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Sodium in PDB 5hxz: Structure-Function Analysis of Functionally Diverse Members of the Cyclic Amide Hydrolase Family of Toblerone Fold Enzymes

Enzymatic activity of Structure-Function Analysis of Functionally Diverse Members of the Cyclic Amide Hydrolase Family of Toblerone Fold Enzymes

All present enzymatic activity of Structure-Function Analysis of Functionally Diverse Members of the Cyclic Amide Hydrolase Family of Toblerone Fold Enzymes:
3.5.2.1;

Protein crystallography data

The structure of Structure-Function Analysis of Functionally Diverse Members of the Cyclic Amide Hydrolase Family of Toblerone Fold Enzymes, PDB code: 5hxz was solved by T.S.Peat, S.Balotra, M.Wilding, J.Newman, C.Scott, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.30 / 2.36
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 81.630, 83.732, 215.102, 90.00, 90.00, 90.00
R / Rfree (%) 22.4 / 25.5

Other elements in 5hxz:

The structure of Structure-Function Analysis of Functionally Diverse Members of the Cyclic Amide Hydrolase Family of Toblerone Fold Enzymes also contains other interesting chemical elements:

Chlorine (Cl) 4 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Structure-Function Analysis of Functionally Diverse Members of the Cyclic Amide Hydrolase Family of Toblerone Fold Enzymes (pdb code 5hxz). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Structure-Function Analysis of Functionally Diverse Members of the Cyclic Amide Hydrolase Family of Toblerone Fold Enzymes, PDB code: 5hxz:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 5hxz

Go back to Sodium Binding Sites List in 5hxz
Sodium binding site 1 out of 4 in the Structure-Function Analysis of Functionally Diverse Members of the Cyclic Amide Hydrolase Family of Toblerone Fold Enzymes


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure-Function Analysis of Functionally Diverse Members of the Cyclic Amide Hydrolase Family of Toblerone Fold Enzymes within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na404

b:23.5
occ:1.00
 O A:ALA350 2.7 24.0 1.0
OE2 A:GLU301 2.7 25.2 1.0
O A:GLN353 2.8 22.2 1.0
O A:GLY358 2.8 17.7 1.0
O A:PRO355 3.0 26.9 1.0
CD A:GLU301 3.2 26.5 1.0
O A:GLY354 3.4 25.7 1.0
CB A:ALA350 3.4 21.3 1.0
OE1 A:GLU301 3.7 19.4 1.0
C A:ALA350 3.7 21.8 1.0
C A:PRO355 3.7 29.0 1.0
C A:GLN353 3.7 21.6 1.0
C A:GLY358 3.8 16.8 1.0
C A:GLY354 3.9 28.6 1.0
CG A:GLU301 4.0 25.6 1.0
CA A:ALA350 4.2 20.8 1.0
CA A:GLU356 4.2 26.7 1.0
N A:GLU356 4.3 29.1 1.0
N A:GLY358 4.3 27.8 1.0
N A:GLY357 4.3 25.7 1.0
N A:GLN353 4.3 23.7 1.0
N A:PRO355 4.5 26.4 1.0
CA A:GLY354 4.5 21.6 1.0
N A:GLY354 4.5 26.7 1.0
CA A:GLY359 4.5 19.4 1.0
N A:GLY359 4.6 17.9 1.0
CA A:GLN353 4.6 21.9 1.0
C A:GLU356 4.7 30.3 1.0
CA A:PRO355 4.7 24.9 1.0
CA A:GLY358 4.7 23.0 1.0
N A:ALA351 4.7 20.0 1.0
NH1 A:ARG220 4.8 41.6 1.0
CB A:GLU301 5.0 15.7 1.0
CB A:GLN353 5.0 22.2 1.0

Sodium binding site 2 out of 4 in 5hxz

Go back to Sodium Binding Sites List in 5hxz
Sodium binding site 2 out of 4 in the Structure-Function Analysis of Functionally Diverse Members of the Cyclic Amide Hydrolase Family of Toblerone Fold Enzymes


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structure-Function Analysis of Functionally Diverse Members of the Cyclic Amide Hydrolase Family of Toblerone Fold Enzymes within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na402

b:26.0
occ:1.00
 O B:GLN353 2.7 26.4 1.0
O B:GLY358 2.7 15.6 1.0
O B:PRO355 2.8 20.6 1.0
O B:ALA350 2.8 31.5 1.0
OE2 B:GLU301 2.9 27.4 1.0
O B:GLY354 3.1 20.8 1.0
CD B:GLU301 3.5 25.7 1.0
C B:PRO355 3.5 23.7 1.0
CB B:ALA350 3.6 23.8 1.0
C B:GLY354 3.6 26.1 1.0
C B:GLN353 3.6 28.6 1.0
C B:GLY358 3.7 17.2 1.0
C B:ALA350 3.8 28.9 1.0
OE1 B:GLU301 4.0 21.2 1.0
N B:GLU356 4.1 20.7 1.0
CA B:GLU356 4.1 26.4 1.0
N B:GLY358 4.2 23.5 1.0
N B:PRO355 4.2 23.8 1.0
CA B:GLY354 4.3 23.4 1.0
CG B:GLU301 4.3 23.9 1.0
N B:GLY357 4.3 19.9 1.0
N B:GLN353 4.3 26.6 1.0
CA B:ALA350 4.3 28.2 1.0
N B:GLY354 4.3 23.2 1.0
CA B:PRO355 4.4 21.6 1.0
N B:GLY359 4.5 21.0 1.0
CA B:GLY359 4.5 23.6 1.0
CA B:GLN353 4.5 23.9 1.0
C B:GLU356 4.6 27.7 1.0
CA B:GLY358 4.6 21.7 1.0
N B:ALA351 4.8 24.8 1.0
NH1 B:ARG220 4.9 41.8 1.0
CB B:GLN353 5.0 25.3 1.0
N B:HIS352 5.0 22.8 1.0

Sodium binding site 3 out of 4 in 5hxz

Go back to Sodium Binding Sites List in 5hxz
Sodium binding site 3 out of 4 in the Structure-Function Analysis of Functionally Diverse Members of the Cyclic Amide Hydrolase Family of Toblerone Fold Enzymes


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Structure-Function Analysis of Functionally Diverse Members of the Cyclic Amide Hydrolase Family of Toblerone Fold Enzymes within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na401

b:38.0
occ:1.00
 OE2 C:GLU301 2.7 30.5 1.0
O C:PRO355 2.7 30.4 1.0
O C:GLY358 2.8 25.9 1.0
O C:ALA350 2.9 23.9 1.0
O C:GLN353 3.0 23.1 1.0
CD C:GLU301 3.2 24.6 1.0
O C:GLY354 3.3 28.5 1.0
C C:PRO355 3.5 31.7 1.0
CB C:ALA350 3.6 23.6 1.0
C C:GLY358 3.7 25.3 1.0
OE1 C:GLU301 3.8 23.7 1.0
C C:GLY354 3.8 29.6 1.0
C C:ALA350 3.8 30.1 1.0
C C:GLN353 3.9 27.9 1.0
CA C:GLU356 3.9 36.1 1.0
N C:GLU356 4.0 28.3 1.0
N C:GLY357 4.0 30.2 1.0
CG C:GLU301 4.0 22.7 1.0
N C:GLY358 4.0 31.4 1.0
C C:GLU356 4.3 37.6 1.0
N C:PRO355 4.3 35.4 1.0
CA C:ALA350 4.3 23.6 1.0
CA C:PRO355 4.5 31.9 1.0
N C:GLN353 4.5 29.4 1.0
CA C:GLY358 4.5 27.5 1.0
CA C:GLY354 4.5 29.7 1.0
N C:GLY359 4.5 21.9 1.0
N C:GLY354 4.6 34.6 1.0
CA C:GLY359 4.6 21.4 1.0
CA C:GLN353 4.8 24.7 1.0
N C:ALA351 4.8 29.0 1.0
C C:GLY357 4.9 31.9 1.0
CA C:GLY357 5.0 29.0 1.0

Sodium binding site 4 out of 4 in 5hxz

Go back to Sodium Binding Sites List in 5hxz
Sodium binding site 4 out of 4 in the Structure-Function Analysis of Functionally Diverse Members of the Cyclic Amide Hydrolase Family of Toblerone Fold Enzymes


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Structure-Function Analysis of Functionally Diverse Members of the Cyclic Amide Hydrolase Family of Toblerone Fold Enzymes within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na403

b:27.1
occ:1.00
 O D:ALA350 2.4 23.4 1.0
O D:GLN353 2.7 26.7 1.0
OE2 D:GLU301 3.0 30.3 1.0
O D:GLY354 3.1 23.9 1.0
O D:GLY358 3.2 23.5 1.0
O D:PRO355 3.2 22.1 1.0
C D:ALA350 3.4 24.6 1.0
CD D:GLU301 3.5 23.0 1.0
C D:GLN353 3.5 28.2 1.0
CB D:ALA350 3.5 19.5 1.0
OE1 D:GLU301 3.7 19.7 1.0
C D:GLY354 3.7 25.1 1.0
C D:PRO355 3.7 27.2 1.0
N D:GLN353 3.9 18.8 1.0
CA D:ALA350 4.1 23.0 1.0
C D:GLY358 4.2 22.4 1.0
N D:GLU356 4.2 26.4 1.0
CA D:GLU356 4.2 31.9 1.0
CA D:GLN353 4.2 21.1 1.0
N D:GLY354 4.3 28.0 1.0
CA D:GLY354 4.4 22.6 1.0
N D:ALA351 4.4 20.8 1.0
N D:PRO355 4.4 30.0 1.0
CG D:GLU301 4.4 21.2 1.0
N D:HIS352 4.5 21.6 1.0
CA D:PRO355 4.6 30.4 1.0
N D:GLY357 4.6 29.5 1.0
CA D:ALA351 4.6 27.7 1.0
CB D:GLN353 4.7 24.3 1.0
N D:GLY358 4.7 23.3 1.0
NH1 D:ARG220 4.7 42.9 1.0
CA D:GLY359 4.8 21.5 1.0
C D:ALA351 4.8 25.0 1.0
C D:GLU356 4.8 26.2 1.0
N D:GLY359 4.9 18.2 1.0
C D:HIS352 4.9 24.2 1.0

Reference:

T.S.Peat, S.Balotra, M.Wilding, C.J.Hartley, J.Newman, C.Scott. High-Resolution X-Ray Structures of Two Functionally Distinct Members of the Cyclic Amide Hydrolase Family of Toblerone Fold Enzymes. Appl. Environ. Microbiol. V. 83 2017.
ISSN: ESSN 1098-5336
PubMed: 28235873
DOI: 10.1128/AEM.03365-16
Page generated: Mon Oct 7 21:29:54 2024

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