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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

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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

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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

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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

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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

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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

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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

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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

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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: Tue Dec 15 07:05:17 2020

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