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Sodium in PDB 4df9: Crystal Structure of A Putative Peptidase (BF3526) From Bacteroides Fragilis Nctc 9343 at 2.17 A Resolution

Protein crystallography data

The structure of Crystal Structure of A Putative Peptidase (BF3526) From Bacteroides Fragilis Nctc 9343 at 2.17 A Resolution, PDB code: 4df9 was solved by Joint Center For Structural Genomics (Jcsg), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.73 / 2.17
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 238.730, 92.820, 173.890, 90.00, 125.26, 90.00
R / Rfree (%) 15.6 / 18.8

Other elements in 4df9:

The structure of Crystal Structure of A Putative Peptidase (BF3526) From Bacteroides Fragilis Nctc 9343 at 2.17 A Resolution also contains other interesting chemical elements:

Zinc (Zn) 12 atoms
Chlorine (Cl) 15 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of A Putative Peptidase (BF3526) From Bacteroides Fragilis Nctc 9343 at 2.17 A Resolution (pdb code 4df9). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 6 binding sites of Sodium where determined in the Crystal Structure of A Putative Peptidase (BF3526) From Bacteroides Fragilis Nctc 9343 at 2.17 A Resolution, PDB code: 4df9:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6;

Sodium binding site 1 out of 6 in 4df9

Go back to Sodium Binding Sites List in 4df9
Sodium binding site 1 out of 6 in the Crystal Structure of A Putative Peptidase (BF3526) From Bacteroides Fragilis Nctc 9343 at 2.17 A Resolution


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 Putative Peptidase (BF3526) From Bacteroides Fragilis Nctc 9343 at 2.17 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na501

b:44.0
occ:1.00
 O A:CYS175 2.2 50.3 1.0
O A:GLU172 2.3 58.0 1.0
O A:ALA58 2.3 45.4 1.0
OE2 A:GLU275 2.4 41.3 1.0
OD2 A:ASP177 2.4 51.9 1.0
CD A:GLU275 3.2 57.1 1.0
C A:GLU172 3.4 59.5 1.0
O A:HOH782 3.4 54.5 1.0
C A:CYS175 3.4 50.6 1.0
C A:ALA58 3.5 46.0 1.0
CG A:ASP177 3.6 48.2 1.0
N A:ASP177 3.8 36.9 1.0
OE1 A:GLU275 3.9 42.2 1.0
CA A:GLU172 4.0 55.2 1.0
CA A:ILE176 4.1 39.7 1.0
CG A:GLU275 4.1 42.7 1.0
N A:ILE176 4.2 43.2 1.0
CA A:ALA58 4.2 41.8 1.0
CB A:ALA58 4.3 41.4 1.0
C A:ILE176 4.3 41.6 1.0
OD1 A:ASP177 4.4 50.6 1.0
N A:CYS175 4.4 52.2 1.0
CB A:ASP177 4.4 38.4 1.0
N A:GLU173 4.5 58.8 1.0
N A:GLY59 4.5 43.0 1.0
CA A:CYS175 4.5 50.0 1.0
CB A:GLU172 4.5 56.0 1.0
O A:GLY59 4.6 42.6 1.0
CA A:GLY59 4.7 42.0 1.0
CA A:ASP177 4.8 35.9 1.0
CA A:GLU173 4.8 59.8 1.0
C A:GLU173 4.9 64.6 1.0
C A:GLY59 4.9 44.3 1.0

Sodium binding site 2 out of 6 in 4df9

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Sodium binding site 2 out of 6 in the Crystal Structure of A Putative Peptidase (BF3526) From Bacteroides Fragilis Nctc 9343 at 2.17 A Resolution


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 Putative Peptidase (BF3526) From Bacteroides Fragilis Nctc 9343 at 2.17 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na501

b:27.7
occ:1.00
 O B:ALA58 2.2 31.0 1.0
O B:GLU172 2.2 40.0 1.0
O B:CYS175 2.3 28.6 1.0
OD2 B:ASP177 2.3 38.9 1.0
OE2 B:GLU275 2.5 22.3 1.0
O B:HOH836 2.9 47.6 1.0
CD B:GLU275 3.3 41.6 1.0
C B:GLU172 3.3 39.6 1.0
C B:ALA58 3.4 30.9 1.0
CG B:ASP177 3.5 35.8 1.0
C B:CYS175 3.5 30.2 1.0
N B:ASP177 3.8 25.8 1.0
CA B:GLU172 3.9 30.9 1.0
OE1 B:GLU275 4.0 28.7 1.0
CA B:ALA58 4.1 27.6 1.0
O B:HOH721 4.1 35.2 1.0
CA B:ILE176 4.1 24.7 1.0
CG B:GLU275 4.1 29.5 1.0
CB B:ALA58 4.2 27.3 1.0
N B:ILE176 4.2 26.1 1.0
CB B:ASP177 4.2 26.4 1.0
C B:ILE176 4.3 26.9 1.0
OD1 B:ASP177 4.3 34.3 1.0
CB B:GLU172 4.4 30.8 1.0
N B:GLU173 4.4 40.1 1.0
N B:GLY59 4.5 26.8 1.0
N B:CYS175 4.5 32.3 1.0
CA B:CYS175 4.6 31.3 1.0
CA B:ASP177 4.6 24.9 1.0
O B:GLY59 4.7 33.0 1.0
CA B:GLY59 4.8 25.8 1.0
CA B:GLU173 4.8 40.7 1.0
C B:GLU173 4.9 44.6 1.0
C B:GLY59 5.0 33.0 1.0

Sodium binding site 3 out of 6 in 4df9

Go back to Sodium Binding Sites List in 4df9
Sodium binding site 3 out of 6 in the Crystal Structure of A Putative Peptidase (BF3526) From Bacteroides Fragilis Nctc 9343 at 2.17 A Resolution


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 Putative Peptidase (BF3526) From Bacteroides Fragilis Nctc 9343 at 2.17 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na501

b:27.3
occ:1.00
 O C:CYS175 2.2 31.3 1.0
O C:ALA58 2.2 24.9 1.0
O C:GLU172 2.3 41.7 1.0
OE2 C:GLU275 2.4 35.3 1.0
OD2 C:ASP177 2.5 28.9 1.0
O C:HOH670 2.5 33.4 1.0
CD C:GLU275 3.2 45.9 1.0
C C:ALA58 3.4 27.0 1.0
C C:CYS175 3.4 30.7 1.0
C C:GLU172 3.4 40.7 1.0
CG C:ASP177 3.6 32.1 1.0
N C:ASP177 3.8 22.7 1.0
O C:HOH649 3.8 29.7 1.0
OE1 C:GLU275 4.0 28.6 1.0
CA C:GLU172 4.0 33.3 1.0
CA C:ALA58 4.1 22.8 1.0
CG C:GLU275 4.1 23.8 1.0
CA C:ILE176 4.1 24.8 1.0
CB C:ASP177 4.2 23.5 1.0
CB C:ALA58 4.2 22.0 1.0
N C:ILE176 4.2 26.4 1.0
C C:ILE176 4.3 25.5 1.0
N C:CYS175 4.4 30.8 1.0
N C:GLY59 4.5 26.0 1.0
CA C:CYS175 4.5 28.2 1.0
CB C:GLU172 4.5 34.3 1.0
N C:GLU173 4.5 38.0 1.0
OD1 C:ASP177 4.6 31.8 1.0
CA C:ASP177 4.6 21.7 1.0
O C:GLY59 4.7 28.6 1.0
CA C:GLY59 4.7 25.2 1.0
CA C:GLU173 4.9 38.9 1.0
C C:GLU173 4.9 44.5 1.0
C C:GLY59 5.0 30.4 1.0

Sodium binding site 4 out of 6 in 4df9

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Sodium binding site 4 out of 6 in the Crystal Structure of A Putative Peptidase (BF3526) From Bacteroides Fragilis Nctc 9343 at 2.17 A Resolution


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 Putative Peptidase (BF3526) From Bacteroides Fragilis Nctc 9343 at 2.17 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na501

b:25.8
occ:1.00
 O D:ALA58 2.2 25.6 1.0
O D:CYS175 2.3 25.3 1.0
O D:GLU172 2.3 35.4 1.0
OD2 D:ASP177 2.3 29.2 1.0
OE2 D:GLU275 2.4 30.5 1.0
O D:HOH746 2.6 40.1 1.0
CD D:GLU275 3.3 35.2 1.0
C D:GLU172 3.3 37.3 1.0
C D:ALA58 3.4 25.0 1.0
C D:CYS175 3.5 29.5 1.0
CG D:ASP177 3.5 28.1 1.0
N D:ASP177 3.8 22.1 1.0
O D:HOH701 3.8 36.8 1.0
CA D:GLU172 3.9 35.4 1.0
OE1 D:GLU275 4.0 28.9 1.0
CA D:ALA58 4.1 20.1 1.0
CA D:ILE176 4.1 22.7 1.0
CG D:GLU275 4.1 27.8 1.0
CB D:ALA58 4.2 20.4 1.0
N D:ILE176 4.2 24.3 1.0
CB D:ASP177 4.2 22.7 1.0
C D:ILE176 4.3 25.1 1.0
CB D:GLU172 4.4 37.0 1.0
OD1 D:ASP177 4.4 30.9 1.0
N D:GLY59 4.4 23.1 1.0
N D:GLU173 4.5 33.0 1.0
N D:CYS175 4.5 30.3 1.0
CA D:CYS175 4.6 28.1 1.0
CA D:ASP177 4.6 21.3 1.0
O D:GLY59 4.7 26.2 1.0
CA D:GLY59 4.7 21.5 1.0
CA D:GLU173 4.9 33.4 1.0
C D:GLY59 5.0 26.4 1.0

Sodium binding site 5 out of 6 in 4df9

Go back to Sodium Binding Sites List in 4df9
Sodium binding site 5 out of 6 in the Crystal Structure of A Putative Peptidase (BF3526) From Bacteroides Fragilis Nctc 9343 at 2.17 A Resolution


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 A Putative Peptidase (BF3526) From Bacteroides Fragilis Nctc 9343 at 2.17 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Na501

b:41.9
occ:1.00
 O E:CYS175 2.2 42.9 1.0
O E:GLU172 2.2 53.8 1.0
OD2 E:ASP177 2.3 45.0 1.0
O E:ALA58 2.4 38.0 1.0
OE2 E:GLU275 2.4 43.3 1.0
CD E:GLU275 3.3 57.3 1.0
C E:GLU172 3.3 54.3 1.0
C E:CYS175 3.4 44.7 1.0
CG E:ASP177 3.5 41.2 1.0
C E:ALA58 3.5 39.8 1.0
O E:HOH694 3.8 41.4 1.0
N E:ASP177 3.8 35.3 1.0
CA E:GLU172 3.9 49.3 1.0
OE1 E:GLU275 4.0 40.1 1.0
CA E:ILE176 4.1 37.0 1.0
N E:ILE176 4.2 39.0 1.0
CG E:GLU275 4.2 40.0 1.0
CA E:ALA58 4.2 37.4 1.0
CB E:ASP177 4.3 36.2 1.0
C E:ILE176 4.3 39.3 1.0
CB E:ALA58 4.3 37.3 1.0
OD1 E:ASP177 4.4 40.3 1.0
N E:CYS175 4.4 47.4 1.0
N E:GLU173 4.4 52.2 1.0
CB E:GLU172 4.5 49.9 1.0
CA E:CYS175 4.5 45.0 1.0
N E:GLY59 4.6 37.0 1.0
CA E:ASP177 4.7 34.9 1.0
O E:GLY59 4.7 42.4 1.0
CA E:GLU173 4.8 52.2 1.0
CA E:GLY59 4.8 37.0 1.0
C E:GLU173 4.9 56.0 1.0
C E:GLY59 5.0 42.2 1.0

Sodium binding site 6 out of 6 in 4df9

Go back to Sodium Binding Sites List in 4df9
Sodium binding site 6 out of 6 in the Crystal Structure of A Putative Peptidase (BF3526) From Bacteroides Fragilis Nctc 9343 at 2.17 A Resolution


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 A Putative Peptidase (BF3526) From Bacteroides Fragilis Nctc 9343 at 2.17 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Na501

b:30.0
occ:1.00
 O F:CYS175 2.2 30.8 1.0
O F:GLU172 2.2 37.4 1.0
OD2 F:ASP177 2.3 37.0 1.0
O F:ALA58 2.3 33.1 1.0
OE2 F:GLU275 2.4 39.0 1.0
CD F:GLU275 3.3 50.1 1.0
C F:GLU172 3.3 39.4 1.0
C F:CYS175 3.4 33.7 1.0
CG F:ASP177 3.4 33.9 1.0
C F:ALA58 3.5 34.1 1.0
N F:ASP177 3.8 26.7 1.0
CA F:GLU172 3.9 36.4 1.0
OE1 F:GLU275 4.0 40.8 1.0
O F:HOH718 4.0 38.4 1.0
CA F:ILE176 4.1 27.3 1.0
CG F:GLU275 4.2 31.4 1.0
N F:ILE176 4.2 28.8 1.0
CA F:ALA58 4.2 31.6 1.0
CB F:ASP177 4.2 27.4 1.0
OD1 F:ASP177 4.3 34.1 1.0
C F:ILE176 4.3 28.6 1.0
CB F:ALA58 4.3 31.4 1.0
CB F:GLU172 4.4 37.4 1.0
N F:GLU173 4.4 37.8 1.0
N F:CYS175 4.4 35.1 1.0
CA F:CYS175 4.5 32.6 1.0
N F:GLY59 4.6 31.0 1.0
CA F:ASP177 4.6 26.2 1.0
O F:GLY59 4.8 35.1 1.0
CA F:GLU173 4.8 38.3 1.0
CA F:GLY59 4.8 29.9 1.0
C F:GLU173 4.9 42.5 1.0

Reference:

Joint Center For Structural Genomics (Jcsg), Joint Center For Structural Genomics (Jcsg). N/A N/A.
Page generated: Mon Oct 7 14:56:21 2024

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