Atomistry » Sodium » PDB 6nxy-6oog » 6ome
Atomistry »
  Sodium »
    PDB 6nxy-6oog »
      6ome »

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

Go back to Sodium Binding Sites List in 6ome
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: Tue Dec 15 12:43:13 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy