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

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

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

Protein crystallography data

The structure of Crystal Structure of E. Coli Aminopeptidase N in Complex with L-Beta Homotryptophan, PDB code: 4xnd 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) 20.00 / 1.93
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 121.120, 121.120, 170.781, 90.00, 90.00, 120.00
R / Rfree (%) 13.3 / 16.6

Other elements in 4xnd:

The structure of Crystal Structure of E. Coli Aminopeptidase N in Complex with L-Beta Homotryptophan 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 Homotryptophan (pdb code 4xnd). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 8 binding sites of Sodium where determined in the Crystal Structure of E. Coli Aminopeptidase N in Complex with L-Beta Homotryptophan, PDB code: 4xnd:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Sodium binding site 1 out of 8 in 4xnd

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Sodium binding site 1 out of 8 in the Crystal Structure of E. Coli Aminopeptidase N in Complex with L-Beta Homotryptophan


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

b:21.7
occ:1.00
 O A:LEU138 2.3 14.7 1.0
O A:HOH1549 2.4 17.5 1.0
O A:HOH1753 2.4 29.4 1.0
O A:ILE20 2.4 19.3 1.0
OE1 A:GLN19 2.5 18.5 1.0
C A:LEU138 3.4 14.8 1.0
CD A:GLN19 3.4 19.1 1.0
C A:ILE20 3.5 16.6 1.0
N A:LEU138 3.5 13.9 1.0
O A:HOH1740 3.5 47.0 1.0
CA A:LEU138 4.0 15.3 1.0
O A:HOH1756 4.0 38.0 1.0
N A:ILE20 4.0 16.4 1.0
CB A:GLN19 4.1 16.4 1.0
CG A:GLN19 4.2 19.1 1.0
NE2 A:GLN19 4.2 18.3 1.0
CA A:THR21 4.2 16.1 1.0
CG1 A:VAL137 4.2 15.6 1.0
N A:THR21 4.2 16.3 1.0
C A:VAL137 4.3 14.1 1.0
CA A:VAL137 4.4 14.9 1.0
N A:ALA139 4.4 13.4 1.0
CA A:ILE20 4.4 16.4 1.0
CB A:LEU138 4.5 17.2 1.0
CA A:GLN19 4.7 16.4 1.0
CA A:ALA139 4.7 14.7 1.0
C A:GLN19 4.8 18.8 1.0
CG2 A:THR21 4.8 21.1 1.0
CB A:VAL137 5.0 14.2 1.0

Sodium binding site 2 out of 8 in 4xnd

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Sodium binding site 2 out of 8 in the Crystal Structure of E. Coli Aminopeptidase N in Complex with L-Beta Homotryptophan


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

b:30.3
occ:1.00
 O1 A:GOL932 2.6 53.2 1.0
C1 A:GOL932 3.8 61.6 1.0
C2 A:GOL932 3.9 54.0 1.0
O2 A:GOL932 4.1 58.3 1.0
O A:HOH1064 4.7 30.2 1.0

Sodium binding site 3 out of 8 in 4xnd

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Sodium binding site 3 out of 8 in the Crystal Structure of E. Coli Aminopeptidase N in Complex with L-Beta Homotryptophan


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 Homotryptophan within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na905

b:53.5
occ:1.00
 O A:HOH1665 2.1 55.8 1.0
O A:HOH1419 2.3 34.7 1.0
O A:HOH1694 2.4 51.4 1.0
O A:HOH1552 2.5 43.7 1.0
O A:SER429 2.6 25.3 1.0
OD1 A:ASN399 2.8 28.1 1.0
ND2 A:ASN399 3.4 32.3 1.0
CG A:ASN399 3.5 29.0 1.0
C A:SER429 3.5 24.9 1.0
CA A:SER429 3.9 22.1 1.0
NZ A:LYS402 4.3 60.9 1.0
OD1 A:ASN430 4.4 49.6 1.0
O A:ALA428 4.5 23.2 1.0
N A:ASN430 4.5 22.2 1.0
CB A:SER429 4.7 19.5 1.0
CB A:ASN430 4.7 33.2 1.0
CB A:ASN399 4.9 21.6 1.0
O A:HOH1758 4.9 54.4 1.0
CG A:ASN430 5.0 38.1 1.0

Sodium binding site 4 out of 8 in 4xnd

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Sodium binding site 4 out of 8 in the Crystal Structure of E. Coli Aminopeptidase N in Complex with L-Beta Homotryptophan


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 Homotryptophan within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na906

b:39.4
occ:1.00
 O A:HOH1161 2.3 48.6 1.0
O A:HOH1339 2.5 49.3 1.0
O A:HOH1079 2.6 27.2 1.0
OD1 A:ASN344 2.7 19.7 1.0
O A:HOH1344 2.8 19.1 1.0
OE1 A:GLU382 3.3 29.9 0.8
O A:HOH1575 3.3 31.8 1.0
CG A:ASN344 3.6 16.6 1.0
CD A:GLU382 3.7 27.5 0.8
CG A:GLU382 3.8 9.6 0.2
CA A:ASN344 3.9 15.7 1.0
CB A:THR347 3.9 17.4 1.0
OG1 A:THR347 3.9 16.5 1.0
CB A:ASN344 3.9 16.8 1.0
OE2 A:GLU382 4.0 33.1 0.8
CG2 A:THR347 4.0 18.8 1.0
NE2 A:GLN328 4.2 14.6 1.0
O A:HOH1047 4.4 29.0 1.0
OE1 A:GLU382 4.4 8.0 0.2
O A:HOH1376 4.4 47.6 1.0
CD A:GLU382 4.5 9.3 0.2
O A:ASN344 4.6 13.9 1.0
ND2 A:ASN344 4.6 16.5 1.0
CG A:GLU382 4.7 26.3 0.8
N A:ASN344 4.8 15.0 1.0
C A:ASN344 4.8 15.1 1.0
O A:ASN343 4.8 14.9 1.0
O A:HOH1166 5.0 14.1 1.0

Sodium binding site 5 out of 8 in 4xnd

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Sodium binding site 5 out of 8 in the Crystal Structure of E. Coli Aminopeptidase N in Complex with L-Beta Homotryptophan


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Crystal Structure of E. Coli Aminopeptidase N in Complex with L-Beta Homotryptophan within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na907

b:22.0
occ:1.00
 O A:HOH1177 2.3 29.4 1.0
O A:GLY335 2.3 16.9 1.0
O A:HOH1648 2.4 27.4 1.0
O A:SER332 2.4 17.6 1.0
O9 A:MLI936 2.5 25.1 1.0
O A:ASP333 2.7 16.6 1.0
C A:ASP333 3.4 18.1 1.0
C A:GLY335 3.4 17.1 1.0
O A:HOH1139 3.4 53.2 1.0
C3 A:MLI936 3.4 34.1 1.0
C A:SER332 3.5 19.2 1.0
O8 A:MLI936 3.6 54.0 1.0
CA A:ASP333 3.7 17.7 1.0
N A:GLY335 3.9 16.0 1.0
N A:ARG337 3.9 17.1 1.0
N A:ASP333 4.1 17.2 1.0
O A:HOH1425 4.2 31.3 1.0
N A:LEU334 4.2 16.3 1.0
C A:LEU334 4.2 18.2 1.0
CA A:GLY335 4.3 17.7 1.0
N A:SER336 4.3 16.8 1.0
O A:HOH1581 4.3 48.3 1.0
CA A:SER336 4.4 17.4 1.0
C A:SER336 4.5 17.7 1.0
O A:HOH1497 4.5 48.4 1.0
CB A:ARG337 4.6 16.5 1.0
CA A:LEU334 4.7 17.4 1.0
CA A:ARG337 4.7 18.2 1.0
O A:LEU334 4.8 16.7 1.0
CA A:SER332 4.8 16.7 1.0
C1 A:MLI936 4.8 38.2 1.0

Sodium binding site 6 out of 8 in 4xnd

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Sodium binding site 6 out of 8 in the Crystal Structure of E. Coli Aminopeptidase N in Complex with L-Beta Homotryptophan


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Crystal Structure of E. Coli Aminopeptidase N in Complex with L-Beta Homotryptophan within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na908

b:32.0
occ:1.00
 O A:HOH1645 2.4 40.9 1.0
O A:ASN623 2.4 20.6 1.0
O A:HOH1028 2.4 28.9 1.0
O A:GLY350 2.6 23.2 1.0
O A:HOH1223 2.7 27.1 1.0
C A:ASN623 3.4 23.6 1.0
C A:GLY350 3.5 23.9 1.0
CB A:ALA354 3.7 20.3 1.0
OE1 A:GLU627 3.9 32.1 1.0
CA A:ASN623 3.9 25.2 1.0
CB A:ASN623 4.0 29.7 1.0
CA A:GLY350 4.0 21.3 1.0
N A:GLU627 4.1 20.4 1.0
CB A:GLU627 4.2 27.2 1.0
CB A:ALA626 4.2 19.4 1.0
O9 A:MLI933 4.4 37.0 1.0
N A:GLU624 4.4 21.3 1.0
CA A:GLU627 4.5 22.3 1.0
N A:LEU351 4.6 19.2 1.0
O A:ARG349 4.6 22.6 1.0
C1 A:MLI933 4.6 38.6 1.0
C A:ALA626 4.7 20.1 1.0
C3 A:MLI933 4.7 37.3 1.0
CA A:GLU624 4.8 21.8 1.0
CA A:LEU351 4.8 17.1 1.0
CA A:ALA354 4.8 18.9 1.0
CD A:GLU627 4.8 34.7 1.0
ND2 A:ASN623 4.9 34.3 1.0
CA A:ALA626 4.9 20.5 1.0
N A:ALA354 4.9 16.3 1.0
CG A:ASN623 5.0 29.2 1.0

Sodium binding site 7 out of 8 in 4xnd

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Sodium binding site 7 out of 8 in the Crystal Structure of E. Coli Aminopeptidase N in Complex with L-Beta Homotryptophan


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of Crystal Structure of E. Coli Aminopeptidase N in Complex with L-Beta Homotryptophan within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na909

b:43.4
occ:1.00
 O A:HOH1710 2.4 56.1 1.0
O A:HOH1724 2.5 34.3 1.0
OD1 A:ASN67 2.5 20.5 1.0
O A:HOH1745 2.6 40.6 1.0
OG1 A:THR91 2.7 19.2 1.0
CG A:ASN67 3.4 24.8 1.0
CB A:THR91 3.4 18.0 1.0
N A:THR91 3.8 16.3 1.0
CB A:ASN67 4.2 22.9 1.0
CA A:THR91 4.2 18.1 1.0
ND2 A:ASN67 4.2 22.3 1.0
CA A:ASN67 4.4 21.5 1.0
O A:HOH1785 4.4 58.4 1.0
O A:HOH1248 4.5 29.8 1.0
C A:PHE90 4.5 16.8 1.0
CG2 A:THR91 4.6 21.0 1.0
CA A:PHE90 4.7 18.4 1.0
OE1 A:GLN41 4.8 24.9 1.0

Sodium binding site 8 out of 8 in 4xnd

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Sodium binding site 8 out of 8 in the Crystal Structure of E. Coli Aminopeptidase N in Complex with L-Beta Homotryptophan


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of Crystal Structure of E. Coli Aminopeptidase N in Complex with L-Beta Homotryptophan within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na910

b:33.5
occ:1.00
 OG1 A:THR574 2.3 19.6 1.0
O A:HOH1328 2.3 31.4 1.0
O A:HOH1390 2.4 27.3 1.0
O A:SER570 2.6 20.8 1.0
CB A:THR574 3.3 21.4 1.0
C A:SER570 3.6 19.4 1.0
CD1 A:LEU551 3.6 17.3 1.0
CA A:LEU571 3.9 18.5 1.0
O A:LEU571 4.1 22.7 1.0
N A:LEU571 4.1 17.8 1.0
CG2 A:THR574 4.2 25.1 1.0
N A:THR574 4.2 17.6 1.0
OD1 A:ASP548 4.2 24.4 1.0
C A:LEU571 4.3 20.0 1.0
CA A:THR574 4.4 19.0 1.0
O A:HOH1500 4.5 41.9 1.0
CA A:SER570 4.7 16.5 1.0
CB A:SER570 4.8 18.0 1.0
CB A:TRP546 5.0 24.9 1.0

Reference:

A.Addlagatta, R.Gumpena. Crystal Structure of E. Coli Aminopeptidase N in Complex with L-Beta Homotryptophan To Be Published.
Page generated: Mon Oct 7 19:15:47 2024

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