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

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

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

Protein crystallography data

The structure of Crystal Structure of E. Coli Aminopeptidase N in Complex with L-Beta Homophenylalanine, PDB code: 4xnb 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) 19.16 / 1.95
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 120.191, 120.191, 169.921, 90.00, 90.00, 120.00
R / Rfree (%) 13.2 / 16.5

Other elements in 4xnb:

The structure of Crystal Structure of E. Coli Aminopeptidase N in Complex with L-Beta Homophenylalanine 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 Homophenylalanine (pdb code 4xnb). 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 Homophenylalanine, PDB code: 4xnb:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Sodium binding site 1 out of 8 in 4xnb

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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 Homophenylalanine


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

b:28.1
occ:1.00
 O A:HOH1906 2.3 33.3 1.0
O A:HOH1738 2.4 20.8 1.0
O A:LEU138 2.4 16.7 1.0
OE1 A:GLN19 2.5 19.8 1.0
O A:ILE20 2.6 21.7 1.0
CD A:GLN19 3.4 20.4 1.0
C A:LEU138 3.5 15.8 1.0
N A:LEU138 3.5 14.3 1.0
C A:ILE20 3.6 20.3 1.0
O A:HOH2005 3.8 53.0 1.0
CB A:GLN19 4.0 16.9 1.0
CA A:LEU138 4.0 15.5 1.0
O A:HOH1967 4.0 37.5 1.0
N A:ILE20 4.1 17.1 1.0
CG A:GLN19 4.1 19.5 1.0
CA A:THR21 4.2 17.8 1.0
NE2 A:GLN19 4.3 19.0 1.0
N A:THR21 4.3 17.1 1.0
C A:VAL137 4.4 15.7 1.0
O A:HOH1555 4.4 43.4 1.0
CG1 A:VAL137 4.4 17.8 1.0
CA A:ILE20 4.5 18.2 1.0
CA A:VAL137 4.5 16.7 1.0
N A:ALA139 4.5 15.9 1.0
CB A:LEU138 4.5 17.7 1.0
O A:HOH1971 4.6 37.2 1.0
CG2 A:THR21 4.7 21.9 1.0
CA A:GLN19 4.7 16.5 1.0
C A:GLN19 4.7 18.7 1.0
O A:HOH1871 4.8 43.4 1.0
CA A:ALA139 4.8 15.5 1.0

Sodium binding site 2 out of 8 in 4xnb

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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 Homophenylalanine


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

b:45.9
occ:1.00
 O A:HOH1872 2.4 53.2 1.0
OG1 A:THR91 2.6 20.6 1.0
OD1 A:ASN67 2.7 23.8 1.0
O A:HOH1887 2.7 34.9 1.0
O A:HOH1907 2.7 43.2 1.0
CB A:THR91 3.5 20.6 1.0
CG A:ASN67 3.6 26.7 1.0
N A:THR91 3.8 18.6 1.0
CA A:THR91 4.3 19.2 1.0
CB A:ASN67 4.3 24.9 1.0
O A:HOH1952 4.3 55.7 1.0
O A:HOH1216 4.4 31.8 1.0
O A:HOH1754 4.4 53.8 1.0
ND2 A:ASN67 4.5 27.8 1.0
CA A:ASN67 4.5 23.3 1.0
C A:PHE90 4.6 18.3 1.0
CG2 A:THR91 4.7 19.8 1.0
NE2 A:GLN41 4.7 23.6 1.0
CA A:PHE90 4.8 19.4 1.0

Sodium binding site 3 out of 8 in 4xnb

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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 Homophenylalanine


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

b:55.2
occ:1.00
 O A:HOH1810 2.3 50.1 1.0
O A:HOH1716 2.4 48.1 1.0
O A:HOH1172 2.4 32.9 1.0
O A:HIS771 2.6 22.6 1.0
O A:PHE774 2.6 22.2 1.0
C A:HIS771 3.6 23.6 1.0
C A:PHE774 3.7 23.7 1.0
O A:ARG772 3.8 30.3 1.0
C A:ARG772 4.0 26.3 1.0
N A:PHE774 4.0 21.0 1.0
CA A:ARG772 4.0 28.2 1.0
N A:ARG772 4.3 26.5 1.0
O A:HOH1758 4.3 48.3 1.0
O A:GLN770 4.3 23.6 1.0
CA A:PHE774 4.4 23.0 1.0
C A:GLN770 4.4 28.1 1.0
N A:HIS771 4.6 25.1 1.0
N A:SER773 4.6 25.0 1.0
CB A:PHE774 4.7 23.1 1.0
N A:THR775 4.8 21.7 1.0
CA A:HIS771 4.8 24.1 1.0
O A:LEU769 4.8 23.5 1.0
C A:SER773 4.9 23.7 1.0
CA A:THR775 4.9 22.4 1.0

Sodium binding site 4 out of 8 in 4xnb

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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 Homophenylalanine


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

b:35.8
occ:1.00
 O A:HOH1058 2.4 36.3 1.0
O2 A:GOL915 3.3 33.6 1.0
C3 A:GOL915 3.5 34.8 1.0
NA A:NA910 3.7 60.5 1.0
C2 A:GOL915 3.8 47.6 1.0
O A:HOH1517 4.2 41.0 1.0
O A:HOH2040 4.4 29.2 0.5
O A:HOH1023 4.5 35.9 1.0
O A:HOH1999 4.6 31.2 0.5
O3 A:GOL915 4.7 55.4 1.0
O A:HOH1791 4.9 26.8 0.5

Sodium binding site 5 out of 8 in 4xnb

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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 Homophenylalanine


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 Homophenylalanine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na907

b:52.8
occ:1.00
 O A:HOH1247 2.3 45.7 1.0
OE1 A:GLN164 3.8 29.3 1.0
NE2 A:GLN164 4.0 30.3 1.0
CD A:GLN164 4.2 33.0 1.0

Sodium binding site 6 out of 8 in 4xnb

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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 Homophenylalanine


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 Homophenylalanine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na908

b:25.2
occ:1.00
 O A:HOH1846 2.2 31.8 1.0
O A:GLY335 2.3 16.9 1.0
O A:HOH1773 2.4 27.4 1.0
O A:SER332 2.5 19.8 1.0
O A:HOH1513 2.5 22.0 1.0
O A:ASP333 2.8 18.3 1.0
O A:HOH1038 3.1 42.7 1.0
C A:GLY335 3.4 18.7 1.0
C A:ASP333 3.4 18.5 1.0
C A:SER332 3.6 19.3 1.0
CA A:ASP333 3.8 19.1 1.0
N A:GLY335 3.9 18.0 1.0
N A:ARG337 3.9 19.1 1.0
O A:HOH1562 4.1 27.1 1.0
N A:ASP333 4.1 17.6 1.0
CA A:GLY335 4.2 18.5 1.0
C A:LEU334 4.2 20.4 1.0
O A:HOH2036 4.2 47.6 1.0
N A:LEU334 4.3 17.5 1.0
O A:HOH1911 4.3 43.0 1.0
N A:SER336 4.3 18.6 1.0
CA A:SER336 4.4 19.1 1.0
C A:SER336 4.5 18.8 1.0
O A:HOH1400 4.5 33.1 1.0
CB A:ARG337 4.5 19.4 1.0
O A:HOH1835 4.7 48.3 1.0
CA A:ARG337 4.7 20.4 1.0
O A:LEU334 4.7 19.5 1.0
CA A:LEU334 4.8 18.7 1.0
CA A:SER332 4.8 17.5 1.0

Sodium binding site 7 out of 8 in 4xnb

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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 Homophenylalanine


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 Homophenylalanine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na909

b:49.5
occ:1.00
 O A:HOH1460 2.1 36.1 1.0
O A:HOH1144 2.6 44.1 1.0
O A:HOH1143 2.7 30.7 1.0
O A:HOH1228 2.9 37.3 1.0
OE1 A:GLU371 2.9 22.6 1.0
CD A:GLU371 3.4 22.8 1.0
OE1 A:GLU107 3.6 29.3 0.5
OE2 A:GLU371 3.7 22.9 1.0
O A:HOH1104 3.9 41.2 1.0
O A:HOH1039 4.0 39.8 1.0
OE2 A:GLU107 4.0 22.2 0.5
OE1 A:GLU107 4.1 26.4 0.5
O A:HOH1094 4.1 35.1 1.0
O A:HOH1149 4.2 24.2 1.0
ND2 A:ASN373 4.2 39.2 1.0
OD1 A:ASP860 4.3 22.2 1.0
O A:HOH1213 4.3 45.0 1.0
CD A:GLU107 4.4 23.1 0.5
CG A:GLU371 4.6 24.3 1.0
OD2 A:ASP860 4.6 19.9 1.0
CD A:GLU107 4.6 24.8 0.5
O A:HOH1080 4.7 37.0 1.0
CG A:ASP860 4.8 22.3 1.0
OE2 A:GLU107 4.9 22.2 0.5

Sodium binding site 8 out of 8 in 4xnb

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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 Homophenylalanine


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 Homophenylalanine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na910

b:60.5
occ:1.00
 NA A:NA906 3.7 35.8 1.0
O A:HOH2040 4.7 29.2 0.5

Reference:

A.Addlagatta, R.Gumpena. Crystal Structure of E. Coli Aminopeptidase N in Complex with L-Beta Homophenylalanine To Be Published.
Page generated: Mon Oct 7 19:15:33 2024

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