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Sodium in PDB 6ome: Crystal Structure of A Probable Cytosol Aminopeptidase (Leucine Aminopeptidase, Lap) From Chlamydia Trachomatis D/Uw-3/Cx

Enzymatic activity of Crystal Structure of A Probable Cytosol Aminopeptidase (Leucine Aminopeptidase, Lap) From Chlamydia Trachomatis D/Uw-3/Cx

All present enzymatic activity of Crystal Structure of A Probable Cytosol Aminopeptidase (Leucine Aminopeptidase, Lap) From Chlamydia Trachomatis D/Uw-3/Cx:
3.4.11.1; 3.4.11.10;

Protein crystallography data

The structure of Crystal Structure of A Probable Cytosol Aminopeptidase (Leucine Aminopeptidase, Lap) From Chlamydia Trachomatis D/Uw-3/Cx, PDB code: 6ome was solved by Seattle Structural Genomics Center For Infectious Disease (Ssgcid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.16 / 1.95
Space group P 63 2 2
Cell size a, b, c (Å), α, β, γ (°) 137.960, 137.960, 128.140, 90.00, 90.00, 120.00
R / Rfree (%) 14.3 / 17.1

Other elements in 6ome:

The structure of Crystal Structure of A Probable Cytosol Aminopeptidase (Leucine Aminopeptidase, Lap) From Chlamydia Trachomatis D/Uw-3/Cx also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms
Zinc (Zn) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of A Probable Cytosol Aminopeptidase (Leucine Aminopeptidase, Lap) From Chlamydia Trachomatis D/Uw-3/Cx (pdb code 6ome). 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 A Probable Cytosol Aminopeptidase (Leucine Aminopeptidase, Lap) From Chlamydia Trachomatis D/Uw-3/Cx, PDB code: 6ome:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 6ome

Go back to Sodium Binding Sites List in 6ome
Sodium binding site 1 out of 4 in the Crystal Structure of A Probable Cytosol Aminopeptidase (Leucine Aminopeptidase, Lap) From Chlamydia Trachomatis D/Uw-3/Cx


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 A Probable Cytosol Aminopeptidase (Leucine Aminopeptidase, Lap) From Chlamydia Trachomatis D/Uw-3/Cx within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na508

b:48.8
occ:1.00
 O A:HOH901 2.4 59.3 1.0
OE2 A:GLU177 2.5 79.6 1.0
OE1 A:GLU177 2.7 82.8 1.0
O A:HOH899 2.9 70.1 1.0
CD A:GLU177 2.9 76.5 1.0
CG A:GLU177 4.4 53.7 1.0
CD2 A:TYR180 4.5 35.3 1.0
O A:HOH743 4.5 51.0 1.0
CE2 A:TYR180 4.9 42.5 1.0
O A:HOH757 4.9 45.4 1.0

Sodium binding site 2 out of 4 in 6ome

Go back to Sodium Binding Sites List in 6ome
Sodium binding site 2 out of 4 in the Crystal Structure of A Probable Cytosol Aminopeptidase (Leucine Aminopeptidase, Lap) From Chlamydia Trachomatis D/Uw-3/Cx


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 A Probable Cytosol Aminopeptidase (Leucine Aminopeptidase, Lap) From Chlamydia Trachomatis D/Uw-3/Cx within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na509

b:36.1
occ:1.00
 O A:ALA206 2.2 40.0 1.0
O A:LEU212 2.3 35.6 1.0
O A:HOH710 2.3 53.4 1.0
O A:PHE209 2.3 35.7 1.0
C A:ALA206 3.3 43.5 1.0
C A:PHE209 3.4 36.0 1.0
C A:LEU212 3.4 36.2 1.0
CA A:ALA210 3.8 38.6 1.0
N A:LEU212 3.9 36.5 1.0
O A:ALA210 3.9 46.7 1.0
C A:ALA210 3.9 39.7 1.0
CA A:ALA206 4.0 39.5 1.0
N A:ALA210 4.0 38.5 1.0
CA A:LEU212 4.1 31.7 1.0
CB A:ALA206 4.4 39.2 1.0
N A:GLY207 4.4 36.8 1.0
CB A:LEU212 4.4 39.1 1.0
N A:ASP213 4.5 30.6 1.0
CA A:PHE209 4.5 37.7 1.0
N A:PHE209 4.5 36.3 1.0
OD1 A:ASP213 4.6 61.5 1.0
CA A:GLY207 4.6 39.8 1.0
O A:GLY207 4.6 44.2 1.0
N A:SER211 4.7 40.4 1.0
C A:GLY207 4.7 37.2 1.0
CA A:ASP213 4.7 28.4 1.0
C A:SER211 5.0 36.2 1.0
CG A:ASP213 5.0 57.4 1.0

Sodium binding site 3 out of 4 in 6ome

Go back to Sodium Binding Sites List in 6ome
Sodium binding site 3 out of 4 in the Crystal Structure of A Probable Cytosol Aminopeptidase (Leucine Aminopeptidase, Lap) From Chlamydia Trachomatis D/Uw-3/Cx


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 A Probable Cytosol Aminopeptidase (Leucine Aminopeptidase, Lap) From Chlamydia Trachomatis D/Uw-3/Cx within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na510

b:36.8
occ:1.00
 O A:HOH663 2.4 33.5 1.0
OD1 A:ASP273 2.4 23.0 1.0
O A:HOH840 2.4 32.6 1.0
O A:LEU514 2.5 40.4 1.0
CL A:CL512 2.8 49.6 1.0
C A:LEU514 3.1 55.0 1.0
CG A:ASP273 3.3 29.1 1.0
CA A:LEU514 3.4 47.8 1.0
O A:HOH869 3.5 55.1 1.0
OD2 A:ASP273 3.5 25.6 1.0
N A:LEU514 3.6 54.2 1.0
O A:HOH672 3.8 32.1 1.0
O A:HOH718 3.8 30.2 1.0
O A:HOH685 3.9 25.5 1.0
OXT A:LEU514 4.1 40.3 1.0
O A:HOH613 4.6 45.9 1.0
CB A:ASP273 4.6 17.9 1.0
O A:LEU274 4.8 17.7 1.0
O A:ASP273 4.8 20.5 1.0
C A:ASP273 4.9 23.3 1.0
CB A:LEU514 4.9 55.9 1.0
CA A:ASP273 5.0 18.2 1.0

Sodium binding site 4 out of 4 in 6ome

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Sodium binding site 4 out of 4 in the Crystal Structure of A Probable Cytosol Aminopeptidase (Leucine Aminopeptidase, Lap) From Chlamydia Trachomatis D/Uw-3/Cx


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 A Probable Cytosol Aminopeptidase (Leucine Aminopeptidase, Lap) From Chlamydia Trachomatis D/Uw-3/Cx within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na511

b:39.8
occ:1.00
 O A:TYR469 2.3 23.8 1.0
O A:HOH858 2.4 32.6 1.0
O A:HOH894 2.4 36.4 1.0
O A:HOH617 2.5 22.6 1.0
O A:HOH683 2.6 27.8 1.0
O A:GLY466 2.7 24.2 1.0
O A:HOH777 3.3 43.4 1.0
C A:GLY466 3.5 21.2 1.0
C A:TYR469 3.5 26.6 1.0
O A:ALA465 3.7 24.7 1.0
CA A:GLY466 3.9 23.1 1.0
N A:TYR469 4.0 22.5 1.0
CA A:TYR469 4.2 23.8 1.0
CD2 A:HIS470 4.4 24.9 1.0
CB A:TYR469 4.5 23.7 1.0
OE1 A:GLU285 4.5 29.4 1.0
N A:HIS470 4.5 22.1 1.0
N A:THR467 4.6 22.0 1.0
C A:ALA465 4.6 27.1 1.0
CA A:HIS470 4.7 23.4 1.0
OE2 A:GLU285 4.7 27.6 1.0
N A:GLY466 4.8 22.9 1.0
O A:HOH842 4.8 58.6 1.0
N A:ALA468 4.8 21.4 1.0
CB A:GLU384 4.9 28.4 1.0

Reference:

T.E.Edwards, D.M.Dranow, D.D.Lorimer, P.S.Horanyi, Seattle Structural Genomics Center For Infectious Disease(Ssgcid). Crystal Structure of A Probable Cytosol Aminopeptidase (Leucine Aminopeptidase, Lap) From Chlamydia Trachomatis D/Uw-3/Cx To Be Published.
Page generated: Mon Aug 18 06:28:18 2025

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