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Sodium in PDB 8dla: CLPP2 From Chlamydia Trachomatis Bound By MAS1-12

Enzymatic activity of CLPP2 From Chlamydia Trachomatis Bound By MAS1-12

All present enzymatic activity of CLPP2 From Chlamydia Trachomatis Bound By MAS1-12:
3.4.21.92;

Protein crystallography data

The structure of CLPP2 From Chlamydia Trachomatis Bound By MAS1-12, PDB code: 8dla was solved by J.Azadmanesh, L.R.Struble, M.A.Seleem, S.Ouellette, M.Conda-Sheridan, G.E.O.Borgstahl, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 33.09 / 2.66
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 97, 98.01, 97.97, 97.16, 114.15, 114.16
R / Rfree (%) 17.4 / 21

Other elements in 8dla:

The structure of CLPP2 From Chlamydia Trachomatis Bound By MAS1-12 also contains other interesting chemical elements:

Fluorine (F) 18 atoms
Chlorine (Cl) 6 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the CLPP2 From Chlamydia Trachomatis Bound By MAS1-12 (pdb code 8dla). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 8 binding sites of Sodium where determined in the CLPP2 From Chlamydia Trachomatis Bound By MAS1-12, PDB code: 8dla:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Sodium binding site 1 out of 8 in 8dla

Go back to Sodium Binding Sites List in 8dla
Sodium binding site 1 out of 8 in the CLPP2 From Chlamydia Trachomatis Bound By MAS1-12


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of CLPP2 From Chlamydia Trachomatis Bound By MAS1-12 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na302

b:41.5
occ:1.00
 NE2 B:HIS123 2.6 33.9 1.0
O M:PRO125 2.8 64.4 1.0
N B:SER126 2.8 64.7 1.0
OD2 B:ASP172 3.2 36.0 1.0
CE1 M:HIS123 3.3 37.6 1.0
OD2 M:ASP172 3.3 44.6 1.0
CA B:PRO125 3.4 63.3 1.0
CE1 B:HIS123 3.5 28.8 1.0
C B:PRO125 3.6 65.3 1.0
CD2 B:HIS123 3.6 27.2 1.0
C M:PRO125 3.6 63.9 1.0
CB B:SER126 3.7 61.7 1.0
CA B:SER126 3.8 70.5 1.0
NE2 M:HIS123 3.8 36.9 1.0
CA M:PRO125 3.8 51.2 1.0
CG B:ASP172 4.0 28.8 1.0
CB B:PRO125 4.1 68.9 1.0
CG M:ASP172 4.2 42.5 1.0
O B:GLN124 4.3 42.2 1.0
OG B:SER126 4.4 58.5 1.0
CB M:PRO125 4.5 47.3 1.0
CB B:ASP172 4.5 26.5 1.0
ND1 M:HIS123 4.5 36.1 1.0
C B:SER126 4.6 69.3 1.0
CB M:ASP172 4.6 40.0 1.0
N B:PRO125 4.6 62.2 1.0
O B:SER126 4.6 72.9 1.0
ND1 B:HIS123 4.7 25.8 1.0
N M:SER126 4.8 82.1 1.0
CG B:HIS123 4.8 24.5 1.0
OD1 B:ASP172 4.8 24.9 1.0
O B:PRO125 4.8 73.1 1.0
C B:GLN124 4.8 44.1 1.0
O M:GLN124 4.9 50.0 1.0
O B:HOH420 4.9 38.6 1.0
NE2 D:GLN139 5.0 44.7 1.0

Sodium binding site 2 out of 8 in 8dla

Go back to Sodium Binding Sites List in 8dla
Sodium binding site 2 out of 8 in the CLPP2 From Chlamydia Trachomatis Bound By MAS1-12


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of CLPP2 From Chlamydia Trachomatis Bound By MAS1-12 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na302

b:64.5
occ:1.00
 OD2 D:ASP172 2.5 37.1 1.0
NE2 N:HIS123 2.6 39.1 1.0
CE1 N:HIS123 3.3 36.8 1.0
NE2 D:HIS123 3.4 43.3 1.0
CG D:ASP172 3.5 39.0 1.0
OD2 N:ASP172 3.6 36.4 1.0
O N:HOH421 3.7 51.5 1.0
CD2 N:HIS123 3.7 37.4 1.0
CB D:ASP172 4.1 38.2 1.0
O N:GLN124 4.2 68.5 1.0
CE1 D:HIS123 4.2 41.0 1.0
CG N:ASP172 4.3 36.3 1.0
OD1 D:ASP172 4.3 38.6 1.0
CD2 D:HIS123 4.4 45.6 1.0
ND1 N:HIS123 4.5 40.3 1.0
CA D:PRO125 4.5 76.0 1.0
CB N:ASP172 4.6 36.5 1.0
N N:SER126 4.6 80.1 1.0
C N:PRO125 4.7 91.0 1.0
CG N:HIS123 4.7 40.0 1.0
O N:HOH401 4.8 77.2 1.0
O D:GLN124 4.9 93.6 1.0
CA N:PRO125 4.9 83.8 1.0

Sodium binding site 3 out of 8 in 8dla

Go back to Sodium Binding Sites List in 8dla
Sodium binding site 3 out of 8 in the CLPP2 From Chlamydia Trachomatis Bound By MAS1-12


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of CLPP2 From Chlamydia Trachomatis Bound By MAS1-12 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Na301

b:20.8
occ:1.00
 OE1 E:GLU179 2.4 37.9 1.0
O E:HOH427 2.4 15.5 1.0
N E:GLU179 2.6 38.3 1.0
CG E:GLU179 2.7 36.3 1.0
CD E:GLU179 2.8 40.2 1.0
CB E:GLU179 3.3 33.4 1.0
CB E:GLU178 3.4 24.0 1.0
CA E:GLU179 3.5 37.6 1.0
C E:GLU178 3.5 26.8 1.0
N E:GLU178 3.5 24.2 1.0
CA E:GLU178 3.6 20.4 1.0
CA E:GLY176 3.8 21.0 1.0
C E:GLY176 3.8 30.0 1.0
N E:GLY176 4.0 21.6 1.0
OE2 E:GLU179 4.0 38.5 1.0
O E:GLY176 4.0 33.8 1.0
CG E:GLU178 4.0 24.7 1.0
CD E:GLU178 4.1 29.6 1.0
OE1 E:GLU178 4.3 34.1 1.0
N E:ALA177 4.3 22.3 1.0
C E:ALA177 4.5 26.8 1.0
O E:GLU178 4.6 27.2 1.0
OE2 E:GLU178 4.6 29.9 1.0
C E:GLU179 4.8 34.4 1.0

Sodium binding site 4 out of 8 in 8dla

Go back to Sodium Binding Sites List in 8dla
Sodium binding site 4 out of 8 in the CLPP2 From Chlamydia Trachomatis Bound By MAS1-12


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of CLPP2 From Chlamydia Trachomatis Bound By MAS1-12 within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Na301

b:20.0
occ:1.00
 O F:HOH444 2.3 17.0 1.0
N F:GLU179 2.5 22.7 1.0
C F:GLY176 2.6 25.1 1.0
N F:GLU178 2.8 23.7 1.0
CA F:GLY176 2.8 22.4 1.0
O F:GLY176 2.9 22.3 1.0
N F:ALA177 3.0 32.1 1.0
N F:GLY176 3.3 22.9 1.0
CA F:GLU178 3.3 23.8 1.0
C F:GLU178 3.3 23.2 1.0
CB F:GLU179 3.3 21.6 1.0
CA F:GLU179 3.5 22.1 1.0
C F:ALA177 3.5 31.3 1.0
CB F:GLU178 3.5 25.3 1.0
O F:HOH443 3.7 12.1 1.0
CA F:ALA177 3.8 31.3 1.0
N F:ALA180 4.4 25.4 1.0
O F:ALA177 4.4 31.7 1.0
C F:GLU179 4.5 24.2 1.0
C F:MET175 4.5 23.8 1.0
O F:GLU178 4.5 27.1 1.0
O F:HOH421 4.8 24.9 1.0
CG F:GLU179 4.8 23.1 1.0
CG F:GLU178 4.8 24.8 1.0
CB F:ALA177 4.9 31.9 1.0
OE1 F:GLU179 5.0 34.7 1.0

Sodium binding site 5 out of 8 in 8dla

Go back to Sodium Binding Sites List in 8dla
Sodium binding site 5 out of 8 in the CLPP2 From Chlamydia Trachomatis Bound By MAS1-12


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of CLPP2 From Chlamydia Trachomatis Bound By MAS1-12 within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Na303

b:32.8
occ:1.00
 N G:SER126 2.4 59.2 1.0
OD2 K:ASP172 2.5 40.8 1.0
NE2 G:HIS123 2.8 28.3 1.0
CA G:SER126 3.1 64.4 1.0
C G:PRO125 3.4 63.0 1.0
NE2 K:HIS123 3.5 31.0 1.0
OD2 G:ASP172 3.6 41.6 1.0
CE1 G:HIS123 3.6 28.8 1.0
CG K:ASP172 3.6 32.5 1.0
CA G:PRO125 3.6 61.3 1.0
OE1 N:GLN139 3.7 47.7 1.0
CD2 G:HIS123 3.9 25.8 1.0
C G:SER126 4.0 63.1 1.0
O G:SER126 4.1 72.0 1.0
O G:GLN124 4.2 38.1 1.0
CB K:ASP172 4.2 27.2 1.0
CD N:GLN139 4.2 42.3 1.0
CA K:PRO125 4.2 75.9 1.0
CD2 K:HIS123 4.2 35.1 1.0
CG G:ASP172 4.3 34.5 1.0
CB G:SER126 4.3 67.3 1.0
CE1 K:HIS123 4.3 32.8 1.0
OD1 K:ASP172 4.5 27.4 1.0
C K:PRO125 4.5 80.7 1.0
CB K:PRO125 4.5 72.2 1.0
CB G:PRO125 4.5 55.8 1.0
O G:PRO125 4.5 60.2 1.0
OG K:SER126 4.6 67.0 1.0
NE2 N:GLN139 4.7 45.9 1.0
CB K:SER126 4.7 63.2 1.0
N K:SER126 4.7 65.7 1.0
N G:PRO125 4.8 56.0 1.0
ND1 G:HIS123 4.8 25.0 1.0
CB G:ASP172 4.8 32.5 1.0
C G:GLN124 4.9 37.6 1.0
O K:PRO125 4.9 82.8 1.0
CG G:HIS123 5.0 24.6 1.0

Sodium binding site 6 out of 8 in 8dla

Go back to Sodium Binding Sites List in 8dla
Sodium binding site 6 out of 8 in the CLPP2 From Chlamydia Trachomatis Bound By MAS1-12


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of CLPP2 From Chlamydia Trachomatis Bound By MAS1-12 within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Na301

b:21.8
occ:1.00
 O H:SER169 2.4 28.4 1.0
NE2 C:GLN139 2.4 36.1 1.0
N H:GLN124 2.6 37.2 1.0
ND1 H:HIS123 2.6 32.6 1.0
OE1 C:GLN139 3.0 32.4 1.0
CD C:GLN139 3.1 31.3 1.0
O H:GLN124 3.1 44.0 1.0
CE1 H:HIS123 3.2 32.1 1.0
CG H:HIS123 3.3 27.9 1.0
CA H:GLN124 3.4 38.8 1.0
C H:HIS123 3.5 31.4 1.0
CA H:HIS123 3.5 30.6 1.0
C H:SER169 3.5 33.4 1.0
C H:GLN124 3.6 40.6 1.0
CB H:GLN124 3.7 38.4 1.0
CB H:HIS123 3.8 28.6 1.0
OE1 H:GLN124 3.9 39.0 1.0
NE2 H:HIS123 4.0 34.6 1.0
CD2 H:HIS123 4.1 29.9 1.0
CB H:SER169 4.3 32.1 1.0
CA H:SER169 4.3 36.9 1.0
NZ H:LYS147 4.4 24.8 1.0
N H:GLU170 4.5 36.1 1.0
CG C:GLN139 4.6 32.7 1.0
O H:HIS123 4.6 36.2 1.0
O H:HOH426 4.6 19.4 1.0
CA H:GLU170 4.7 35.0 1.0
N H:PRO125 4.7 45.4 1.0
CD H:GLN124 4.7 41.9 1.0
CG H:GLN124 4.8 37.8 1.0
N H:HIS123 4.8 34.3 1.0
O H:ILE122 4.9 38.1 1.0
O C:HOH416 5.0 30.9 1.0

Sodium binding site 7 out of 8 in 8dla

Go back to Sodium Binding Sites List in 8dla
Sodium binding site 7 out of 8 in the CLPP2 From Chlamydia Trachomatis Bound By MAS1-12


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of CLPP2 From Chlamydia Trachomatis Bound By MAS1-12 within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Na301

b:38.4
occ:1.00
 OD2 H:ASP172 2.5 36.4 1.0
N L:SER126 2.6 65.1 1.0
NE2 L:HIS123 2.8 19.4 1.0
CA L:SER126 3.1 68.6 1.0
CE1 L:HIS123 3.5 22.5 1.0
C L:PRO125 3.6 61.2 1.0
CG H:ASP172 3.6 28.5 1.0
OD2 L:ASP172 3.8 31.6 1.0
CA L:PRO125 3.9 51.3 1.0
N L:GLY127 3.9 75.4 1.0
C L:SER126 3.9 78.2 1.0
NE2 H:HIS123 3.9 34.6 1.0
CD2 L:HIS123 4.0 25.4 1.0
O H:HOH425 4.1 54.4 1.0
O L:GLN124 4.1 55.8 1.0
CB H:ASP172 4.3 25.1 1.0
CB L:SER126 4.4 66.2 1.0
OD1 H:ASP172 4.5 28.7 1.0
CB H:PRO125 4.5 43.3 1.0
CG L:ASP172 4.6 27.9 1.0
OG L:SER126 4.6 57.9 1.0
O L:PRO125 4.6 62.0 1.0
OE1 M:GLN137 4.7 94.1 1.0
CD2 H:HIS123 4.7 29.9 1.0
ND1 L:HIS123 4.8 30.4 1.0
CE1 H:HIS123 4.8 32.1 1.0
CA H:PRO125 4.8 48.6 1.0
CB L:PRO125 4.9 60.0 1.0
N L:PRO125 4.9 49.7 1.0
C L:GLN124 4.9 49.0 1.0
O L:SER126 5.0 78.0 1.0

Sodium binding site 8 out of 8 in 8dla

Go back to Sodium Binding Sites List in 8dla
Sodium binding site 8 out of 8 in the CLPP2 From Chlamydia Trachomatis Bound By MAS1-12


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of CLPP2 From Chlamydia Trachomatis Bound By MAS1-12 within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Na302

b:15.6
occ:1.00
 O N:HOH412 2.8 17.5 1.0
N N:GLU178 3.1 29.5 1.0
N N:ALA177 3.3 26.3 1.0
CG N:GLU178 3.4 39.5 1.0
O B:HOH438 3.5 9.8 1.0
CB N:GLU178 3.6 31.8 1.0
C N:GLY176 3.9 22.2 1.0
CA N:GLU178 3.9 29.4 1.0
CA N:ALA177 4.0 28.1 1.0
CA N:GLY176 4.0 23.8 1.0
C N:ALA177 4.0 25.8 1.0
CB N:ALA177 4.2 27.0 1.0
O B:HOH423 4.3 16.5 1.0
O N:PRO116 4.6 24.8 1.0
N N:GLU179 4.8 33.5 1.0
O N:GLY176 4.8 26.4 1.0
CD N:GLU178 4.8 49.2 1.0
C N:GLU178 4.9 30.6 1.0
OE2 N:GLU179 5.0 37.8 1.0

Reference:

J.Azadmanesh, L.R.Struble, G.E.O.Borgstahl, S.Ouellette, M.Conda Sheridan. CLPP2 From Chlamydia Trachomatis with Resolved Handle Loop To Be Published.
Page generated: Wed Oct 9 11:31:45 2024

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