Atomistry » Sodium » PDB 5g3g-5gwa » 5gt6
Atomistry »
  Sodium »
    PDB 5g3g-5gwa »
      5gt6 »

Sodium in PDB 5gt6: Apo Structure of Aldehyde Dehydrogenase From Bacillus Cereus

Protein crystallography data

The structure of Apo Structure of Aldehyde Dehydrogenase From Bacillus Cereus, PDB code: 5gt6 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) 49.57 / 2.60
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 83.527, 93.284, 145.472, 90.00, 98.05, 90.00
R / Rfree (%) 18.2 / 25.1

Sodium Binding Sites:

The binding sites of Sodium atom in the Apo Structure of Aldehyde Dehydrogenase From Bacillus Cereus (pdb code 5gt6). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Apo Structure of Aldehyde Dehydrogenase From Bacillus Cereus, PDB code: 5gt6:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 5gt6

Go back to Sodium Binding Sites List in 5gt6
Sodium binding site 1 out of 4 in the Apo 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 Apo Structure of Aldehyde Dehydrogenase From Bacillus Cereus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na501

b:16.9
occ:1.00
OD1 A:ASP108 2.3 15.2 1.0
O A:GLN195 2.3 16.3 1.0
O A:HOH607 2.3 15.5 1.0
O A:ASP108 2.3 16.2 1.0
O A:TYR40 2.4 18.3 1.0
OG1 A:THR39 2.8 18.1 1.0
C A:ASP108 3.3 15.4 1.0
CG A:ASP108 3.4 15.2 1.0
C A:TYR40 3.4 18.5 1.0
N A:TYR40 3.4 19.4 1.0
C A:GLN195 3.5 15.9 1.0
CA A:ASP108 3.6 15.8 1.0
CA A:TYR40 3.9 19.9 1.0
CB A:ASP108 4.1 15.4 1.0
CB A:THR39 4.1 17.7 1.0
C A:THR39 4.2 19.1 1.0
OD2 A:ASP108 4.4 15.3 1.0
N A:THR196 4.4 15.1 1.0
CA A:GLN195 4.4 16.0 1.0
CA A:THR39 4.5 19.3 1.0
N A:ASN109 4.5 14.2 1.0
CA A:THR196 4.5 14.7 1.0
N A:ASN41 4.6 18.4 1.0
CG2 A:THR196 4.6 14.4 1.0
CD A:PRO42 4.7 17.1 1.0
CG2 A:THR39 4.7 17.3 1.0
CB A:TYR40 4.8 21.4 1.0
CB A:GLN195 4.9 15.7 1.0
N A:ASP108 5.0 16.0 1.0
O A:LEU107 5.0 17.5 1.0

Sodium binding site 2 out of 4 in 5gt6

Go back to Sodium Binding Sites List in 5gt6
Sodium binding site 2 out of 4 in the Apo 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 Apo Structure of Aldehyde Dehydrogenase From Bacillus Cereus within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na501

b:19.1
occ:1.00
OD1 B:ASP108 2.3 16.4 1.0
O B:HOH608 2.3 20.1 1.0
O B:TYR40 2.3 19.7 1.0
O B:ASP108 2.3 16.7 1.0
O B:GLN195 2.3 18.7 1.0
OG1 B:THR39 2.7 21.0 1.0
C B:ASP108 3.3 14.6 1.0
CG B:ASP108 3.4 14.8 1.0
C B:TYR40 3.4 18.8 1.0
N B:TYR40 3.4 18.6 1.0
C B:GLN195 3.5 18.3 1.0
CA B:ASP108 3.7 14.9 1.0
CA B:TYR40 4.0 19.5 1.0
CB B:THR39 4.0 20.2 1.0
C B:THR39 4.1 19.0 1.0
CB B:ASP108 4.1 15.0 1.0
OD2 B:ASP108 4.3 15.5 1.0
CA B:THR39 4.3 20.1 1.0
CA B:GLN195 4.4 18.0 1.0
N B:ASN109 4.5 14.0 1.0
N B:THR196 4.5 17.8 1.0
N B:ASN41 4.5 18.4 1.0
CG2 B:THR39 4.6 19.4 1.0
CD B:PRO42 4.6 16.2 1.0
CA B:THR196 4.7 17.0 1.0
CG2 B:THR196 4.7 16.3 1.0
CB B:TYR40 4.8 19.8 1.0
CB B:GLN195 4.9 18.1 1.0
O B:THR39 5.0 18.6 1.0

Sodium binding site 3 out of 4 in 5gt6

Go back to Sodium Binding Sites List in 5gt6
Sodium binding site 3 out of 4 in the Apo 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 Apo Structure of Aldehyde Dehydrogenase From Bacillus Cereus within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na501

b:18.3
occ:1.00
O C:GLN195 2.3 18.8 1.0
OD1 C:ASP108 2.3 19.2 1.0
O C:HOH602 2.3 16.2 1.0
O C:TYR40 2.3 20.0 1.0
O C:ASP108 2.3 17.9 1.0
OG1 C:THR39 2.9 20.4 1.0
C C:ASP108 3.3 16.9 1.0
CG C:ASP108 3.3 18.5 1.0
C C:TYR40 3.5 19.8 1.0
C C:GLN195 3.5 18.4 1.0
N C:TYR40 3.6 20.7 1.0
CA C:ASP108 3.6 17.2 1.0
CB C:ASP108 4.1 17.8 1.0
CA C:TYR40 4.1 21.0 1.0
CB C:THR39 4.1 19.5 1.0
OD2 C:ASP108 4.3 18.8 1.0
C C:THR39 4.3 20.2 1.0
CA C:GLN195 4.4 19.7 1.0
N C:THR196 4.4 16.4 1.0
CG2 C:THR196 4.5 15.2 1.0
CA C:THR196 4.5 15.8 1.0
CA C:THR39 4.5 20.4 1.0
N C:ASN109 4.5 16.4 1.0
CG2 C:THR39 4.6 19.5 1.0
N C:ASN41 4.6 19.2 1.0
CB C:TYR40 4.9 22.3 1.0
CD C:PRO42 4.9 17.2 1.0
CG C:PRO42 4.9 17.6 1.0
CB C:GLN195 4.9 19.8 1.0
O C:LEU107 4.9 19.6 1.0
N C:ASP108 5.0 18.2 1.0

Sodium binding site 4 out of 4 in 5gt6

Go back to Sodium Binding Sites List in 5gt6
Sodium binding site 4 out of 4 in the Apo 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 Apo Structure of Aldehyde Dehydrogenase From Bacillus Cereus within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na501

b:20.1
occ:1.00
O D:GLN195 2.3 19.2 1.0
OD1 D:ASP108 2.3 19.8 1.0
O D:HOH602 2.3 17.3 1.0
O D:ASP108 2.3 21.3 1.0
O D:TYR40 2.5 21.3 1.0
OG1 D:THR39 2.6 18.9 1.0
C D:ASP108 3.3 19.7 1.0
CG D:ASP108 3.3 20.7 1.0
C D:GLN195 3.5 18.8 1.0
N D:TYR40 3.5 21.0 1.0
C D:TYR40 3.6 20.8 1.0
CA D:ASP108 3.7 20.5 1.0
CB D:THR39 3.9 19.8 1.0
CA D:TYR40 4.0 22.3 1.0
CB D:ASP108 4.1 20.2 1.0
C D:THR39 4.2 20.9 1.0
OD2 D:ASP108 4.2 21.3 1.0
CG2 D:THR196 4.3 19.9 1.0
CA D:GLN195 4.4 18.7 1.0
CA D:THR39 4.4 20.6 1.0
N D:THR196 4.4 18.8 1.0
N D:ASN109 4.5 18.7 1.0
CA D:THR196 4.6 19.3 1.0
CG2 D:THR39 4.6 20.0 1.0
CD D:PRO42 4.7 18.0 1.0
N D:ASN41 4.7 19.9 1.0
CB D:GLN195 4.8 19.3 1.0
CB D:TYR40 4.8 24.1 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 Oct 7 21:15:16 2024

Last articles

Zn in 9FD2
Zn in 9GUW
Zn in 9GUX
Zn in 9F7C
Zn in 9GUR
Zn in 9F7A
Zn in 9DDE
Zn in 9DBY
Zn in 9EBZ
Zn in 9DGG
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy