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Sodium in PDB 4o5h: X-Ray Crystal Structure of A Putative Phenylacetaldehyde Dehydrogenase From Burkholderia Cenocepacia

Enzymatic activity of X-Ray Crystal Structure of A Putative Phenylacetaldehyde Dehydrogenase From Burkholderia Cenocepacia

All present enzymatic activity of X-Ray Crystal Structure of A Putative Phenylacetaldehyde Dehydrogenase From Burkholderia Cenocepacia:
1.2.1.39;

Protein crystallography data

The structure of X-Ray Crystal Structure of A Putative Phenylacetaldehyde Dehydrogenase From Burkholderia Cenocepacia, PDB code: 4o5h was solved by Seattle Structural 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) 50.00 / 2.00
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 112.620, 150.070, 345.910, 90.00, 90.00, 90.00
R / Rfree (%) 16.9 / 19.3

Sodium Binding Sites:

The binding sites of Sodium atom in the X-Ray Crystal Structure of A Putative Phenylacetaldehyde Dehydrogenase From Burkholderia Cenocepacia (pdb code 4o5h). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the X-Ray Crystal Structure of A Putative Phenylacetaldehyde Dehydrogenase From Burkholderia Cenocepacia, PDB code: 4o5h:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 4o5h

Go back to Sodium Binding Sites List in 4o5h
Sodium binding site 1 out of 4 in the X-Ray Crystal Structure of A Putative Phenylacetaldehyde Dehydrogenase From Burkholderia Cenocepacia


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of X-Ray Crystal Structure of A Putative Phenylacetaldehyde Dehydrogenase From Burkholderia Cenocepacia within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na605

b:15.3
occ:1.00
 O A:ASP204 2.2 12.1 1.0
OD1 A:ASP111 2.3 13.7 1.0
O A:HOH764 2.4 19.4 1.0
O A:HOH716 2.4 11.1 1.0
O A:ASP111 2.4 12.4 1.0
O A:VAL43 3.0 13.1 1.0
C A:ASP111 3.4 12.2 1.0
C A:ASP204 3.5 12.0 1.0
CG A:ASP111 3.5 13.1 1.0
CA A:ASP111 3.8 12.6 1.0
CG1 A:VAL42 3.9 14.3 1.0
N A:VAL43 4.1 13.5 1.0
C A:VAL43 4.1 13.4 1.0
CB A:ASP111 4.2 12.5 1.0
CG2 A:THR205 4.3 11.1 1.0
O A:HOH822 4.3 15.4 1.0
N A:THR205 4.3 11.2 1.0
CA A:THR205 4.3 10.9 1.0
O A:HOH940 4.4 22.8 1.0
CA A:ASP204 4.4 12.6 1.0
OD2 A:ASP111 4.5 12.5 1.0
N A:ASN112 4.5 12.0 1.0
CA A:VAL43 4.6 13.8 1.0
CD A:PRO45 4.8 12.8 1.0
CB A:ASP204 4.8 12.6 1.0
C A:VAL42 4.9 14.3 1.0
CB A:THR205 4.9 10.7 1.0
CA A:VAL42 5.0 14.4 1.0
CD A:PRO206 5.0 10.9 1.0

Sodium binding site 2 out of 4 in 4o5h

Go back to Sodium Binding Sites List in 4o5h
Sodium binding site 2 out of 4 in the X-Ray Crystal Structure of A Putative Phenylacetaldehyde Dehydrogenase From Burkholderia Cenocepacia


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of X-Ray Crystal Structure of A Putative Phenylacetaldehyde Dehydrogenase From Burkholderia Cenocepacia within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na602

b:19.6
occ:1.00
 O B:ASP204 2.3 19.9 1.0
O B:ASP111 2.3 16.9 1.0
OD1 B:ASP111 2.4 17.3 1.0
O B:HOH955 2.4 25.6 1.0
O B:HOH707 2.4 17.7 1.0
O B:VAL43 3.0 18.9 1.0
C B:ASP111 3.3 16.7 1.0
CG B:ASP111 3.5 17.1 1.0
C B:ASP204 3.5 18.9 1.0
CA B:ASP111 3.7 17.1 1.0
CG1 B:VAL42 4.0 21.7 1.0
C B:VAL43 4.1 19.7 1.0
N B:VAL43 4.1 19.7 1.0
CB B:ASP111 4.2 16.8 1.0
CG2 B:THR205 4.2 17.0 1.0
CA B:THR205 4.3 16.8 1.0
N B:THR205 4.4 17.4 1.0
N B:ASN112 4.4 16.2 1.0
O B:HOH958 4.4 27.0 1.0
OD2 B:ASP111 4.5 17.0 1.0
O B:HOH889 4.5 22.9 1.0
CA B:ASP204 4.5 19.5 1.0
CA B:VAL43 4.6 20.3 1.0
CD B:PRO45 4.8 18.6 1.0
CB B:ASP204 4.8 19.9 1.0
CA B:ASN112 4.9 15.9 1.0
CB B:THR205 4.9 16.6 1.0
C B:VAL42 4.9 22.1 1.0
CG2 B:VAL352 5.0 19.4 1.0

Sodium binding site 3 out of 4 in 4o5h

Go back to Sodium Binding Sites List in 4o5h
Sodium binding site 3 out of 4 in the X-Ray Crystal Structure of A Putative Phenylacetaldehyde Dehydrogenase From Burkholderia Cenocepacia


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of X-Ray Crystal Structure of A Putative Phenylacetaldehyde Dehydrogenase From Burkholderia Cenocepacia within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na602

b:16.4
occ:1.00
 O C:ASP111 2.3 12.8 1.0
OD1 C:ASP111 2.4 13.9 1.0
O C:HOH781 2.4 16.3 1.0
O C:HOH833 2.5 16.7 1.0
O C:ASP204 2.5 13.9 1.0
O C:VAL43 2.7 14.8 1.0
C C:ASP111 3.3 12.8 1.0
CG C:ASP111 3.5 13.2 1.0
CA C:ASP111 3.7 12.9 1.0
CG1 C:VAL42 3.7 14.1 1.0
C C:ASP204 3.8 14.0 1.0
C C:VAL43 3.8 14.2 1.0
N C:VAL43 3.9 13.9 1.0
CB C:ASP111 4.2 12.8 1.0
O C:HOH800 4.3 16.0 1.0
CA C:VAL43 4.4 14.1 1.0
CG2 C:THR205 4.5 13.6 1.0
N C:ASN112 4.5 12.3 1.0
OD2 C:ASP111 4.5 13.0 1.0
CA C:THR205 4.6 13.6 1.0
CD C:PRO45 4.6 13.3 1.0
N C:THR205 4.6 13.4 1.0
O C:HOH729 4.7 15.5 1.0
C C:VAL42 4.7 13.8 1.0
CA C:ASP204 4.8 14.2 1.0
CG2 C:VAL43 4.8 15.0 1.0
CA C:VAL42 4.9 13.9 1.0
N C:ASN44 4.9 13.9 1.0
O C:LEU110 4.9 13.6 1.0
CB C:VAL42 4.9 14.1 1.0
CA C:ASN112 5.0 12.2 1.0
N C:ASP111 5.0 12.9 1.0

Sodium binding site 4 out of 4 in 4o5h

Go back to Sodium Binding Sites List in 4o5h
Sodium binding site 4 out of 4 in the X-Ray Crystal Structure of A Putative Phenylacetaldehyde Dehydrogenase From Burkholderia Cenocepacia


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of X-Ray Crystal Structure of A Putative Phenylacetaldehyde Dehydrogenase From Burkholderia Cenocepacia within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na603

b:10.8
occ:1.00
 O D:ASP204 2.3 12.9 1.0
O D:ASP111 2.3 11.9 1.0
O D:HOH850 2.4 9.3 1.0
OD1 D:ASP111 2.4 13.0 1.0
O D:HOH895 2.4 16.1 1.0
O D:VAL43 3.0 13.8 1.0
C D:ASP111 3.3 12.0 1.0
CG D:ASP111 3.5 12.4 1.0
C D:ASP204 3.6 12.3 1.0
CA D:ASP111 3.7 12.2 1.0
CG1 D:VAL42 4.0 13.4 1.0
N D:VAL43 4.1 13.8 1.0
C D:VAL43 4.1 14.1 1.0
CB D:ASP111 4.2 12.2 1.0
CG2 D:THR205 4.2 10.7 1.0
O D:HOH1063 4.3 31.6 1.0
CA D:THR205 4.4 10.8 1.0
N D:THR205 4.4 11.2 1.0
N D:ASN112 4.4 11.7 1.0
O D:HOH741 4.5 13.6 1.0
OD2 D:ASP111 4.5 12.5 1.0
CA D:ASP204 4.5 12.9 1.0
CA D:VAL43 4.6 14.4 1.0
CD D:PRO45 4.8 13.3 1.0
CB D:ASP204 4.8 13.0 1.0
C D:VAL42 4.9 14.2 1.0
CA D:ASN112 4.9 11.5 1.0
CG2 D:VAL352 4.9 12.4 1.0
CB D:THR205 5.0 10.5 1.0

Reference:

J.W.Fairman, J.Abendroth, T.E.Edwards, D.Lorimer. X-Ray Crystal Structure of A Putative Phenylacetaldehyde Dehydrogenase From Burkholderia Cenocepacia To Be Published.
Page generated: Mon Oct 7 17:24:58 2024

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