:LYS261 4.9 28.6 1.0
N C:ILE471 5.0 24.9 1.0
CA C:TYR466 5.0 21.2 1.0

Sodium binding site 7 out of 8 in 4qet

Go back to Sodium Binding Sites List in 4qet
Sodium binding site 7 out of 8 in the Structure of Aldehyde Dehydrogenase From Bacillus Cereus, G224D 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, G224D Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na501

b:36.1
occ:1.00
 O D:GLN195 2.3 22.9 1.0
O D:TYR40 2.5 23.8 1.0
O D:ASP108 2.6 29.4 1.0
O D:HOH626 2.6 24.6 1.0
OD1 D:ASP108 2.7 27.8 1.0
OG1 D:THR39 2.8 21.9 1.0
C D:GLN195 3.5 22.5 1.0
C D:ASP108 3.5 23.4 1.0
N D:TYR40 3.5 25.7 1.0
C D:TYR40 3.6 22.8 1.0
CG D:ASP108 3.7 25.4 1.0
CA D:ASP108 3.9 24.8 1.0
CA D:TYR40 4.1 25.1 1.0
CB D:THR39 4.2 23.6 1.0
CA D:GLN195 4.2 20.2 1.0
CD D:PRO42 4.3 22.4 1.0
CB D:ASP108 4.4 24.7 1.0
C D:THR39 4.4 23.3 1.0
N D:THR196 4.5 21.8 1.0
OD2 D:ASP108 4.6 25.4 1.0
CB D:GLN195 4.6 19.7 1.0
CA D:THR39 4.6 23.4 1.0
CG2 D:THR196 4.7 17.2 1.0
CB D:TYR40 4.7 27.7 1.0
N D:ASN109 4.7 21.9 1.0
N D:ASN41 4.8 24.1 1.0
CA D:THR196 4.8 20.1 1.0
O D:VAL343 4.9 25.5 1.0

Sodium binding site 8 out of 8 in 4qet

Go back to Sodium Binding Sites List in 4qet
Sodium binding site 8 out of 8 in the Structure of Aldehyde Dehydrogenase From Bacillus Cereus, G224D 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, G224D Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na502

b:38.2
occ:1.00
 O D:GLY470 2.3 25.3 1.0
O B:HOH634 2.3 30.0 1.0
O D:LYS467 2.4 26.4 1.0
O B:HOH628 2.5 33.3 1.0
O B:ILE260 2.8 35.4 1.0
C D:LYS467 3.4 24.3 1.0
C D:GLY470 3.5 25.8 1.0
N D:LYS467 3.7 24.2 1.0
CA D:LYS467 3.9 24.0 1.0
C D:TYR466 4.0 22.8 1.0
CG2 B:ILE260 4.0 34.1 1.0
C B:ILE260 4.0 36.6 1.0
CG1 D:ILE471 4.1 24.1 1.0
N D:ILE471 4.3 25.2 1.0
O D:GLY465 4.3 27.4 1.0
N D:GLY470 4.3 24.7 1.0
OE2 B:GLU485 4.4 23.2 1.0
CA D:ILE471 4.4 24.3 1.0
O D:TYR466 4.5 22.6 1.0
CA D:GLY470 4.5 25.2 1.0
CA D:TYR466 4.6 23.3 1.0
N D:GLN468 4.6 25.6 1.0
CB B:ILE260 4.7 32.9 1.0
N B:LYS261 4.9 34.1 1.0
CB D:ILE471 4.9 22.8 1.0
N B:HIS262 5.0 29.8 1.0
C D:GLY465 5.0 26.6 1.0
CA B:ILE260 5.0 34.8 1.0
CA B:LYS261 5.0 35.0 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 17:58:15 2024

Last articles

Zn in 9MJ5
Zn in 9HNW
Zn in 9G0L
Zn in 9FNE
Zn in 9DZN
Zn in 9E0I
Zn in 9D32
Zn in 9DAK
Zn in 8ZXC
Zn in 8ZUF
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy