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Sodium in PDB 4zla: Bestatin Complex Structure of Leucine Aminopeptidase From Helicobacter Pylori

Enzymatic activity of Bestatin Complex Structure of Leucine Aminopeptidase From Helicobacter Pylori

All present enzymatic activity of Bestatin Complex Structure of Leucine Aminopeptidase From Helicobacter Pylori:
3.4.11.1; 3.4.11.10;

Protein crystallography data

The structure of Bestatin Complex Structure of Leucine Aminopeptidase From Helicobacter Pylori, PDB code: 4zla was solved by J.K.Modak, A.Roujeinikova, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.55 / 1.90
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 99.770, 99.690, 96.780, 81.89, 60.97, 75.39
R / Rfree (%) 17.6 / 21.9

Other elements in 4zla:

The structure of Bestatin Complex Structure of Leucine Aminopeptidase From Helicobacter Pylori also contains other interesting chemical elements:

Zinc (Zn) 12 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Bestatin Complex Structure of Leucine Aminopeptidase From Helicobacter Pylori (pdb code 4zla). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 6 binding sites of Sodium where determined in the Bestatin Complex Structure of Leucine Aminopeptidase From Helicobacter Pylori, PDB code: 4zla:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6;

Sodium binding site 1 out of 6 in 4zla

Go back to Sodium Binding Sites List in 4zla
Sodium binding site 1 out of 6 in the Bestatin Complex Structure of Leucine Aminopeptidase From Helicobacter Pylori


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Bestatin Complex Structure of Leucine Aminopeptidase From Helicobacter Pylori within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na503

b:12.9
occ:1.00
 O A:HOH611 2.2 14.0 1.0
O A:HOH627 2.3 16.0 1.0
O A:TYR465 2.4 6.5 1.0
O A:GLY462 2.4 8.1 1.0
O A:ALA461 2.6 10.4 1.0
O A:HOH912 2.6 26.4 1.0
C A:GLY462 3.3 11.9 1.0
C A:TYR465 3.5 12.5 1.0
C A:ALA461 3.7 8.5 1.0
CA A:GLY462 3.7 9.9 1.0
N A:TYR465 3.9 7.8 1.0
CA A:TYR465 4.1 10.6 1.0
N A:GLY462 4.2 7.5 1.0
O A:HOH914 4.2 25.5 1.0
O A:HOH877 4.3 28.6 1.0
OE2 A:GLU378 4.3 14.8 1.0
CB A:TYR465 4.4 11.1 1.0
N A:PRO463 4.5 7.2 1.0
N A:VAL466 4.6 7.8 1.0
C11 A:BES505 4.6 25.6 1.0
CG2 A:VAL466 4.7 8.5 1.0
N A:ALA464 4.8 8.9 1.0
C10 A:BES505 4.9 23.3 1.0
CA A:VAL466 4.9 9.4 1.0
CA A:ALA461 5.0 9.1 1.0

Sodium binding site 2 out of 6 in 4zla

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Sodium binding site 2 out of 6 in the Bestatin Complex Structure of Leucine Aminopeptidase From Helicobacter Pylori


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Bestatin Complex Structure of Leucine Aminopeptidase From Helicobacter Pylori within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na503

b:14.3
occ:1.00
 O B:HOH681 2.3 15.0 1.0
O B:HOH931 2.3 19.7 1.0
O B:TYR465 2.4 7.0 1.0
O B:GLY462 2.4 6.8 1.0
O B:HOH647 2.5 12.3 1.0
O B:ALA461 2.6 6.5 1.0
C B:GLY462 3.3 8.2 1.0
C B:TYR465 3.5 8.7 1.0
CA B:GLY462 3.7 8.5 1.0
C B:ALA461 3.7 8.8 1.0
N B:TYR465 3.8 7.5 1.0
O B:HOH921 4.0 21.3 1.0
CA B:TYR465 4.0 7.0 1.0
N B:GLY462 4.2 6.8 1.0
CB B:TYR465 4.3 6.1 1.0
OE2 B:GLU378 4.4 10.7 1.0
C10 B:BES505 4.5 20.8 1.0
N B:PRO463 4.5 7.2 1.0
N B:VAL466 4.6 8.8 1.0
C11 B:BES505 4.6 23.6 1.0
N B:ALA464 4.7 8.0 1.0
CG2 B:VAL466 4.7 7.3 1.0
CA B:VAL466 4.9 6.8 1.0
C B:PRO463 4.9 10.6 1.0
C B:ALA464 5.0 6.8 1.0
CA B:ALA461 5.0 7.4 1.0

Sodium binding site 3 out of 6 in 4zla

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Sodium binding site 3 out of 6 in the Bestatin Complex Structure of Leucine Aminopeptidase From Helicobacter Pylori


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Bestatin Complex Structure of Leucine Aminopeptidase From Helicobacter Pylori within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na503

b:15.0
occ:1.00
 O C:HOH2571 2.3 18.0 1.0
O C:HOH2562 2.3 17.3 1.0
O C:HOH2787 2.3 21.7 1.0
O C:GLY462 2.4 8.4 1.0
O C:TYR465 2.4 11.2 1.0
O C:ALA461 2.5 9.6 1.0
C C:GLY462 3.3 11.3 1.0
O C:HOH2796 3.4 29.9 1.0
C C:TYR465 3.5 12.5 1.0
C C:ALA461 3.5 10.7 1.0
CA C:GLY462 3.6 9.5 1.0
N C:TYR465 3.8 9.8 1.0
N C:GLY462 4.0 9.0 1.0
CA C:TYR465 4.0 10.3 1.0
CB C:TYR465 4.3 9.1 1.0
C10 C:BES505 4.4 26.5 1.0
N C:PRO463 4.5 11.0 1.0
OE2 C:GLU378 4.5 14.7 1.0
C11 C:BES505 4.5 19.3 1.0
N C:VAL466 4.7 7.0 1.0
N C:ALA464 4.7 9.4 1.0
CG2 C:VAL466 4.8 8.0 1.0
CA C:ALA461 4.8 10.5 1.0
O C:HOH2591 4.8 20.2 1.0
C C:ALA464 4.9 10.8 1.0
C C:PRO463 5.0 12.4 1.0

Sodium binding site 4 out of 6 in 4zla

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Sodium binding site 4 out of 6 in the Bestatin Complex Structure of Leucine Aminopeptidase From Helicobacter Pylori


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Bestatin Complex Structure of Leucine Aminopeptidase From Helicobacter Pylori within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na503

b:13.8
occ:1.00
 O D:GLY462 2.4 7.3 1.0
O D:HOH935 2.4 24.4 1.0
O D:HOH692 2.4 12.2 1.0
O D:TYR465 2.4 8.1 1.0
O D:HOH618 2.5 15.0 1.0
O D:ALA461 2.5 5.4 1.0
C D:GLY462 3.3 9.3 1.0
O D:HOH942 3.4 29.3 1.0
C D:TYR465 3.5 11.8 1.0
C D:ALA461 3.6 9.7 1.0
CA D:GLY462 3.7 10.5 1.0
N D:TYR465 3.8 6.6 1.0
CA D:TYR465 4.1 5.8 1.0
O D:HOH889 4.1 19.6 1.0
N D:GLY462 4.1 6.5 1.0
CB D:TYR465 4.4 8.5 1.0
N D:PRO463 4.5 9.3 1.0
C11 D:BES505 4.5 21.8 1.0
OE2 D:GLU378 4.5 15.4 1.0
C10 D:BES505 4.6 15.5 1.0
N D:VAL466 4.7 8.0 1.0
N D:ALA464 4.7 11.5 1.0
CG2 D:VAL466 4.7 4.3 1.0
CA D:ALA461 4.9 10.6 1.0
C D:ALA464 4.9 7.9 1.0
C D:PRO463 5.0 10.5 1.0
CA D:PRO463 5.0 8.3 1.0
CA D:VAL466 5.0 7.5 1.0

Sodium binding site 5 out of 6 in 4zla

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Sodium binding site 5 out of 6 in the Bestatin Complex Structure of Leucine Aminopeptidase From Helicobacter Pylori


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Bestatin Complex Structure of Leucine Aminopeptidase From Helicobacter Pylori within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Na503

b:12.1
occ:1.00
 O E:GLY462 2.3 8.9 1.0
O E:HOH634 2.3 15.2 1.0
O E:HOH923 2.4 22.5 1.0
O E:HOH856 2.4 16.4 1.0
O E:TYR465 2.4 8.1 1.0
O E:ALA461 2.5 6.5 1.0
C E:GLY462 3.2 10.4 1.0
C E:TYR465 3.5 7.4 1.0
C E:ALA461 3.6 9.3 1.0
CA E:GLY462 3.6 8.0 1.0
N E:TYR465 3.8 6.9 1.0
CA E:TYR465 4.1 9.6 1.0
N E:GLY462 4.1 7.6 1.0
O E:HOH922 4.2 24.5 1.0
CB E:TYR465 4.3 7.1 1.0
O E:HOH862 4.4 27.1 1.0
N E:PRO463 4.4 5.5 1.0
OE2 E:GLU378 4.4 12.2 1.0
N E:VAL466 4.6 8.2 1.0
N E:ALA464 4.7 7.9 1.0
C10 E:BES505 4.7 23.6 1.0
C11 E:BES505 4.7 24.2 1.0
CG2 E:VAL466 4.7 5.2 1.0
CA E:ALA461 4.9 8.2 1.0
CA E:VAL466 5.0 10.2 1.0
C E:PRO463 5.0 7.7 1.0
CA E:PRO463 5.0 8.1 1.0
C E:ALA464 5.0 10.1 1.0

Sodium binding site 6 out of 6 in 4zla

Go back to Sodium Binding Sites List in 4zla
Sodium binding site 6 out of 6 in the Bestatin Complex Structure of Leucine Aminopeptidase From Helicobacter Pylori


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Bestatin Complex Structure of Leucine Aminopeptidase From Helicobacter Pylori within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Na503

b:12.0
occ:1.00
 O F:HOH919 2.2 26.5 1.0
O F:HOH614 2.3 14.8 1.0
O F:GLY462 2.3 6.7 1.0
O F:TYR465 2.4 8.8 1.0
O F:HOH878 2.5 28.1 1.0
O F:ALA461 2.5 8.8 1.0
C F:GLY462 3.2 9.7 1.0
C F:TYR465 3.5 7.7 1.0
CA F:GLY462 3.6 6.5 1.0
C F:ALA461 3.6 7.8 1.0
N F:TYR465 3.8 5.4 1.0
O F:HOH932 3.9 29.4 1.0
N F:GLY462 4.1 7.1 1.0
CA F:TYR465 4.1 8.0 1.0
C10 F:BES505 4.3 15.7 1.0
CB F:TYR465 4.3 5.7 1.0
N F:PRO463 4.5 7.2 1.0
OE2 F:GLU378 4.5 12.6 1.0
N F:VAL466 4.6 6.9 1.0
C11 F:BES505 4.7 20.7 1.0
N F:ALA464 4.7 5.0 1.0
CG2 F:VAL466 4.8 4.6 1.0
CA F:ALA461 4.9 7.1 1.0
CA F:VAL466 5.0 8.3 1.0
C F:PRO463 5.0 7.4 1.0
C F:ALA464 5.0 6.6 1.0

Reference:

J.K.Modak, W.Rut, L.C.Wijeyewickrema, R.N.Pike, M.Drag, A.Roujeinikova. Structural Basis For Substrate Specificity of Helicobacter Pylori M17 Aminopeptidase. Biochimie V. 121 60 2016.
ISSN: ISSN 0300-9084
PubMed: 26616008
DOI: 10.1016/J.BIOCHI.2015.11.021
Page generated: Mon Oct 7 19:43:58 2024

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