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Sodium in PDB 4xn7: Crystal Structure of E. Coli Aminopeptidase N in Complex with L-2,3- Diaminopropionic Acid

Enzymatic activity of Crystal Structure of E. Coli Aminopeptidase N in Complex with L-2,3- Diaminopropionic Acid

All present enzymatic activity of Crystal Structure of E. Coli Aminopeptidase N in Complex with L-2,3- Diaminopropionic Acid:
3.4.11.2;

Protein crystallography data

The structure of Crystal Structure of E. Coli Aminopeptidase N in Complex with L-2,3- Diaminopropionic Acid, PDB code: 4xn7 was solved by A.Addlagatta, R.Gumpena, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.25 / 2.22
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 120.690, 120.690, 170.460, 90.00, 90.00, 120.00
R / Rfree (%) 19.9 / 24.6

Other elements in 4xn7:

The structure of Crystal Structure of E. Coli Aminopeptidase N in Complex with L-2,3- Diaminopropionic Acid also contains other interesting chemical elements:

Zinc (Zn) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of E. Coli Aminopeptidase N in Complex with L-2,3- Diaminopropionic Acid (pdb code 4xn7). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Crystal Structure of E. Coli Aminopeptidase N in Complex with L-2,3- Diaminopropionic Acid, PDB code: 4xn7:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 4xn7

Go back to Sodium Binding Sites List in 4xn7
Sodium binding site 1 out of 4 in the Crystal Structure of E. Coli Aminopeptidase N in Complex with L-2,3- Diaminopropionic Acid


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 E. Coli Aminopeptidase N in Complex with L-2,3- Diaminopropionic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na903

b:28.4
occ:1.00
 O A:HOH1371 2.2 21.3 1.0
O A:GLY335 2.4 19.2 1.0
O A:SER332 2.7 19.1 1.0
O A:HOH1332 2.7 12.7 1.0
O A:ASP333 2.9 18.2 1.0
C A:GLY335 3.6 18.4 1.0
C A:ASP333 3.6 17.0 1.0
O A:HOH1147 3.7 28.2 1.0
O A:HOH1301 3.9 20.8 1.0
C A:SER332 3.9 17.5 1.0
O A:HOH1391 3.9 35.7 1.0
N A:ARG337 3.9 18.5 1.0
CA A:ASP333 4.0 16.9 1.0
N A:GLY335 4.2 18.9 1.0
N A:ASP333 4.4 17.1 1.0
N A:SER336 4.4 18.3 1.0
CA A:GLY335 4.5 18.3 1.0
N A:LEU334 4.5 17.4 1.0
C A:LEU334 4.5 18.6 1.0
CA A:SER336 4.5 18.7 1.0
C A:SER336 4.6 18.9 1.0
CB A:ARG337 4.6 18.2 1.0
O A:HOH1362 4.7 30.7 1.0
CA A:ARG337 4.8 18.7 1.0
CA A:LEU334 5.0 17.9 1.0
O A:LEU334 5.0 19.2 1.0

Sodium binding site 2 out of 4 in 4xn7

Go back to Sodium Binding Sites List in 4xn7
Sodium binding site 2 out of 4 in the Crystal Structure of E. Coli Aminopeptidase N in Complex with L-2,3- Diaminopropionic Acid


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 E. Coli Aminopeptidase N in Complex with L-2,3- Diaminopropionic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na904

b:31.1
occ:1.00
 O A:HOH1419 2.3 26.5 1.0
O1 A:GOL924 2.5 49.3 1.0
OD1 A:ASP452 2.6 20.1 1.0
O A:HOH1344 2.7 18.8 1.0
O A:ASP452 2.8 18.4 1.0
O2 A:GOL924 3.0 56.9 1.0
C1 A:GOL924 3.3 52.6 1.0
O A:HOH1372 3.5 27.3 1.0
C A:ASP452 3.7 18.2 1.0
CG A:ASP452 3.7 20.4 1.0
C2 A:GOL924 3.8 53.5 1.0
N A:ASP452 4.3 19.7 1.0
CA A:ASP452 4.4 19.1 1.0
OD2 A:ASP452 4.5 20.6 1.0
N A:ASP453 4.5 19.1 1.0
CB A:ASP452 4.6 19.8 1.0
O A:HOH1269 4.7 32.6 1.0
CA A:ASP453 4.8 20.1 1.0
C3 A:GOL924 5.0 51.2 1.0

Sodium binding site 3 out of 4 in 4xn7

Go back to Sodium Binding Sites List in 4xn7
Sodium binding site 3 out of 4 in the Crystal Structure of E. Coli Aminopeptidase N in Complex with L-2,3- Diaminopropionic Acid


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 E. Coli Aminopeptidase N in Complex with L-2,3- Diaminopropionic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na905

b:38.3
occ:1.00
 OE2 A:GLU627 2.8 24.5 0.8
O A:HOH1392 3.0 40.1 1.0
O A:GLY350 3.0 25.9 1.0
O A:ASN623 3.1 20.6 1.0
CB A:ALA354 3.6 16.2 1.0
O A:HOH1172 3.7 26.0 1.0
CD A:GLU627 3.7 24.2 0.8
C A:ASN623 3.8 20.3 1.0
CA A:ASN623 4.0 21.6 1.0
O3 A:GOL927 4.0 35.7 1.0
ND2 A:ASN623 4.0 27.7 1.0
C3 A:GOL927 4.0 40.3 1.0
CG A:GLU627 4.0 22.8 0.8
CB A:ASN623 4.1 22.6 1.0
CB A:ALA626 4.1 18.7 1.0
C A:GLY350 4.2 21.5 1.0
O2 A:GOL927 4.2 50.5 1.0
CG A:ASN623 4.5 24.7 1.0
C2 A:GOL927 4.6 39.7 1.0
N A:GLU627 4.7 19.5 1.0
OE1 A:GLU627 4.8 24.2 0.8
CA A:LEU351 4.9 19.5 1.0
CA A:ALA354 4.9 16.1 1.0
N A:LEU351 4.9 20.2 1.0

Sodium binding site 4 out of 4 in 4xn7

Go back to Sodium Binding Sites List in 4xn7
Sodium binding site 4 out of 4 in the Crystal Structure of E. Coli Aminopeptidase N in Complex with L-2,3- Diaminopropionic Acid


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 E. Coli Aminopeptidase N in Complex with L-2,3- Diaminopropionic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na906

b:23.9
occ:1.00
 O A:ILE20 2.4 16.1 1.0
O A:LEU138 2.5 17.4 1.0
OE1 A:GLN19 2.5 17.9 1.0
O A:HOH1338 2.5 15.0 1.0
C A:ILE20 3.4 15.2 1.0
CD A:GLN19 3.4 17.6 1.0
C A:LEU138 3.5 16.5 1.0
O A:HOH1445 3.6 32.4 1.0
N A:LEU138 3.6 16.1 1.0
N A:ILE20 3.9 17.2 1.0
CB A:GLN19 3.9 18.3 1.0
CG A:GLN19 4.1 18.1 1.0
CA A:LEU138 4.1 16.6 1.0
N A:THR21 4.2 14.6 1.0
CA A:THR21 4.2 14.1 1.0
CA A:ILE20 4.3 16.1 1.0
CG1 A:VAL137 4.3 14.1 1.0
NE2 A:GLN19 4.3 16.5 1.0
O A:HOH1461 4.4 21.6 1.0
C A:VAL137 4.4 15.6 1.0
N A:ALA139 4.6 16.8 1.0
CA A:VAL137 4.6 13.8 1.0
C A:GLN19 4.6 18.0 1.0
CA A:GLN19 4.6 17.8 1.0
CG2 A:THR21 4.6 14.6 1.0
CB A:LEU138 4.6 17.0 1.0
CA A:ALA139 4.9 16.7 1.0

Reference:

A.Addlagatta, R.Gumpena. Crystal Structure of E. Coli Aminopeptidase N in Complex with L-2,3-Diaminopropionic Acid To Be Published.
Page generated: Mon Oct 7 19:13:51 2024

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