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Sodium in PDB 4xna: Crystal Structure of E. Coli Aminopeptidase N in Complex with L-Beta Homolysine

Enzymatic activity of Crystal Structure of E. Coli Aminopeptidase N in Complex with L-Beta Homolysine

All present enzymatic activity of Crystal Structure of E. Coli Aminopeptidase N in Complex with L-Beta Homolysine:
3.4.11.2;

Protein crystallography data

The structure of Crystal Structure of E. Coli Aminopeptidase N in Complex with L-Beta Homolysine, PDB code: 4xna 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) 19.98 / 2.40
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 120.330, 120.330, 170.919, 90.00, 90.00, 120.00
R / Rfree (%) 13.3 / 18

Other elements in 4xna:

The structure of Crystal Structure of E. Coli Aminopeptidase N in Complex with L-Beta Homolysine 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-Beta Homolysine (pdb code 4xna). 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-Beta Homolysine, PDB code: 4xna:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 4xna

Go back to Sodium Binding Sites List in 4xna
Sodium binding site 1 out of 4 in the Crystal Structure of E. Coli Aminopeptidase N in Complex with L-Beta Homolysine


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-Beta Homolysine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na903

b:25.7
occ:1.00
 O A:HOH1687 2.5 26.3 1.0
O A:HOH1390 2.5 24.2 1.0
O A:LEU138 2.6 22.9 1.0
OE1 A:GLN19 2.6 18.1 1.0
O A:ILE20 2.6 20.4 1.0
CD A:GLN19 3.4 17.3 1.0
C A:ILE20 3.5 19.0 1.0
C A:LEU138 3.6 18.0 1.0
N A:LEU138 3.6 17.9 1.0
CB A:GLN19 4.0 16.9 1.0
CG A:GLN19 4.0 16.3 1.0
N A:ILE20 4.1 19.1 1.0
CA A:THR21 4.1 17.7 1.0
CA A:LEU138 4.1 19.2 1.0
N A:THR21 4.2 18.1 1.0
O A:HOH1546 4.2 43.1 1.0
O A:HOH1646 4.2 43.0 1.0
NE2 A:GLN19 4.3 17.7 1.0
CA A:ILE20 4.5 19.1 1.0
CG2 A:THR21 4.5 17.9 1.0
C A:VAL137 4.6 16.6 1.0
O A:HOH1632 4.6 35.5 1.0
CB A:LEU138 4.6 21.4 1.0
N A:ALA139 4.6 16.6 1.0
CG1 A:VAL137 4.7 16.0 1.0
CA A:VAL137 4.7 16.2 1.0
CA A:GLN19 4.7 16.4 1.0
C A:GLN19 4.8 17.6 1.0
CB A:THR21 4.9 19.2 1.0
CA A:ALA139 5.0 15.8 1.0
O A:HOH1270 5.0 17.0 1.0

Sodium binding site 2 out of 4 in 4xna

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Sodium binding site 2 out of 4 in the Crystal Structure of E. Coli Aminopeptidase N in Complex with L-Beta Homolysine


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-Beta Homolysine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na904

b:30.8
occ:1.00
 O A:HOH1530 2.1 48.8 1.0
O A:HOH1532 2.3 33.4 1.0
O A:GLY335 2.3 19.7 1.0
O A:HOH1301 2.6 22.1 1.0
O A:SER332 2.6 22.4 1.0
O A:ASP333 2.9 26.8 1.0
C A:GLY335 3.5 19.1 1.0
C A:ASP333 3.6 21.3 1.0
C A:SER332 3.7 20.2 1.0
CA A:ASP333 3.9 21.4 1.0
N A:ARG337 4.0 19.1 1.0
N A:GLY335 4.0 21.5 1.0
N A:ASP333 4.3 21.1 1.0
O A:HOH1280 4.3 37.8 1.0
CA A:GLY335 4.3 19.9 1.0
N A:SER336 4.3 20.3 1.0
C A:LEU334 4.4 21.2 1.0
N A:LEU334 4.4 19.8 1.0
CA A:SER336 4.4 21.1 1.0
C A:SER336 4.6 21.1 1.0
O A:HOH1727 4.6 36.0 1.0
CB A:ARG337 4.8 20.8 1.0
CA A:LEU334 4.8 20.9 1.0
CA A:ARG337 4.9 21.4 1.0
O A:LEU334 4.9 23.2 1.0
CA A:SER332 4.9 19.6 1.0

Sodium binding site 3 out of 4 in 4xna

Go back to Sodium Binding Sites List in 4xna
Sodium binding site 3 out of 4 in the Crystal Structure of E. Coli Aminopeptidase N in Complex with L-Beta Homolysine


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-Beta Homolysine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na905

b:31.8
occ:1.00
 OH A:TYR185 2.7 13.0 1.0
OD1 A:ASN306 2.7 15.4 1.0
OE2 A:GLU264 2.8 13.4 1.0
O A:GLY305 3.1 14.5 1.0
C A:GLY305 3.1 14.2 1.0
CA A:GLY305 3.3 14.0 1.0
CD A:LYS319 3.5 11.8 1.0
CG A:GLU264 3.5 14.6 1.0
CZ A:TYR185 3.6 13.6 1.0
CE1 A:TYR185 3.6 12.9 1.0
CD A:GLU264 3.6 14.1 1.0
N A:ASN306 3.8 14.2 1.0
CE A:LYS319 3.8 11.5 1.0
CD2 A:LEU186 3.9 16.6 1.0
CG A:ASN306 4.0 16.2 1.0
NZ A:LYS319 4.0 10.8 1.0
ND1 A:HIS301 4.1 15.3 1.0
CD1 A:LEU186 4.2 18.7 1.0
CA A:ASN306 4.4 15.5 1.0
CG A:HIS301 4.5 14.4 1.0
CG A:LEU186 4.5 16.8 1.0
N A:GLY305 4.6 13.5 1.0
CB A:HIS301 4.7 14.9 1.0
CE1 A:HIS301 4.7 14.7 1.0
O A:HIS301 4.7 16.7 1.0
CG A:LYS319 4.8 12.2 1.0
CB A:ASN306 4.8 16.1 1.0
OG1 A:THR309 4.8 15.3 1.0
OE1 A:GLU264 4.9 14.4 1.0
ND2 A:ASN306 4.9 16.6 1.0
CD1 A:TYR185 4.9 13.0 1.0
CE2 A:TYR185 4.9 14.0 1.0
CB A:LYS319 5.0 12.4 1.0

Sodium binding site 4 out of 4 in 4xna

Go back to Sodium Binding Sites List in 4xna
Sodium binding site 4 out of 4 in the Crystal Structure of E. Coli Aminopeptidase N in Complex with L-Beta Homolysine


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-Beta Homolysine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na906

b:38.4
occ:1.00
 O A:HOH1358 2.3 35.2 1.0
OG1 A:THR574 2.3 18.6 1.0
O A:HOH1338 2.5 36.4 1.0
O A:SER570 2.6 20.2 1.0
O A:HOH1692 2.7 44.8 1.0
CB A:THR574 3.4 18.7 1.0
C A:SER570 3.5 21.3 1.0
CD1 A:LEU551 3.7 18.6 1.0
CA A:LEU571 4.0 21.9 1.0
N A:THR574 4.1 18.9 1.0
N A:LEU571 4.1 22.5 1.0
O A:LEU571 4.1 22.5 1.0
O A:HOH1432 4.3 36.3 1.0
CA A:THR574 4.4 18.4 1.0
CG2 A:THR574 4.4 18.4 1.0
C A:LEU571 4.4 23.4 1.0
O A:HOH1314 4.4 35.2 1.0
OD1 A:ASP548 4.5 21.4 1.0
CA A:SER570 4.6 19.4 1.0
CB A:SER570 4.8 21.2 1.0
CB A:TRP546 4.9 31.6 1.0
O A:TRP546 4.9 34.3 1.0

Reference:

A.Addlagatta, R.Gumpena. Crystal Structure of E. Coli Aminopeptidase N in Complex with L-Beta Homolysin To Be Published.
Page generated: Mon Oct 7 19:15:05 2024

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