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Sodium in PDB 5gtl: Nadph Complex Structure of Aldehyde Dehydrogenase From Bacillus Cereus

Protein crystallography data

The structure of Nadph Complex Structure of Aldehyde Dehydrogenase From Bacillus Cereus, PDB code: 5gtl was solved by H.P.T.Ngo, S.H.Hong, T.H.Ho, 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) 47.88 / 2.00
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 83.887, 93.940, 144.934, 90.00, 97.67, 90.00
R / Rfree (%) 18.9 / 25.2

Sodium Binding Sites:

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

Sodium binding site 1 out of 7 in 5gtl

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Sodium binding site 1 out of 7 in the Nadph Complex Structure of Aldehyde Dehydrogenase From Bacillus Cereus


Mono view


Stereo pair view

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

b:23.9
occ:1.00
 O A:GLN195 2.3 26.5 1.0
O A:HOH647 2.4 21.0 1.0
O A:TYR40 2.5 29.9 1.0
O A:HOH665 2.7 26.8 1.0
OG1 A:THR39 2.7 20.1 1.0
OD1 A:ASP108 2.7 24.5 1.0
O A:ASP108 2.7 19.9 1.0
C A:GLN195 3.4 25.0 1.0
N A:TYR40 3.5 26.1 1.0
C A:TYR40 3.6 27.7 1.0
C A:ASP108 3.6 21.8 1.0
CG A:ASP108 3.7 26.4 1.0
CA A:ASP108 3.8 22.5 1.0
CA A:TYR40 4.0 28.5 1.0
CB A:THR39 4.1 24.8 1.0
CA A:GLN195 4.1 26.2 1.0
C A:THR39 4.2 26.4 1.0
O A:HOH757 4.3 30.9 1.0
CB A:ASP108 4.4 23.3 1.0
CA A:THR39 4.5 27.2 1.0
CB A:GLN195 4.5 30.8 1.0
N A:THR196 4.5 21.4 1.0
OD2 A:ASP108 4.5 24.4 1.0
CD A:PRO42 4.6 30.0 1.0
N A:ASN41 4.7 25.6 1.0
CG2 A:THR39 4.8 24.8 1.0
N A:ASN109 4.8 18.8 1.0
CA A:THR196 4.8 20.1 1.0
CB A:TYR40 4.8 30.1 1.0
CG2 A:THR196 4.8 21.8 1.0

Sodium binding site 2 out of 7 in 5gtl

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Sodium binding site 2 out of 7 in the Nadph Complex Structure of Aldehyde Dehydrogenase From Bacillus Cereus


Mono view


Stereo pair view

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

b:28.9
occ:1.00
 O B:HOH914 2.3 24.1 1.0
O A:LYS467 2.3 22.8 1.0
O A:HOH801 2.3 23.4 1.0
O B:ILE260 2.4 24.2 1.0
O A:GLY470 2.4 25.4 1.0
C A:LYS467 3.3 21.1 1.0
C A:GLY470 3.5 25.0 1.0
C B:ILE260 3.6 26.2 1.0
N A:LYS467 3.8 21.2 1.0
CA A:LYS467 3.8 20.4 1.0
O B:HOH791 3.9 24.9 1.0
CG2 B:ILE260 3.9 29.2 1.0
CG1 A:ILE471 4.1 31.5 1.0
C A:TYR466 4.1 20.7 1.0
O A:HOH672 4.2 34.4 1.0
CB B:ILE260 4.3 28.1 1.0
N A:ILE471 4.4 26.0 1.0
O A:TYR466 4.5 18.9 1.0
N A:GLN468 4.5 25.8 1.0
N A:GLY470 4.5 25.2 1.0
O A:GLY465 4.5 20.9 1.0
CA A:GLY470 4.5 25.1 1.0
N B:LYS261 4.5 26.3 1.0
CA A:ILE471 4.5 26.8 1.0
CA B:ILE260 4.6 26.7 1.0
CA B:LYS261 4.7 28.1 1.0
O B:MET259 4.9 30.2 1.0
CA A:GLN468 4.9 25.4 1.0
CA A:TYR466 4.9 19.0 1.0
CB A:ILE471 5.0 30.9 1.0
N B:HIS262 5.0 27.1 1.0

Sodium binding site 3 out of 7 in 5gtl

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Sodium binding site 3 out of 7 in the Nadph Complex Structure of Aldehyde Dehydrogenase From Bacillus Cereus


Mono view


Stereo pair view

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

b:27.1
occ:1.00
 O B:GLN195 2.4 25.1 1.0
O B:HOH777 2.4 20.8 1.0
O B:HOH638 2.4 34.9 1.0
O B:TYR40 2.5 27.5 1.0
OG1 B:THR39 2.6 23.5 1.0
O B:ASP108 2.8 26.2 1.0
OD1 B:ASP108 3.0 26.3 1.0
C B:GLN195 3.5 24.7 1.0
N B:TYR40 3.5 27.7 1.0
C B:TYR40 3.5 26.9 1.0
O B:HOH926 3.7 39.4 1.0
C B:ASP108 3.7 26.9 1.0
CG B:ASP108 3.9 27.0 1.0
CB B:THR39 3.9 23.3 1.0
CA B:TYR40 4.0 30.0 1.0
CA B:ASP108 4.0 27.4 1.0
CA B:GLN195 4.1 25.6 1.0
C B:THR39 4.1 26.2 1.0
O B:HOH763 4.3 29.2 1.0
CA B:THR39 4.4 26.3 1.0
CB B:GLN195 4.5 31.7 1.0
CB B:ASP108 4.5 28.1 1.0
N B:THR196 4.5 24.0 1.0
OD2 B:ASP108 4.6 24.3 1.0
N B:ASN41 4.6 24.8 1.0
CD B:PRO42 4.6 27.1 1.0
CB B:TYR40 4.7 31.1 1.0
CG2 B:THR39 4.8 25.3 1.0
CA B:THR196 4.8 21.5 1.0
O B:HOH967 4.9 50.8 1.0
N B:ASN109 4.9 26.1 1.0
CG2 B:THR196 4.9 22.1 1.0
O B:THR39 5.0 27.4 1.0

Sodium binding site 4 out of 7 in 5gtl

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Sodium binding site 4 out of 7 in the Nadph Complex Structure of Aldehyde Dehydrogenase From Bacillus Cereus


Mono view


Stereo pair view

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

b:32.2
occ:1.00
 O A:HOH972 2.2 26.7 1.0
O B:LYS467 2.3 26.0 1.0
O A:HOH633 2.3 27.0 1.0
O B:GLY470 2.4 22.6 1.0
O A:ILE260 2.7 24.5 1.0
C B:LYS467 3.4 26.5 1.0
C B:GLY470 3.5 25.1 1.0
N B:LYS467 3.7 26.7 1.0
O A:HOH710 3.8 34.5 1.0
CA B:LYS467 3.8 25.1 1.0
O A:HOH742 3.8 27.5 1.0
C A:ILE260 3.9 26.6 1.0
CG2 A:ILE260 3.9 32.2 1.0
CG1 B:ILE471 4.1 30.2 1.0
C B:TYR466 4.2 23.4 1.0
O B:HOH692 4.4 33.7 1.0
N B:ILE471 4.4 25.0 1.0
CB A:ILE260 4.4 29.3 1.0
N B:GLY470 4.5 29.1 1.0
CA B:ILE471 4.5 25.1 1.0
N B:GLN468 4.5 28.9 1.0
O B:GLY465 4.5 21.0 1.0
CA B:GLY470 4.5 26.4 1.0
OE1 A:GLU485 4.6 29.2 1.0
O B:TYR466 4.6 19.9 1.0
N A:LYS261 4.7 26.8 1.0
CA A:ILE260 4.8 27.4 1.0
CA A:LYS261 4.8 27.7 1.0
O A:HOH649 4.9 22.9 1.0
CA B:TYR466 4.9 20.6 1.0
CA B:GLN468 4.9 30.9 1.0
CB B:ILE471 4.9 27.4 1.0
N A:HIS262 5.0 26.3 1.0

Sodium binding site 5 out of 7 in 5gtl

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Sodium binding site 5 out of 7 in the Nadph Complex Structure of Aldehyde Dehydrogenase From Bacillus Cereus


Mono view


Stereo pair view

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

b:42.2
occ:1.00
 O D:HOH851 2.1 31.2 1.0
O D:HOH619 2.4 27.3 1.0
O C:LYS467 2.4 38.8 1.0
O C:GLY470 2.5 34.4 1.0
O D:ILE260 2.5 38.5 1.0
O C:HOH680 3.2 48.2 1.0
C C:LYS467 3.5 37.1 1.0
C C:GLY470 3.6 31.3 1.0
O D:HOH783 3.7 36.1 1.0
C D:ILE260 3.7 38.2 1.0
N C:LYS467 3.9 33.1 1.0
CG2 D:ILE260 3.9 34.7 1.0
CG1 C:ILE471 3.9 37.7 1.0
CA C:LYS467 3.9 35.1 1.0
C C:TYR466 4.3 30.8 1.0
CB D:ILE260 4.3 38.5 1.0
N C:ILE471 4.5 28.7 1.0
N C:GLY470 4.5 28.6 1.0
CA C:ILE471 4.5 31.1 1.0
O C:TYR466 4.6 32.3 1.0
N C:GLN468 4.6 38.8 1.0
CA C:GLY470 4.6 30.0 1.0
O C:GLY465 4.6 23.2 1.0
N D:LYS261 4.6 38.8 1.0
CA D:ILE260 4.6 35.6 1.0
OE1 D:GLU485 4.6 31.2 1.0
CA D:LYS261 4.7 39.8 1.0
O D:HOH811 4.8 34.4 1.0
CB C:ILE471 4.8 32.9 1.0
CD1 C:ILE471 4.8 35.2 1.0
N D:HIS262 4.9 31.1 1.0
CA C:GLN468 4.9 37.9 1.0
O D:MET259 4.9 35.4 1.0
CA C:TYR466 5.0 26.8 1.0
O D:HOH680 5.0 36.6 1.0

Sodium binding site 6 out of 7 in 5gtl

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Sodium binding site 6 out of 7 in the Nadph Complex Structure of Aldehyde Dehydrogenase From Bacillus Cereus


Mono view


Stereo pair view

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

b:40.8
occ:1.00
 O C:TYR40 2.2 41.1 1.0
O C:ASP108 2.5 34.9 1.0
O C:HOH648 2.5 34.5 1.0
O C:GLN195 2.5 36.0 1.0
OG1 C:THR39 2.7 31.9 1.0
OD1 C:ASP108 2.9 30.9 1.0
C C:TYR40 3.3 40.6 1.0
C C:ASP108 3.4 32.5 1.0
N C:TYR40 3.4 37.1 1.0
C C:GLN195 3.6 36.3 1.0
CA C:ASP108 3.7 32.8 1.0
CG C:ASP108 3.8 31.8 1.0
CA C:TYR40 3.9 40.3 1.0
CB C:THR39 4.0 34.5 1.0
C C:THR39 4.1 34.9 1.0
CA C:GLN195 4.3 36.5 1.0
CB C:ASP108 4.3 29.6 1.0
CA C:THR39 4.4 32.7 1.0
N C:ASN41 4.5 38.5 1.0
CD C:PRO42 4.5 49.8 1.0
CB C:GLN195 4.5 42.1 1.0
N C:ASN109 4.6 33.9 1.0
N C:THR196 4.7 33.6 1.0
OD2 C:ASP108 4.7 30.4 1.0
CB C:TYR40 4.8 45.3 1.0
CG2 C:THR39 4.8 35.5 1.0
CA C:ASN41 4.9 42.3 1.0
O C:LEU107 4.9 42.4 1.0
O C:THR39 4.9 35.2 1.0
CD2 C:LEU48 4.9 38.7 1.0
CA C:THR196 5.0 33.0 1.0

Sodium binding site 7 out of 7 in 5gtl

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Sodium binding site 7 out of 7 in the Nadph Complex Structure of Aldehyde Dehydrogenase From Bacillus Cereus


Mono view


Stereo pair view

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

b:36.0
occ:1.00
 O D:HOH601 1.7 43.5 1.0
O D:HOH646 2.2 26.8 1.0
O D:ASP108 2.2 26.0 1.0
O D:GLN195 2.4 32.6 1.0
O D:TYR40 2.6 36.0 1.0
O D:HOH813 2.6 35.1 1.0
OD1 D:ASP108 3.0 32.4 1.0
OG1 D:THR39 3.2 28.6 1.0
C D:ASP108 3.2 29.6 1.0
C D:GLN195 3.6 34.4 1.0
C D:TYR40 3.6 34.5 1.0
CA D:ASP108 3.7 30.6 1.0
CG D:ASP108 3.8 31.0 1.0
N D:TYR40 3.8 30.9 1.0
O D:HOH873 4.0 34.9 1.0
CD D:PRO42 4.2 41.5 1.0
CA D:TYR40 4.2 32.5 1.0
CB D:ASP108 4.3 27.6 1.0
CA D:GLN195 4.3 33.0 1.0
O D:HOH824 4.4 32.7 1.0
N D:ASN109 4.4 26.5 1.0
CB D:THR39 4.5 29.4 1.0
CG2 D:THR196 4.5 31.5 1.0
N D:THR196 4.6 33.9 1.0
C D:THR39 4.6 26.6 1.0
OD2 D:ASP108 4.7 33.8 1.0
CB D:GLN195 4.7 41.2 1.0
CA D:THR196 4.7 33.6 1.0
N D:ASN41 4.7 34.9 1.0
CB D:TYR40 4.9 37.8 1.0
CA D:THR39 4.9 26.9 1.0
O D:VAL343 4.9 35.2 1.0
O D:LEU107 4.9 35.9 1.0
CA D:ASN109 4.9 27.9 1.0
N D:ASP108 4.9 30.4 1.0
N D:PRO42 5.0 37.3 1.0

Reference:

H.P.T.Ngo, S.H.Hong, T.H.Ho, D.K.Oh, L.W.Kang. Crystal Structures of Aldehyde Dehydrogenase From Bacillus Cereus Having Atypical Bidirectional Oxidizing and Reducing Activities For All-Trans-Retinal To Be Published.
Page generated: Mon Aug 18 00:00:10 2025

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