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Sodium in PDB 4q4i: Crystal Structure of E.Coli Aminopeptidase N in Complex with Amastatin

Enzymatic activity of Crystal Structure of E.Coli Aminopeptidase N in Complex with Amastatin

All present enzymatic activity of Crystal Structure of E.Coli Aminopeptidase N in Complex with Amastatin:
3.4.11.2;

Protein crystallography data

The structure of Crystal Structure of E.Coli Aminopeptidase N in Complex with Amastatin, PDB code: 4q4i was solved by R.Reddi, R.J.Ganji, A.Addlagatta, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.72 / 2.31
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 119.386, 119.386, 170.129, 90.00, 90.00, 120.00
R / Rfree (%) 14 / 17.9

Other elements in 4q4i:

The structure of Crystal Structure of E.Coli Aminopeptidase N in Complex with Amastatin 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 Amastatin (pdb code 4q4i). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Crystal Structure of E.Coli Aminopeptidase N in Complex with Amastatin, PDB code: 4q4i:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in 4q4i

Go back to Sodium Binding Sites List in 4q4i
Sodium binding site 1 out of 3 in the Crystal Structure of E.Coli Aminopeptidase N in Complex with Amastatin


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 Amastatin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na902

b:31.5
occ:1.00
O A:GLY335 2.4 19.1 1.0
O A:HOH1284 2.4 29.5 1.0
O A:SER332 2.5 21.3 1.0
O A:ASP333 2.8 17.0 1.0
C A:ASP333 3.4 18.9 1.0
C A:GLY335 3.5 19.5 1.0
C A:SER332 3.6 18.1 1.0
O A:HOH1322 3.6 35.6 1.0
CA A:ASP333 3.7 18.1 1.0
N A:ARG337 3.9 19.0 1.0
N A:GLY335 4.0 21.2 1.0
N A:ASP333 4.1 19.8 1.0
N A:LEU334 4.3 19.7 1.0
C A:LEU334 4.3 21.6 1.0
CA A:GLY335 4.4 19.4 1.0
N A:SER336 4.4 21.3 1.0
CA A:SER336 4.5 21.2 1.0
C A:SER336 4.6 21.8 1.0
CB A:ARG337 4.6 19.4 1.0
CA A:ARG337 4.8 20.2 1.0
CA A:LEU334 4.8 20.7 1.0
CA A:SER332 4.8 18.6 1.0
O A:LEU334 4.8 21.8 1.0

Sodium binding site 2 out of 3 in 4q4i

Go back to Sodium Binding Sites List in 4q4i
Sodium binding site 2 out of 3 in the Crystal Structure of E.Coli Aminopeptidase N in Complex with Amastatin


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 Amastatin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na903

b:32.1
occ:1.00
O A:HOH1387 2.3 11.7 0.5
O A:ASP452 2.3 25.4 1.0
OD1 A:ASP452 2.4 25.4 1.0
O A:HOH1176 2.4 26.8 1.0
C A:ASP452 3.1 24.0 1.0
O A:HOH1304 3.4 38.1 1.0
CG A:ASP452 3.5 25.9 1.0
N A:ASP452 3.7 22.9 1.0
CA A:ASP452 3.8 24.5 1.0
O A:HOH1260 3.9 35.1 1.0
N A:ASP453 4.1 25.5 1.0
CB A:ASP452 4.2 25.1 1.0
OD2 A:ASP452 4.4 27.0 1.0
CA A:ASP453 4.5 24.4 1.0
C A:LYS451 5.0 27.3 1.0

Sodium binding site 3 out of 3 in 4q4i

Go back to Sodium Binding Sites List in 4q4i
Sodium binding site 3 out of 3 in the Crystal Structure of E.Coli Aminopeptidase N in Complex with Amastatin


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 Amastatin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na904

b:26.2
occ:1.00
O A:HOH1224 2.3 30.7 1.0
O A:ILE20 2.4 21.7 1.0
O A:LEU138 2.4 18.6 1.0
OE1 A:GLN19 2.4 20.0 1.0
O A:HOH1158 2.5 18.7 1.0
C A:LEU138 3.3 17.8 1.0
CD A:GLN19 3.4 21.6 1.0
N A:LEU138 3.4 16.7 1.0
C A:ILE20 3.5 21.4 1.0
O A:HOH1442 3.7 40.8 1.0
CA A:LEU138 3.9 17.4 1.0
N A:ILE20 4.0 21.8 1.0
CB A:GLN19 4.1 20.2 1.0
CG A:GLN19 4.1 20.9 1.0
CA A:THR21 4.1 20.7 1.0
N A:THR21 4.2 20.0 1.0
C A:VAL137 4.3 18.7 1.0
NE2 A:GLN19 4.3 20.1 1.0
CG1 A:VAL137 4.4 19.0 1.0
N A:ALA139 4.4 17.4 1.0
CA A:ILE20 4.4 21.3 1.0
CB A:LEU138 4.4 19.3 1.0
CA A:VAL137 4.5 18.4 1.0
CA A:ALA139 4.7 18.8 1.0
CA A:GLN19 4.8 21.1 1.0
C A:GLN19 4.8 22.0 1.0
CG2 A:THR21 4.9 18.9 1.0
O A:HOH1318 5.0 35.8 1.0

Reference:

R.J.Ganji, R.Reddi, R.Gumpena, A.K.Marapaka, T.Arya, P.Sankoju, S.Bhukya, A.Addlagatta. Structural Basis For the Inhibition of M1 Family Aminopeptidases By the Natural Product Actinonin: Crystal Structure in Complex with E. Coli Aminopeptidase N Protein Sci. 2015.
ISSN: ESSN 1469-896X
PubMed: 25644575
DOI: 10.1002/PRO.2653
Page generated: Tue Dec 15 07:04:58 2020

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