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Sodium in PDB 4xo5: Crystal Structure of E. Coli Aminopeptidase N in Complex with L- Glutamate

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

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

Protein crystallography data

The structure of Crystal Structure of E. Coli Aminopeptidase N in Complex with L- Glutamate, PDB code: 4xo5 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) 19.59 / 1.98
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 120.482, 120.482, 170.424, 90.00, 90.00, 120.00
R / Rfree (%) 12.8 / 15.8

Other elements in 4xo5:

The structure of Crystal Structure of E. Coli Aminopeptidase N in Complex with L- Glutamate 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- Glutamate (pdb code 4xo5). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 10 binding sites of Sodium where determined in the Crystal Structure of E. Coli Aminopeptidase N in Complex with L- Glutamate, PDB code: 4xo5:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Sodium binding site 1 out of 10 in 4xo5

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Sodium binding site 1 out of 10 in the Crystal Structure of E. Coli Aminopeptidase N in Complex with L- Glutamate


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

b:35.2
occ:1.00
 O A:HOH1783 2.3 35.0 1.0
O A:ASP452 2.4 19.8 1.0
OD1 A:ASP452 2.4 23.6 1.0
O A:HOH1804 2.4 25.3 0.8
O A:HOH1591 2.5 26.1 1.0
C1 A:GOL918 2.8 48.7 1.0
O1 A:GOL918 3.2 64.5 1.0
C A:ASP452 3.2 22.0 1.0
NA A:NA906 3.5 33.6 1.0
O A:HOH1127 3.5 40.1 1.0
CG A:ASP452 3.5 23.6 1.0
N A:ASP452 3.8 22.6 1.0
CA A:ASP452 3.8 19.8 1.0
O A:HOH1788 3.8 24.9 1.0
O A:HOH1167 4.0 42.9 1.0
O A:HOH1916 4.0 37.3 1.0
C2 A:GOL918 4.1 57.6 1.0
N A:ASP453 4.2 22.0 1.0
CB A:ASP452 4.2 21.7 1.0
O A:HOH1703 4.5 31.1 1.0
OD2 A:ASP452 4.5 23.4 1.0
CA A:ASP453 4.5 23.9 1.0
O3 A:GOL918 4.5 48.6 1.0
O2 A:GOL918 4.9 34.1 1.0
C3 A:GOL918 4.9 51.5 1.0

Sodium binding site 2 out of 10 in 4xo5

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Sodium binding site 2 out of 10 in the Crystal Structure of E. Coli Aminopeptidase N in Complex with L- Glutamate


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

b:23.4
occ:1.00
 O A:HOH1795 2.2 32.9 1.0
O A:GLY335 2.3 17.9 1.0
O A:SER332 2.4 15.5 1.0
O A:HOH1691 2.4 27.6 1.0
O A:HOH1597 2.5 21.8 1.0
O A:ASP333 2.8 16.3 1.0
O A:HOH1032 3.3 50.6 1.0
C A:GLY335 3.4 18.4 1.0
C A:ASP333 3.4 17.4 1.0
C A:SER332 3.5 17.6 1.0
CA A:ASP333 3.7 17.5 1.0
N A:GLY335 3.9 16.3 1.0
N A:ARG337 4.0 16.4 1.0
O A:HOH1470 4.1 33.0 1.0
N A:ASP333 4.1 16.9 1.0
O A:HOH1828 4.2 43.5 1.0
O A:HOH1928 4.2 49.9 1.0
C A:LEU334 4.3 18.8 1.0
CA A:GLY335 4.3 17.2 1.0
N A:LEU334 4.3 15.6 1.0
N A:SER336 4.3 18.7 1.0
CA A:SER336 4.4 19.2 1.0
O A:HOH1411 4.5 35.5 1.0
C A:SER336 4.5 18.2 1.0
CB A:ARG337 4.6 18.2 1.0
CA A:ARG337 4.8 19.8 1.0
CA A:LEU334 4.8 17.5 1.0
O A:LEU334 4.8 18.4 1.0
CA A:SER332 4.8 16.9 1.0

Sodium binding site 3 out of 10 in 4xo5

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Sodium binding site 3 out of 10 in the Crystal Structure of E. Coli Aminopeptidase N in Complex with L- Glutamate


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

b:33.6
occ:1.00
 O A:HOH1788 2.4 24.9 1.0
O A:HOH1804 2.4 25.3 0.8
O A:HOH1234 2.4 21.8 1.0
O A:HOH1703 2.5 31.1 1.0
OH A:TYR544 2.5 20.9 1.0
OD1 A:ASP452 2.7 23.6 1.0
CZ A:TYR544 3.3 21.4 1.0
NA A:NA904 3.5 35.2 1.0
CG A:ASP452 3.5 23.6 1.0
OD2 A:ASP452 3.5 23.4 1.0
O A:HOH1916 3.9 37.3 1.0
O A:HOH1890 4.0 40.6 1.0
CE1 A:TYR544 4.0 21.4 1.0
CE2 A:TYR544 4.1 19.0 1.0
NE2 A:GLN550 4.1 27.7 1.0
O A:HOH1591 4.1 26.1 1.0
O1 A:GOL918 4.2 64.5 1.0
O A:LYS545 4.4 20.8 1.0
O A:HOH1491 4.4 36.3 1.0
OE1 A:GLN550 4.5 21.2 1.0
CD A:GLN550 4.8 22.9 1.0
C1 A:GOL918 4.8 48.7 1.0
CB A:ASP452 5.0 21.7 1.0

Sodium binding site 4 out of 10 in 4xo5

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Sodium binding site 4 out of 10 in the Crystal Structure of E. Coli Aminopeptidase N in Complex with L- Glutamate


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

b:32.3
occ:1.00
 O A:HOH1082 2.7 26.3 1.0
O A:HOH1758 2.7 41.1 1.0
O A:ARG140 2.9 16.1 1.0
OG1 A:THR142 3.0 24.0 1.0
O A:ILE23 3.1 17.1 1.0
N A:THR142 3.5 14.0 1.0
C A:ARG140 3.7 16.4 1.0
C A:PHE141 3.7 15.9 1.0
CB A:THR142 3.7 21.8 1.0
C A:ILE23 3.8 17.4 1.0
N A:ILE23 3.8 16.7 1.0
O A:HOH1149 3.9 49.1 1.0
CA A:PHE141 4.0 14.3 1.0
CB A:ASP22 4.1 20.4 1.0
N A:PHE141 4.1 14.4 1.0
CA A:THR142 4.2 15.2 1.0
O A:PHE141 4.3 16.3 1.0
O A:HOH1251 4.3 31.8 1.0
OD1 A:ASP22 4.4 24.7 1.0
CA A:ASP22 4.4 17.2 1.0
N A:ASP24 4.4 16.4 1.0
CB A:ARG140 4.5 21.2 1.0
C A:ASP22 4.5 18.2 1.0
CA A:ILE23 4.5 16.6 1.0
OD2 A:ASP24 4.6 67.1 1.0
CA A:ARG140 4.7 17.9 1.0
CA A:ASP24 4.7 19.4 1.0
CG A:ASP22 4.8 22.8 1.0
CG2 A:THR142 4.9 25.8 1.0
CB A:ASP24 5.0 25.4 1.0

Sodium binding site 5 out of 10 in 4xo5

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Sodium binding site 5 out of 10 in the Crystal Structure of E. Coli Aminopeptidase N in Complex with L- Glutamate


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

b:46.6
occ:1.00
 O A:HOH1017 2.1 43.2 1.0
O A:HOH1520 2.5 42.5 1.0
OE1 A:GLU371 2.7 28.5 1.0
O A:HOH1111 2.8 35.8 1.0
O A:HOH1070 2.9 27.7 1.0
CD A:GLU371 3.5 24.7 1.0
O A:HOH1029 3.8 30.5 0.8
OE2 A:GLU371 3.8 25.4 1.0
O A:HOH1145 4.0 35.0 1.0
OE2 A:GLU107 4.0 42.5 1.0
OE1 A:GLU107 4.1 38.3 1.0
OD1 A:ASP860 4.2 26.1 1.0
O A:HOH1340 4.2 24.8 1.0
O A:HOH1108 4.3 42.8 1.0
CD A:GLU107 4.5 45.1 1.0
ND2 A:ASN373 4.5 35.2 1.0
OD2 A:ASP860 4.6 24.4 1.0
O A:HOH1079 4.6 45.7 1.0
CG A:GLU371 4.6 23.8 1.0
CG A:ASP860 4.8 25.3 1.0

Sodium binding site 6 out of 10 in 4xo5

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Sodium binding site 6 out of 10 in the Crystal Structure of E. Coli Aminopeptidase N in Complex with L- Glutamate


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

b:31.9
occ:1.00
 OXT A:GLU903 2.2 34.4 0.8
O A:HOH1627 2.7 19.8 1.0
OG1 A:THR645 2.9 17.9 1.0
C A:GLU903 2.9 24.9 0.8
O A:GLU903 3.4 46.8 0.8
CG2 A:THR645 3.6 21.5 1.0
CD1 A:LEU619 3.7 26.1 1.0
O A:HOH1432 3.8 18.9 0.5
NH1 A:ARG641 3.8 21.0 1.0
CB A:THR645 3.8 20.3 1.0
CA A:GLU903 3.9 27.6 0.8
CB A:GLU903 3.9 31.4 0.8
O A:HOH1004 4.0 16.9 0.5
CG A:LEU619 4.0 24.2 1.0
CZ A:ARG641 4.0 21.3 1.0
NH2 A:ARG641 4.1 22.6 1.0
CB A:LEU619 4.2 21.9 1.0
CG A:ARG686 4.2 28.9 1.0
O A:HOH1139 4.8 20.9 1.0
NE A:ARG686 4.8 30.9 1.0
NE A:ARG641 4.8 19.8 1.0
CE1 A:PHE687 4.9 20.6 1.0
N A:GLU903 4.9 21.4 0.8
CA A:THR645 4.9 18.7 1.0
N A:LEU619 4.9 17.4 1.0
CG A:ARG641 4.9 17.7 1.0
CZ A:PHE687 5.0 22.9 1.0

Sodium binding site 7 out of 10 in 4xo5

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Sodium binding site 7 out of 10 in the Crystal Structure of E. Coli Aminopeptidase N in Complex with L- Glutamate


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

b:36.2
occ:1.00
 OD1 A:ASP566 2.6 21.6 1.0
OG A:SER570 2.7 19.4 1.0
O A:HOH1829 2.8 29.4 1.0
O A:HOH1872 2.8 39.8 1.0
O A:ASP566 3.1 17.4 1.0
CG A:ASP566 3.4 21.3 1.0
N A:SER570 3.6 16.2 1.0
NH2 A:ARG349 3.6 26.3 1.0
O3 A:GOL917 3.7 34.1 1.0
NH1 A:ARG349 3.7 25.9 1.0
CB A:GLN569 3.8 19.0 1.0
CB A:SER570 3.8 17.5 1.0
CZ A:ARG349 3.9 25.3 1.0
CA A:SER570 4.0 16.9 1.0
OD2 A:ASP566 4.0 27.0 1.0
C A:ASP566 4.0 18.8 1.0
C A:GLN569 4.2 16.5 1.0
O A:HOH1582 4.3 33.0 1.0
CA A:ASP566 4.4 16.8 1.0
C3 A:GOL917 4.4 44.2 1.0
O A:HOH1056 4.5 21.5 0.5
O A:HOH1903 4.5 39.5 1.0
CB A:ASP566 4.5 17.9 1.0
CA A:GLN569 4.6 16.5 1.0
CG A:GLN569 4.8 19.1 1.0
O A:HOH1023 4.9 36.4 1.0
O A:GLN569 4.9 16.2 1.0
NE A:ARG349 4.9 24.8 1.0

Sodium binding site 8 out of 10 in 4xo5

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Sodium binding site 8 out of 10 in the Crystal Structure of E. Coli Aminopeptidase N in Complex with L- Glutamate


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- Glutamate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na911

b:25.8
occ:1.00
 O A:HOH1831 2.4 33.9 1.0
O A:LEU138 2.4 17.6 1.0
O A:HOH1634 2.4 21.0 1.0
OE1 A:GLN19 2.5 19.5 1.0
O A:ILE20 2.5 21.0 1.0
CD A:GLN19 3.3 19.1 1.0
C A:LEU138 3.4 18.3 1.0
C A:ILE20 3.5 18.6 1.0
N A:LEU138 3.5 15.1 1.0
O A:HOH1768 3.5 57.7 1.0
N A:ILE20 4.0 17.3 1.0
O A:HOH1862 4.0 39.3 1.0
CB A:GLN19 4.0 15.8 1.0
CA A:LEU138 4.0 16.1 1.0
CG A:GLN19 4.1 17.9 1.0
NE2 A:GLN19 4.2 17.5 1.0
CA A:THR21 4.2 17.2 1.0
N A:THR21 4.2 15.5 1.0
C A:VAL137 4.3 16.5 1.0
CA A:ILE20 4.4 17.2 1.0
CG1 A:VAL137 4.5 17.4 1.0
CA A:VAL137 4.5 17.5 1.0
N A:ALA139 4.5 16.1 1.0
CB A:LEU138 4.6 17.7 1.0
O A:HOH1812 4.6 41.6 1.0
CA A:GLN19 4.7 16.6 1.0
C A:GLN19 4.7 19.4 1.0
CG2 A:THR21 4.7 22.6 1.0
CA A:ALA139 4.8 15.2 1.0

Sodium binding site 9 out of 10 in 4xo5

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Sodium binding site 9 out of 10 in the Crystal Structure of E. Coli Aminopeptidase N in Complex with L- Glutamate


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 9 of Crystal Structure of E. Coli Aminopeptidase N in Complex with L- Glutamate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na912

b:47.5
occ:1.00
 O A:HOH1780 2.3 42.3 1.0
OD1 A:ASP432 2.4 30.1 1.0
OG A:SER434 2.6 30.0 1.0
O A:HOH1265 2.6 37.5 1.0
OE1 A:GLU426 2.7 25.3 1.0
CD A:GLU426 3.2 32.1 1.0
CG A:ASP432 3.5 28.6 1.0
OE2 A:GLU426 3.7 32.5 1.0
CB A:SER434 3.8 22.5 1.0
N A:SER434 3.8 17.6 1.0
N A:LEU433 4.1 18.7 1.0
CG A:GLU426 4.2 28.9 1.0
CA A:SER434 4.2 19.1 1.0
CA A:ASP432 4.3 23.6 1.0
CB A:ASP432 4.3 27.2 1.0
OD2 A:ASP432 4.3 39.0 1.0
NH1 A:ARG437 4.5 25.0 1.0
C A:ASP432 4.6 20.3 1.0
C A:LEU433 4.7 17.2 1.0
O A:HOH1741 4.9 44.4 1.0
O A:HOH1813 4.9 42.2 1.0

Sodium binding site 10 out of 10 in 4xo5

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Sodium binding site 10 out of 10 in the Crystal Structure of E. Coli Aminopeptidase N in Complex with L- Glutamate


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 10 of Crystal Structure of E. Coli Aminopeptidase N in Complex with L- Glutamate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na913

b:48.8
occ:1.00
 O A:HOH1702 2.2 24.6 0.5
O A:HOH1271 2.3 38.1 1.0
O A:HOH1467 2.5 23.6 0.5
O A:PHE774 2.5 23.2 1.0
O A:HIS771 2.6 20.5 1.0
C A:HIS771 3.7 22.7 1.0
C A:PHE774 3.7 22.4 1.0
O A:HOH1695 3.9 50.6 1.0
O A:ARG772 3.9 28.8 1.0
C A:ARG772 4.0 26.6 1.0
CA A:ARG772 4.1 26.8 1.0
N A:PHE774 4.1 19.1 1.0
O A:GLN770 4.3 23.3 1.0
N A:ARG772 4.3 22.7 1.0
CA A:PHE774 4.4 19.4 1.0
C A:GLN770 4.4 24.2 1.0
N A:HIS771 4.6 21.5 1.0
O A:HOH1477 4.7 57.3 1.0
N A:THR775 4.7 21.5 1.0
CB A:PHE774 4.7 19.2 1.0
N A:SER773 4.7 22.1 1.0
O A:LEU769 4.8 21.3 1.0
CA A:HIS771 4.8 22.2 1.0
CA A:THR775 4.9 22.3 1.0
C A:SER773 5.0 21.7 1.0
CA A:GLN770 5.0 24.2 1.0

Reference:

A.Addlagatta, R.Gumpena. Crystal Structure of E. Coli Aminopeptidase N in Complex with L-Glutamate To Be Published.
Page generated: Mon Oct 7 19:19:29 2024

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