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Sodium in PDB 6mx2: Crystal Structure of CLPP1 From Clostridium Difficile 630.

Enzymatic activity of Crystal Structure of CLPP1 From Clostridium Difficile 630.

All present enzymatic activity of Crystal Structure of CLPP1 From Clostridium Difficile 630.:
3.4.21.92;

Protein crystallography data

The structure of Crystal Structure of CLPP1 From Clostridium Difficile 630., PDB code: 6mx2 was solved by N.P.Lavey, L.M.Thomas, A.S.Duerfeldt, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 34.90 / 2.50
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 97.328, 97.372, 106.494, 113.15, 104.56, 103.21
R / Rfree (%) 19.3 / 24.4

Sodium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 17;

Binding sites:

The binding sites of Sodium atom in the Crystal Structure of CLPP1 From Clostridium Difficile 630. (pdb code 6mx2). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 17 binding sites of Sodium where determined in the Crystal Structure of CLPP1 From Clostridium Difficile 630., PDB code: 6mx2:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Sodium binding site 1 out of 17 in 6mx2

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Sodium binding site 1 out of 17 in the Crystal Structure of CLPP1 From Clostridium Difficile 630.


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 CLPP1 From Clostridium Difficile 630. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na201

b:32.6
occ:1.00
 O A:MET80 2.6 29.8 1.0
O A:ILE83 2.7 32.4 1.0
O A:HOH322 2.8 32.9 1.0
O A:PRO85 2.9 35.5 1.0
NZ B:LYS191 3.7 40.2 1.0
C A:MET80 3.8 32.4 1.0
C A:PRO85 3.9 33.9 1.0
C A:ILE83 3.9 33.9 1.0
O A:HOH345 3.9 31.0 1.0
O A:LYS84 4.0 34.3 1.0
O A:GLN81 4.1 41.9 1.0
CG1 A:ILE83 4.1 27.2 1.0
CA A:GLN81 4.1 33.0 1.0
C A:GLN81 4.2 33.9 1.0
C A:LYS84 4.2 34.6 1.0
CG2 A:VAL87 4.4 32.4 1.0
N A:GLN81 4.4 28.7 1.0
CA A:ASP86 4.5 34.6 1.0
N A:ASP86 4.5 32.0 1.0
N A:PRO85 4.6 33.5 1.0
N A:ILE83 4.6 32.2 1.0
N A:VAL87 4.7 32.9 1.0
CA A:ILE83 4.7 32.5 1.0
CE B:LYS191 4.7 41.4 1.0
O A:HOH311 4.8 33.4 1.0
N A:LYS84 4.8 32.1 1.0
CA A:LYS84 4.8 35.7 1.0
CA A:PRO85 4.9 35.5 1.0
OD1 A:ASP86 4.9 36.5 1.0
CA A:MET80 4.9 31.7 1.0
CD1 A:ILE83 4.9 24.1 1.0
C A:ASP86 5.0 34.9 1.0

Sodium binding site 2 out of 17 in 6mx2

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Sodium binding site 2 out of 17 in the Crystal Structure of CLPP1 From Clostridium Difficile 630.


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 CLPP1 From Clostridium Difficile 630. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na201

b:27.6
occ:1.00
 O B:MET80 2.7 29.5 1.0
O B:PRO85 2.7 35.2 1.0
O B:ILE83 2.7 32.7 1.0
O B:HOH337 2.9 37.9 1.0
C B:PRO85 3.7 36.6 1.0
C B:ILE83 3.8 36.0 1.0
CG1 B:ILE83 3.8 29.2 1.0
C B:MET80 3.8 27.8 1.0
O B:LYS84 4.0 30.5 1.0
O B:HOH325 4.1 34.5 1.0
O B:GLN81 4.1 39.4 1.0
CA B:GLN81 4.1 29.2 1.0
C B:LYS84 4.2 31.9 1.0
C B:GLN81 4.2 27.0 1.0
N B:ILE83 4.4 27.8 1.0
CA B:ASP86 4.4 35.6 1.0
N B:GLN81 4.5 27.2 1.0
N B:ASP86 4.5 38.6 1.0
N B:PRO85 4.5 33.0 1.0
CA B:ILE83 4.5 30.8 1.0
N B:VAL87 4.7 34.7 1.0
N B:LYS84 4.7 31.2 1.0
CA B:PRO85 4.8 33.3 1.0
CA B:LYS84 4.8 32.6 1.0
CD1 B:ILE83 4.8 28.1 1.0
CB B:ILE83 4.8 34.2 1.0
OD1 B:ASP86 4.8 41.0 1.0
CG2 B:VAL87 4.8 31.7 1.0
C B:ASP86 5.0 33.4 1.0
CA B:MET80 5.0 23.7 1.0
N B:TYR82 5.0 30.8 1.0

Sodium binding site 3 out of 17 in 6mx2

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Sodium binding site 3 out of 17 in the Crystal Structure of CLPP1 From Clostridium Difficile 630.


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 CLPP1 From Clostridium Difficile 630. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na201

b:21.4
occ:1.00
 O C:MET80 2.6 33.4 1.0
O C:PRO85 2.8 29.8 1.0
O C:HOH339 2.8 34.0 1.0
O C:ILE83 2.8 33.5 1.0
C C:PRO85 3.8 29.3 1.0
C C:MET80 3.8 28.9 1.0
C C:ILE83 3.8 34.2 1.0
O C:LYS84 4.0 41.3 1.0
CG1 C:ILE83 4.0 22.4 1.0
O C:GLN81 4.1 38.0 1.0
CA C:GLN81 4.2 28.5 1.0
C C:GLN81 4.2 32.4 1.0
C C:LYS84 4.2 33.5 1.0
CA C:ASP86 4.5 32.7 1.0
N C:GLN81 4.5 29.6 1.0
N C:ILE83 4.5 27.9 1.0
N C:ASP86 4.5 31.2 1.0
N C:PRO85 4.6 32.6 1.0
CG2 C:VAL87 4.6 27.4 1.0
CA C:ILE83 4.6 30.2 1.0
N C:VAL87 4.7 33.2 1.0
N C:LYS84 4.7 29.7 1.0
OD1 C:ASP86 4.8 27.4 1.0
CA C:LYS84 4.8 35.2 1.0
CA C:PRO85 4.8 29.3 1.0
N C:TYR82 4.9 33.4 1.0
CD1 C:ILE83 5.0 23.5 1.0
CB C:ILE83 5.0 29.3 1.0
CA C:MET80 5.0 23.3 1.0
C C:ASP86 5.0 32.3 1.0

Sodium binding site 4 out of 17 in 6mx2

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Sodium binding site 4 out of 17 in the Crystal Structure of CLPP1 From Clostridium Difficile 630.


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 CLPP1 From Clostridium Difficile 630. within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na201

b:31.0
occ:1.00
 O D:ILE83 2.6 31.4 1.0
O D:PRO85 2.7 26.4 1.0
O D:MET80 2.8 24.1 1.0
C D:ILE83 3.7 33.7 1.0
C D:PRO85 3.7 27.9 1.0
O D:LYS84 3.8 42.1 1.0
CG1 D:ILE83 4.0 25.5 1.0
C D:MET80 4.0 27.0 1.0
C D:LYS84 4.0 34.4 1.0
O D:GLN81 4.2 31.3 1.0
CA D:GLN81 4.3 23.3 1.0
C D:GLN81 4.4 25.4 1.0
N D:ASP86 4.4 26.6 1.0
CA D:ASP86 4.4 27.7 1.0
N D:PRO85 4.4 32.2 1.0
CG2 D:VAL87 4.5 22.3 1.0
N D:LYS84 4.5 31.9 1.0
CA D:LYS84 4.6 33.7 1.0
N D:ILE83 4.6 31.3 1.0
CA D:ILE83 4.6 25.3 1.0
N D:VAL87 4.6 22.9 1.0
CA D:PRO85 4.7 28.7 1.0
N D:GLN81 4.7 24.2 1.0
OD1 D:ASP86 4.9 26.7 1.0
C D:ASP86 4.9 29.2 1.0
CB D:ILE83 4.9 28.0 1.0
CD1 D:ILE83 4.9 18.9 1.0

Sodium binding site 5 out of 17 in 6mx2

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Sodium binding site 5 out of 17 in the Crystal Structure of CLPP1 From Clostridium Difficile 630.


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 CLPP1 From Clostridium Difficile 630. within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Na201

b:25.2
occ:1.00
 O E:MET80 2.5 29.9 1.0
O E:PRO85 2.6 24.9 1.0
O E:ILE83 2.7 31.0 1.0
O E:HOH351 3.0 30.1 1.0
C E:PRO85 3.7 27.9 1.0
C E:MET80 3.7 29.0 1.0
C E:ILE83 3.8 30.0 1.0
CG1 E:ILE83 3.9 28.1 1.0
O E:LYS84 3.9 30.0 1.0
O E:GLN81 4.0 37.2 1.0
CA E:GLN81 4.0 29.8 1.0
C E:LYS84 4.1 27.1 1.0
C E:GLN81 4.2 30.3 1.0
N E:GLN81 4.3 27.2 1.0
NZ F:LYS191 4.4 43.5 1.0
CG2 E:VAL87 4.4 27.6 1.0
N E:PRO85 4.4 32.1 1.0
N E:ASP86 4.5 30.7 1.0
CA E:ASP86 4.5 29.1 1.0
N E:ILE83 4.5 31.6 1.0
CA E:ILE83 4.6 32.8 1.0
N E:LYS84 4.7 32.3 1.0
CA E:PRO85 4.7 30.3 1.0
N E:VAL87 4.7 25.9 1.0
CA E:LYS84 4.7 31.7 1.0
CD1 E:ILE83 4.8 26.8 1.0
CA E:MET80 4.8 27.1 1.0
CB E:ILE83 4.9 29.0 1.0
O E:HOH317 4.9 33.8 1.0
C E:ASP86 4.9 29.8 1.0
N E:TYR82 5.0 31.8 1.0

Sodium binding site 6 out of 17 in 6mx2

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Sodium binding site 6 out of 17 in the Crystal Structure of CLPP1 From Clostridium Difficile 630.


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 CLPP1 From Clostridium Difficile 630. within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Na201

b:29.3
occ:1.00
 O F:PRO85 2.5 28.1 1.0
O F:HOH320 2.5 41.0 1.0
O F:ILE83 2.7 34.3 1.0
O F:MET80 2.7 34.8 1.0
O F:HOH318 2.9 23.5 1.0
O F:HOH306 3.1 33.2 1.0
C F:PRO85 3.6 27.2 1.0
C F:ILE83 3.7 30.7 1.0
CG1 F:ILE83 3.8 27.9 1.0
C F:MET80 3.9 33.0 1.0
O F:LYS84 4.1 29.8 1.0
O F:GLN81 4.2 37.1 1.0
C F:LYS84 4.2 29.7 1.0
CA F:ASP86 4.3 31.2 1.0
CG2 F:VAL87 4.3 26.7 1.0
N F:ASP86 4.3 30.2 1.0
CA F:GLN81 4.3 33.0 1.0
C F:GLN81 4.3 32.2 1.0
N F:PRO85 4.4 26.2 1.0
N F:VAL87 4.4 30.5 1.0
N F:ILE83 4.5 36.2 1.0
CA F:ILE83 4.5 34.4 1.0
N F:LYS84 4.6 33.0 1.0
CA F:PRO85 4.6 24.8 1.0
N F:GLN81 4.6 30.2 1.0
OD1 F:ASP86 4.6 36.1 1.0
CD1 F:ILE83 4.7 27.0 1.0
CA F:LYS84 4.7 34.0 1.0
C F:ASP86 4.8 28.8 1.0
CB F:ILE83 4.8 34.1 1.0

Sodium binding site 7 out of 17 in 6mx2

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Sodium binding site 7 out of 17 in the Crystal Structure of CLPP1 From Clostridium Difficile 630.


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 CLPP1 From Clostridium Difficile 630. within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Na201

b:18.0
occ:1.00
 O G:MET80 2.5 29.0 1.0
O G:PRO85 2.6 29.4 1.0
O G:HOH333 2.8 28.3 1.0
O G:ILE83 2.9 30.2 1.0
C G:MET80 3.7 25.6 1.0
C G:PRO85 3.7 26.3 1.0
C G:ILE83 3.9 29.0 1.0
CG1 G:ILE83 3.9 23.2 1.0
O G:LYS84 4.1 31.0 1.0
CA G:GLN81 4.2 26.7 1.0
C G:LYS84 4.3 30.0 1.0
CG2 G:VAL87 4.3 19.5 1.0
O G:GLN81 4.3 31.4 1.0
C G:GLN81 4.4 26.6 1.0
CA G:ASP86 4.4 24.8 1.0
N G:GLN81 4.4 23.3 1.0
N G:ASP86 4.5 21.8 1.0
N G:VAL87 4.5 27.0 1.0
N G:PRO85 4.5 28.8 1.0
NZ A:LYS191 4.6 40.0 1.0
N G:ILE83 4.7 30.7 1.0
CA G:ILE83 4.7 27.9 1.0
N G:LYS84 4.7 25.9 1.0
CA G:PRO85 4.8 29.7 1.0
CD1 G:ILE83 4.8 20.8 1.0
CA G:MET80 4.8 24.6 1.0
C G:ASP86 4.8 27.1 1.0
CA G:LYS84 4.8 29.8 1.0
O G:HOH308 4.9 31.8 1.0
CB G:ILE83 5.0 31.4 1.0

Sodium binding site 8 out of 17 in 6mx2

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Sodium binding site 8 out of 17 in the Crystal Structure of CLPP1 From Clostridium Difficile 630.


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 CLPP1 From Clostridium Difficile 630. within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Na202

b:28.3
occ:1.00
 N G:MET98 2.9 20.1 1.0
CB G:SER97 3.0 20.6 1.0
N G:GLY68 3.0 22.7 1.0
O G:GLY68 3.3 27.6 1.0
CB G:MET98 3.3 22.2 1.0
CA G:GLY67 3.7 20.1 1.0
CA G:MET98 3.7 22.4 1.0
C G:GLY67 3.9 25.6 1.0
C G:SER97 3.9 17.1 1.0
C G:GLY68 4.0 22.1 1.0
CA G:SER97 4.0 20.6 1.0
CA G:GLY68 4.0 20.6 1.0
OG G:SER97 4.0 26.4 1.0
CG G:MET98 4.7 33.9 1.0
O G:ALA96 4.7 16.9 1.0
O G:PRO66 4.7 28.0 1.0
NE2 G:HIS122 4.8 24.3 1.0
CE G:MET98 4.8 26.9 1.0
C G:MET98 4.9 22.8 1.0
N G:GLY67 5.0 16.9 1.0
N G:GLY99 5.0 17.6 1.0

Sodium binding site 9 out of 17 in 6mx2

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Sodium binding site 9 out of 17 in the Crystal Structure of CLPP1 From Clostridium Difficile 630.


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 CLPP1 From Clostridium Difficile 630. within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Na201

b:28.2
occ:1.00
 O H:PRO85 2.5 29.9 1.0
O H:MET80 2.6 30.0 1.0
O I:HOH314 2.7 37.6 1.0
O H:ILE83 2.9 35.8 1.0
O H:HOH333 2.9 32.2 1.0
C H:PRO85 3.6 32.7 1.0
O H:HOH332 3.7 27.3 1.0
C H:MET80 3.8 31.8 1.0
O H:LYS84 3.9 31.7 1.0
C H:ILE83 3.9 34.6 1.0
CG1 H:ILE83 3.9 28.3 1.0
O H:GLN81 4.0 41.0 1.0
CA H:GLN81 4.1 32.6 1.0
C H:LYS84 4.2 35.0 1.0
CA H:ASP86 4.2 32.8 1.0
C H:GLN81 4.3 33.4 1.0
N H:ASP86 4.3 29.4 1.0
N H:GLN81 4.4 28.3 1.0
CG2 H:VAL87 4.5 33.7 1.0
N H:PRO85 4.5 32.2 1.0
N H:VAL87 4.5 33.6 1.0
OD2 H:ASP86 4.6 36.0 1.0
CA H:PRO85 4.7 34.0 1.0
N H:ILE83 4.7 27.5 1.0
CD1 H:ILE83 4.7 24.0 1.0
CA H:ILE83 4.7 27.6 1.0
N H:LYS84 4.8 31.9 1.0
C H:ASP86 4.8 34.8 1.0
CA H:LYS84 4.8 37.4 1.0
CA H:MET80 4.9 28.6 1.0
CB H:ILE83 5.0 31.9 1.0

Sodium binding site 10 out of 17 in 6mx2

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Sodium binding site 10 out of 17 in the Crystal Structure of CLPP1 From Clostridium Difficile 630.


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 CLPP1 From Clostridium Difficile 630. within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Na201

b:31.9
occ:1.00
 O I:MET80 2.7 32.1 1.0
O I:PRO85 2.8 26.5 1.0
O I:ILE83 2.9 31.4 1.0
O I:HOH342 3.0 32.5 1.0
O I:HOH354 3.1 32.6 1.0
O I:HOH321 3.4 36.7 1.0
C I:PRO85 3.9 30.6 1.0
C I:MET80 3.9 28.6 1.0
C I:ILE83 4.0 34.0 1.0
O I:LYS84 4.0 33.2 1.0
O I:GLN81 4.2 42.2 1.0
CA I:GLN81 4.2 29.5 1.0
CG1 I:ILE83 4.2 26.7 1.0
C I:LYS84 4.3 25.3 1.0
C I:GLN81 4.3 29.7 1.0
CA I:ASP86 4.5 30.9 1.0
N I:ASP86 4.5 31.2 1.0
N I:GLN81 4.5 25.8 1.0
CG2 I:VAL87 4.6 22.5 1.0
N I:VAL87 4.6 30.2 1.0
N I:PRO85 4.7 27.4 1.0
N I:LYS84 4.8 33.6 1.0
OD1 I:ASP86 4.8 32.4 1.0
N I:ILE83 4.8 33.5 1.0
CA I:LYS84 4.8 30.9 1.0
CA I:ILE83 4.9 31.0 1.0
CA I:PRO85 4.9 29.6 1.0
C I:ASP86 5.0 29.3 1.0

Reference:

N.P.Lavey, L.M.Thomas, A.S.Duerfeldt. Crystal Structure of CLPP1 From Clostridium Difficile 630. To Be Published.
Page generated: Tue Oct 8 12:02:46 2024

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