Atomistry » Sodium » PDB 4xn1-4xtj » 4xn7
Atomistry »
  Sodium »
    PDB 4xn1-4xtj »
      4xn7 »

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: Tue Dec 15 09:59:28 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy