Sodium in PDB 8u9b: Crystal Structure of Betaine Aldehyde Dehydrogenase (Betb) From Klebsiella Aerogenes (Apo, P21 Form)

Protein crystallography data

The structure of Crystal Structure of Betaine Aldehyde Dehydrogenase (Betb) From Klebsiella Aerogenes (Apo, P21 Form), PDB code: 8u9b was solved by Seattle Structural Genomics Center For Infectious Disease, Seattlestructural Genomics Center For Infectious Disease (Ssgcid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 27.39 / 1.90
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 101.27, 161.235, 158.708, 90, 101.11, 90
R / Rfree (%) 14.7 / 17.5

Other elements in 8u9b:

The structure of Crystal Structure of Betaine Aldehyde Dehydrogenase (Betb) From Klebsiella Aerogenes (Apo, P21 Form) also contains other interesting chemical elements:

Chlorine (Cl) 8 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Betaine Aldehyde Dehydrogenase (Betb) From Klebsiella Aerogenes (Apo, P21 Form) (pdb code 8u9b). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 8 binding sites of Sodium where determined in the Crystal Structure of Betaine Aldehyde Dehydrogenase (Betb) From Klebsiella Aerogenes (Apo, P21 Form), PDB code: 8u9b:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Sodium binding site 1 out of 8 in 8u9b

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Sodium binding site 1 out of 8 in the Crystal Structure of Betaine Aldehyde Dehydrogenase (Betb) From Klebsiella Aerogenes (Apo, P21 Form)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of Betaine Aldehyde Dehydrogenase (Betb) From Klebsiella Aerogenes (Apo, P21 Form) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na501

b:29.1
occ:1.00
 OD1 A:ASP93 2.4 27.8 1.0
O A:ASP93 2.4 28.6 1.0
OG1 A:THR26 2.4 32.1 1.0
O A:VAL180 2.5 27.2 1.0
O A:HOH752 2.5 38.7 1.0
O A:ILE27 2.7 35.5 1.0
O A:HOH801 3.1 37.1 1.0
C A:ASP93 3.4 28.3 1.0
CG A:ASP93 3.4 33.0 1.0
CA A:ASP93 3.7 24.0 1.0
N A:ILE27 3.7 31.6 1.0
C A:VAL180 3.7 29.3 1.0
C A:ILE27 3.8 34.0 1.0
CB A:THR26 3.8 35.3 1.0
CB A:ASP93 4.1 28.4 1.0
C A:THR26 4.3 38.2 1.0
CA A:THR26 4.4 29.9 1.0
OD2 A:ASP93 4.4 29.1 1.0
CA A:ILE27 4.4 33.6 1.0
CG2 A:THR181 4.4 29.9 1.0
CA A:THR181 4.4 27.4 1.0
CG1 A:VAL180 4.5 36.5 1.0
N A:THR181 4.5 27.1 1.0
N A:THR94 4.6 24.5 1.0
CD A:PRO29 4.6 27.5 1.0
CA A:VAL180 4.7 29.9 1.0
CD1 A:LEU35 4.7 40.1 1.0
CG2 A:THR26 4.8 34.2 1.0
N A:ASN28 4.9 31.6 1.0
O A:LEU92 4.9 29.7 1.0
N A:ASP93 5.0 24.9 1.0

Sodium binding site 2 out of 8 in 8u9b

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Sodium binding site 2 out of 8 in the Crystal Structure of Betaine Aldehyde Dehydrogenase (Betb) From Klebsiella Aerogenes (Apo, P21 Form)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of Betaine Aldehyde Dehydrogenase (Betb) From Klebsiella Aerogenes (Apo, P21 Form) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na501

b:27.9
occ:1.00
 OD1 B:ASP93 2.4 25.8 1.0
O B:VAL180 2.4 25.4 1.0
OG1 B:THR26 2.5 32.2 1.0
O B:ASP93 2.6 28.2 1.0
O B:HOH849 2.7 41.3 1.0
O B:ILE27 2.7 37.4 1.0
O B:HOH729 2.9 34.3 1.0
CG B:ASP93 3.4 26.5 1.0
C B:ASP93 3.5 26.7 1.0
C B:VAL180 3.6 30.2 1.0
N B:ILE27 3.6 32.2 1.0
C B:ILE27 3.8 33.5 1.0
CA B:ASP93 3.8 26.1 1.0
CB B:THR26 3.8 31.6 1.0
CB B:ASP93 4.2 25.7 1.0
C B:THR26 4.2 36.3 1.0
CA B:ILE27 4.3 36.2 1.0
CA B:THR26 4.3 30.3 1.0
CG2 B:THR181 4.3 23.6 1.0
OD2 B:ASP93 4.3 24.6 1.0
CA B:THR181 4.4 27.6 1.0
N B:THR181 4.4 25.1 1.0
CG1 B:VAL180 4.5 28.5 1.0
CD B:PRO29 4.6 30.7 1.0
CA B:VAL180 4.7 31.8 1.0
N B:THR94 4.8 26.2 1.0
CG2 B:THR26 4.8 33.0 1.0
CD1 B:LEU35 4.9 32.2 1.0
N B:ASN28 4.9 33.4 1.0
CB B:THR181 5.0 24.9 1.0

Sodium binding site 3 out of 8 in 8u9b

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Sodium binding site 3 out of 8 in the Crystal Structure of Betaine Aldehyde Dehydrogenase (Betb) From Klebsiella Aerogenes (Apo, P21 Form)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of Betaine Aldehyde Dehydrogenase (Betb) From Klebsiella Aerogenes (Apo, P21 Form) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na501

b:28.0
occ:1.00
 OD1 C:ASP93 2.4 25.2 1.0
O C:HOH875 2.4 38.6 1.0
O C:ASP93 2.5 25.2 1.0
OG1 C:THR26 2.5 28.5 1.0
O C:VAL180 2.5 25.3 1.0
O C:ILE27 2.6 32.6 1.0
O C:HOH808 3.0 29.0 1.0
C C:ASP93 3.4 23.4 1.0
CG C:ASP93 3.5 29.7 1.0
N C:ILE27 3.7 27.2 1.0
CA C:ASP93 3.7 23.1 1.0
C C:ILE27 3.7 30.3 1.0
C C:VAL180 3.8 27.2 1.0
CB C:THR26 3.9 24.0 1.0
CB C:ASP93 4.1 23.1 1.0
CG2 C:THR181 4.3 26.7 1.0
C C:THR26 4.3 30.4 1.0
CA C:ILE27 4.3 29.4 1.0
OD2 C:ASP93 4.4 24.8 1.0
CA C:THR181 4.4 22.4 1.0
CA C:THR26 4.4 23.9 1.0
N C:THR181 4.5 25.4 1.0
CD C:PRO29 4.6 27.4 1.0
CG1 C:VAL180 4.6 29.6 1.0
N C:THR94 4.7 23.4 1.0
CA C:VAL180 4.8 22.6 1.0
N C:ASN28 4.8 28.9 1.0
CD1 C:LEU35 4.8 28.2 1.0
CG2 C:THR26 4.9 24.1 1.0
CB C:THR181 4.9 23.2 1.0
O C:LEU92 4.9 24.8 1.0

Sodium binding site 4 out of 8 in 8u9b

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Sodium binding site 4 out of 8 in the Crystal Structure of Betaine Aldehyde Dehydrogenase (Betb) From Klebsiella Aerogenes (Apo, P21 Form)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Crystal Structure of Betaine Aldehyde Dehydrogenase (Betb) From Klebsiella Aerogenes (Apo, P21 Form) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na501

b:27.4
occ:1.00
 OD1 D:ASP93 2.3 25.7 1.0
O D:ASP93 2.5 29.8 1.0
OG1 D:THR26 2.5 29.2 1.0
O D:HOH837 2.5 41.4 1.0
O D:VAL180 2.6 25.4 1.0
O D:ILE27 2.6 30.5 1.0
O D:HOH823 3.2 28.1 1.0
CG D:ASP93 3.4 28.0 1.0
C D:ASP93 3.4 28.2 1.0
CA D:ASP93 3.6 25.8 1.0
C D:ILE27 3.7 27.6 1.0
N D:ILE27 3.7 25.4 1.0
C D:VAL180 3.8 24.4 1.0
CB D:THR26 3.9 26.6 1.0
CB D:ASP93 4.1 27.0 1.0
CG2 D:THR181 4.3 26.1 1.0
C D:THR26 4.3 25.2 1.0
CA D:ILE27 4.3 28.3 1.0
OD2 D:ASP93 4.3 25.4 1.0
CA D:THR181 4.4 27.6 1.0
CA D:THR26 4.4 24.7 1.0
N D:THR181 4.6 26.5 1.0
CG1 D:VAL180 4.6 29.1 1.0
N D:THR94 4.7 24.3 1.0
CD D:PRO29 4.7 31.9 1.0
N D:ASN28 4.8 27.4 1.0
CG2 D:THR26 4.8 28.4 1.0
CD1 D:LEU35 4.8 30.7 1.0
CA D:VAL180 4.9 23.1 1.0
CB D:THR181 4.9 24.5 1.0
O D:LEU92 4.9 28.6 1.0
N D:ASP93 5.0 21.8 1.0

Sodium binding site 5 out of 8 in 8u9b

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Sodium binding site 5 out of 8 in the Crystal Structure of Betaine Aldehyde Dehydrogenase (Betb) From Klebsiella Aerogenes (Apo, P21 Form)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Crystal Structure of Betaine Aldehyde Dehydrogenase (Betb) From Klebsiella Aerogenes (Apo, P21 Form) within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Na501

b:34.4
occ:1.00
 OD1 E:ASP93 2.4 33.0 1.0
O E:VAL180 2.4 31.9 1.0
O E:ASP93 2.4 32.4 1.0
OG1 E:THR26 2.5 36.8 1.0
O E:HOH671 2.5 40.1 1.0
O E:ILE27 2.8 40.0 1.0
C E:ASP93 3.4 27.3 1.0
CG E:ASP93 3.4 32.8 1.0
O E:HOH863 3.5 36.9 1.0
CA E:ASP93 3.7 30.9 1.0
C E:VAL180 3.7 31.8 1.0
N E:ILE27 3.8 38.9 1.0
C E:ILE27 3.9 38.9 1.0
CB E:THR26 3.9 30.6 1.0
CB E:ASP93 4.1 28.6 1.0
CG2 E:THR181 4.3 28.5 1.0
C E:THR26 4.3 37.9 1.0
CA E:THR181 4.4 30.7 1.0
OD2 E:ASP93 4.4 32.9 1.0
CA E:THR26 4.4 35.5 1.0
CG1 E:VAL180 4.4 31.8 1.0
N E:THR181 4.5 28.3 1.0
CA E:ILE27 4.5 41.3 1.0
CD E:PRO29 4.6 34.7 1.0
N E:THR94 4.6 29.3 1.0
CA E:VAL180 4.7 28.7 1.0
CD1 E:LEU35 4.8 36.3 1.0
CG2 E:THR26 4.8 37.6 1.0
O E:LEU92 4.9 30.4 1.0
CB E:THR181 4.9 29.2 1.0
N E:ASN28 4.9 40.6 1.0

Sodium binding site 6 out of 8 in 8u9b

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Sodium binding site 6 out of 8 in the Crystal Structure of Betaine Aldehyde Dehydrogenase (Betb) From Klebsiella Aerogenes (Apo, P21 Form)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Crystal Structure of Betaine Aldehyde Dehydrogenase (Betb) From Klebsiella Aerogenes (Apo, P21 Form) within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Na501

b:23.8
occ:1.00
 O F:HOH789 2.3 33.3 1.0
O F:VAL180 2.4 21.1 1.0
O F:ASP93 2.4 24.6 1.0
OD1 F:ASP93 2.5 26.2 1.0
OG1 F:THR26 2.5 29.1 1.0
O F:ILE27 2.8 31.5 1.0
C F:ASP93 3.4 22.5 1.0
CG F:ASP93 3.5 23.2 1.0
O F:HOH888 3.6 32.8 1.0
C F:VAL180 3.6 23.0 1.0
CA F:ASP93 3.7 23.7 1.0
N F:ILE27 3.8 24.5 1.0
C F:ILE27 3.9 28.0 1.0
CB F:THR26 3.9 23.9 1.0
CG2 F:THR181 4.1 26.7 1.0
CB F:ASP93 4.2 22.0 1.0
CA F:THR181 4.3 23.8 1.0
CG1 F:VAL180 4.4 28.4 1.0
C F:THR26 4.4 28.1 1.0
N F:THR181 4.4 21.6 1.0
OD2 F:ASP93 4.4 25.3 1.0
CA F:THR26 4.4 25.5 1.0
CA F:ILE27 4.5 31.1 1.0
N F:THR94 4.6 19.8 1.0
CA F:VAL180 4.6 25.6 1.0
CD F:PRO29 4.7 26.7 1.0
CB F:THR181 4.8 25.0 1.0
CG2 F:THR26 4.9 26.3 1.0
CD1 F:LEU35 4.9 26.4 1.0
N F:ASN28 4.9 27.6 1.0

Sodium binding site 7 out of 8 in 8u9b

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Sodium binding site 7 out of 8 in the Crystal Structure of Betaine Aldehyde Dehydrogenase (Betb) From Klebsiella Aerogenes (Apo, P21 Form)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of Crystal Structure of Betaine Aldehyde Dehydrogenase (Betb) From Klebsiella Aerogenes (Apo, P21 Form) within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Na501

b:26.9
occ:1.00
 OD1 G:ASP93 2.4 27.3 1.0
O G:ASP93 2.4 26.4 1.0
OG1 G:THR26 2.5 28.5 1.0
O G:VAL180 2.6 28.1 1.0
O G:ILE27 2.6 28.7 1.0
O G:HOH864 2.7 35.5 1.0
C G:ASP93 3.4 26.3 1.0
CG G:ASP93 3.4 28.5 1.0
CA G:ASP93 3.6 25.5 1.0
N G:ILE27 3.7 25.1 1.0
C G:ILE27 3.7 28.3 1.0
C G:VAL180 3.8 27.3 1.0
CB G:THR26 3.9 25.0 1.0
CB G:ASP93 4.1 28.6 1.0
C G:THR26 4.3 27.3 1.0
CA G:ILE27 4.3 31.4 1.0
CG2 G:THR181 4.3 29.6 1.0
OD2 G:ASP93 4.4 22.9 1.0
CA G:THR26 4.4 24.4 1.0
CD G:PRO29 4.4 29.2 1.0
CA G:THR181 4.5 26.5 1.0
CG1 G:VAL180 4.6 28.9 1.0
CG G:PRO29 4.6 33.9 1.0
N G:THR181 4.6 26.0 1.0
N G:THR94 4.6 22.2 1.0
O G:HOH660 4.8 44.5 1.0
CA G:VAL180 4.8 25.7 1.0
N G:ASN28 4.8 30.2 1.0
O G:LEU92 4.8 24.2 1.0
CD1 G:LEU35 4.9 32.5 1.0
CG2 G:THR26 4.9 28.2 1.0
N G:ASP93 4.9 23.2 1.0
CB G:THR181 5.0 30.0 1.0

Sodium binding site 8 out of 8 in 8u9b

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Sodium binding site 8 out of 8 in the Crystal Structure of Betaine Aldehyde Dehydrogenase (Betb) From Klebsiella Aerogenes (Apo, P21 Form)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of Crystal Structure of Betaine Aldehyde Dehydrogenase (Betb) From Klebsiella Aerogenes (Apo, P21 Form) within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Na501

b:28.4
occ:1.00
 O H:HOH890 2.2 40.6 1.0
OG1 H:THR26 2.4 26.4 1.0
O H:VAL180 2.5 27.1 1.0
OD1 H:ASP93 2.5 27.6 1.0
O H:ASP93 2.5 27.0 1.0
O H:ILE27 2.6 31.8 1.0
O H:HOH774 2.8 31.2 1.0
C H:ASP93 3.5 24.6 1.0
CG H:ASP93 3.6 29.9 1.0
N H:ILE27 3.6 28.6 1.0
C H:ILE27 3.7 33.5 1.0
C H:VAL180 3.7 26.5 1.0
CA H:ASP93 3.8 24.5 1.0
CB H:THR26 3.8 27.3 1.0
C H:THR26 4.2 29.1 1.0
CB H:ASP93 4.2 24.6 1.0
CA H:ILE27 4.2 33.1 1.0
CA H:THR26 4.3 31.1 1.0
CG2 H:THR181 4.3 28.1 1.0
CA H:THR181 4.5 23.3 1.0
OD2 H:ASP93 4.5 24.4 1.0
CG1 H:VAL180 4.5 28.0 1.0
N H:THR181 4.5 22.3 1.0
CD H:PRO29 4.6 31.6 1.0
CA H:VAL180 4.7 24.3 1.0
N H:THR94 4.7 25.6 1.0
CG H:PRO29 4.7 35.0 1.0
CG2 H:THR26 4.8 28.1 1.0
N H:ASN28 4.8 30.7 1.0
CD1 H:LEU35 4.9 32.7 1.0
O H:LEU92 5.0 27.9 1.0
CB H:THR181 5.0 27.5 1.0

Reference:

S.Lovell, L.Liu, K.P.Battaile, A.Cooper. Crystal Structure of Betaine Aldehyde Dehydrogenase (Betb) From Klebsiella Aerogenes (Apo, P21 Form) To Be Published.
Page generated: Wed Oct 9 13:51:55 2024

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