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Sodium in PDB 9lr7: Crystal Structure of the Basal Pilin Ebpb From Enterococcus Faecalis.

Protein crystallography data

The structure of Crystal Structure of the Basal Pilin Ebpb From Enterococcus Faecalis., PDB code: 9lr7 was solved by V.Sharma, V.Krishnan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 77.15 / 2.43
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 87.307, 158.415, 88.221, 90, 92.09, 90
R / Rfree (%) 21.9 / 25.5

Sodium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 15;

Binding sites:

The binding sites of Sodium atom in the Crystal Structure of the Basal Pilin Ebpb From Enterococcus Faecalis. (pdb code 9lr7). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 15 binding sites of Sodium where determined in the Crystal Structure of the Basal Pilin Ebpb From Enterococcus Faecalis., PDB code: 9lr7:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Sodium binding site 1 out of 15 in 9lr7

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Sodium binding site 1 out of 15 in the Crystal Structure of the Basal Pilin Ebpb From Enterococcus Faecalis.


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 the Basal Pilin Ebpb From Enterococcus Faecalis. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na501

b:32.1
occ:1.00
 OH B:TYR222 2.4 27.5 1.0
O B:ASP186 2.5 38.5 1.0
OD1 B:ASN218 2.5 27.6 1.0
CG B:ASN218 3.3 25.9 1.0
ND2 B:ASN218 3.4 26.8 1.0
CB B:PRO216 3.5 24.5 1.0
CZ B:TYR222 3.5 26.2 1.0
C B:ASP186 3.5 38.1 1.0
CE1 B:TYR222 3.7 25.7 1.0
CB B:TYR185 3.7 31.6 1.0
O B:TYR185 4.1 34.2 1.0
CG B:PRO216 4.1 24.4 1.0
C B:TYR185 4.1 33.8 1.0
N B:LEU187 4.3 38.0 1.0
N B:ASP186 4.3 35.5 1.0
CA B:LEU187 4.4 36.0 1.0
CA B:TYR185 4.5 31.4 1.0
CA B:ASP186 4.6 37.2 1.0
CD B:PRO188 4.6 33.4 1.0
CB B:ASN218 4.8 26.2 1.0
CE2 B:TYR222 4.8 25.6 1.0
CG B:TYR185 4.8 31.9 1.0
C B:LEU187 4.9 34.4 1.0
CA B:PRO216 4.9 24.3 1.0
N B:PRO188 4.9 33.3 1.0

Sodium binding site 2 out of 15 in 9lr7

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Sodium binding site 2 out of 15 in the Crystal Structure of the Basal Pilin Ebpb From Enterococcus Faecalis.


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 the Basal Pilin Ebpb From Enterococcus Faecalis. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na502

b:21.3
occ:1.00
 OG1 B:THR259 2.5 20.8 1.0
O B:GLN260 2.5 20.9 1.0
O C:TYR255 2.6 19.7 1.0
CG B:PRO239 3.3 18.9 1.0
C B:GLN260 3.3 21.1 1.0
CB B:THR259 3.4 20.7 1.0
CA C:THR256 3.5 18.0 1.0
C C:TYR255 3.6 19.1 1.0
C B:THR259 3.8 21.0 1.0
N B:GLN260 3.8 21.2 1.0
CA B:GLN260 4.0 21.2 1.0
N C:THR256 4.0 18.6 1.0
CG2 C:THR256 4.0 17.8 1.0
N B:LYS261 4.1 21.2 1.0
CB C:THR256 4.1 17.8 1.0
O B:THR259 4.2 20.9 1.0
CA B:THR259 4.2 20.8 1.0
CB B:PRO239 4.3 18.9 1.0
CD B:PRO239 4.4 18.9 1.0
CA B:LYS261 4.4 21.5 1.0
CD2 B:LEU237 4.5 19.1 1.0
CG2 B:THR259 4.6 20.5 1.0
C C:THR256 4.6 17.7 1.0
N C:LEU257 4.6 17.4 1.0
O B:LEU237 4.9 19.7 1.0
CA C:TYR255 5.0 19.5 1.0

Sodium binding site 3 out of 15 in 9lr7

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Sodium binding site 3 out of 15 in the Crystal Structure of the Basal Pilin Ebpb From Enterococcus Faecalis.


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 the Basal Pilin Ebpb From Enterococcus Faecalis. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na503

b:23.4
occ:1.00
 OG B:SER324 2.5 21.7 1.0
O B:TYR416 2.5 21.0 1.0
O B:THR423 2.5 22.7 1.0
O B:HOH618 3.2 47.1 1.0
CB B:SER324 3.2 22.1 1.0
N B:THR423 3.4 22.8 1.0
C B:THR423 3.4 22.6 1.0
C B:TYR416 3.5 20.3 1.0
NE B:ARG422 3.6 26.1 1.0
CA B:THR423 3.8 22.5 1.0
CA B:TYR416 3.8 19.9 1.0
CB B:THR423 3.9 22.4 1.0
CD1 B:TYR416 3.9 19.6 1.0
CB B:ARG422 4.0 24.6 1.0
NH2 B:ARG422 4.0 24.3 1.0
C B:ARG422 4.2 23.6 1.0
N B:SER324 4.2 22.1 1.0
CE1 B:TYR416 4.3 19.4 1.0
CZ B:ARG422 4.3 24.8 1.0
O B:SER415 4.3 20.8 1.0
CG B:TYR416 4.3 19.6 1.0
CA B:SER324 4.3 22.0 1.0
CA B:ARG422 4.3 24.2 1.0
CG B:ARG422 4.3 25.1 1.0
CD B:ARG422 4.6 25.9 1.0
CB B:TYR416 4.7 19.6 1.0
N B:ALA424 4.7 22.1 1.0
N B:ALA417 4.7 20.4 1.0
OG1 B:THR423 4.8 24.6 1.0
CG2 B:THR423 4.8 22.4 1.0
N B:TYR416 4.8 20.0 1.0
CD2 B:TYR416 4.8 19.3 1.0
CZ B:TYR416 4.9 19.5 1.0
O B:ALA424 4.9 22.8 1.0
C B:ALA424 4.9 22.0 1.0
C B:SER415 5.0 20.7 1.0

Sodium binding site 4 out of 15 in 9lr7

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Sodium binding site 4 out of 15 in the Crystal Structure of the Basal Pilin Ebpb From Enterococcus Faecalis.


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 the Basal Pilin Ebpb From Enterococcus Faecalis. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na505

b:20.7
occ:1.00
 OD1 B:ASN208 2.5 16.8 1.0
O B:HOH623 2.7 19.3 1.0
O B:HOH609 2.9 20.5 1.0
CG B:ASN208 3.4 16.9 1.0
CG B:GLN286 3.7 17.3 1.0
CB B:ASN208 3.9 17.0 1.0
O B:TYR285 4.0 18.8 1.0
NE2 B:GLN286 4.1 18.1 1.0
CD B:GLN286 4.3 17.7 1.0
C B:TYR285 4.3 18.2 1.0
CB B:SER284 4.4 18.5 1.0
CA B:ASN208 4.4 17.3 1.0
N B:TYR285 4.5 18.0 1.0
ND2 B:ASN208 4.5 16.8 1.0
CA B:TYR285 4.7 17.9 1.0
N B:GLN286 4.8 17.9 1.0
O B:TYR209 4.8 18.5 1.0
C B:SER284 4.9 18.3 1.0
CB B:GLN286 5.0 17.3 1.0

Sodium binding site 5 out of 15 in 9lr7

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Sodium binding site 5 out of 15 in the Crystal Structure of the Basal Pilin Ebpb From Enterococcus Faecalis.


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 the Basal Pilin Ebpb From Enterococcus Faecalis. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na501

b:34.8
occ:1.00
 OH A:TYR222 2.4 39.2 1.0
OD1 A:ASN218 2.5 29.4 1.0
O A:ASP186 2.5 35.4 1.0
CG A:ASN218 3.3 28.4 1.0
CB A:PRO216 3.4 24.4 1.0
ND2 A:ASN218 3.4 28.9 1.0
C A:ASP186 3.5 34.3 1.0
CZ A:TYR222 3.5 36.8 1.0
CE1 A:TYR222 3.7 35.0 1.0
CB A:TYR185 3.7 33.1 1.0
O A:TYR185 4.0 39.2 1.0
CG A:PRO216 4.0 24.9 1.0
C A:TYR185 4.1 35.5 1.0
N A:LEU187 4.2 33.3 1.0
N A:ASP186 4.3 35.2 1.0
CA A:LEU187 4.4 32.8 1.0
CA A:ASP186 4.5 37.2 1.0
CA A:TYR185 4.5 34.3 1.0
CD A:PRO188 4.6 28.4 1.0
CB A:ASN218 4.8 28.7 1.0
CE2 A:TYR222 4.8 35.4 1.0
CG A:TYR185 4.8 33.0 1.0
CA A:PRO216 4.8 24.3 1.0
C A:LEU187 4.9 30.4 1.0
N A:PRO188 4.9 28.1 1.0

Sodium binding site 6 out of 15 in 9lr7

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Sodium binding site 6 out of 15 in the Crystal Structure of the Basal Pilin Ebpb From Enterococcus Faecalis.


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 the Basal Pilin Ebpb From Enterococcus Faecalis. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na502

b:21.9
occ:1.00
 O D:TYR255 2.5 21.4 1.0
O A:GLN260 2.6 18.4 1.0
OG1 A:THR259 2.7 20.1 1.0
C A:GLN260 3.2 18.0 1.0
CG A:PRO239 3.5 20.8 1.0
CA D:THR256 3.5 20.9 1.0
CB A:THR259 3.5 19.1 1.0
C D:TYR255 3.5 21.4 1.0
N A:GLN260 3.6 18.6 1.0
C A:THR259 3.7 18.7 1.0
CA A:GLN260 3.7 18.2 1.0
CG2 D:THR256 3.8 21.3 1.0
N D:THR256 3.9 21.2 1.0
N A:LYS261 3.9 17.7 1.0
O A:THR259 4.0 19.4 1.0
CB D:THR256 4.1 21.2 1.0
CA A:THR259 4.2 18.7 1.0
CA A:LYS261 4.4 17.2 1.0
CB A:PRO239 4.5 20.6 1.0
C D:THR256 4.6 20.5 1.0
CD A:PRO239 4.6 20.1 1.0
N D:LEU257 4.6 20.1 1.0
CD2 A:LEU237 4.7 19.5 1.0
CG2 A:THR259 4.8 18.8 1.0
CA D:TYR255 4.9 21.8 1.0

Sodium binding site 7 out of 15 in 9lr7

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Sodium binding site 7 out of 15 in the Crystal Structure of the Basal Pilin Ebpb From Enterococcus Faecalis.


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 the Basal Pilin Ebpb From Enterococcus Faecalis. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na503

b:26.2
occ:1.00
 OG A:SER324 2.5 21.3 1.0
O A:THR423 2.5 24.4 1.0
O A:TYR416 2.5 23.2 1.0
N A:THR423 3.3 23.1 1.0
CB A:SER324 3.3 20.9 1.0
C A:THR423 3.4 23.6 1.0
C A:TYR416 3.5 21.3 1.0
NE A:ARG422 3.5 27.6 1.0
CA A:THR423 3.7 23.3 1.0
CB A:THR423 3.8 22.7 1.0
CA A:TYR416 3.9 20.5 1.0
NH2 A:ARG422 3.9 26.3 1.0
CB A:ARG422 4.0 25.5 1.0
CD1 A:TYR416 4.0 19.5 1.0
C A:ARG422 4.1 24.3 1.0
CZ A:ARG422 4.2 27.8 1.0
CA A:ARG422 4.3 25.1 1.0
CE1 A:TYR416 4.3 19.5 1.0
N A:SER324 4.3 20.3 1.0
O A:SER415 4.3 21.3 1.0
CG A:TYR416 4.3 19.7 1.0
CA A:SER324 4.4 20.6 1.0
CG A:ARG422 4.4 26.3 1.0
CD A:ARG422 4.6 27.2 1.0
OG1 A:THR423 4.7 24.5 1.0
N A:ALA424 4.7 23.6 1.0
CB A:TYR416 4.7 20.0 1.0
N A:ALA417 4.8 21.6 1.0
CG2 A:THR423 4.8 22.7 1.0
CZ A:TYR416 4.9 20.0 1.0
CD2 A:TYR416 4.9 20.1 1.0
N A:TYR416 4.9 20.7 1.0
O A:ARG422 5.0 25.2 1.0
C A:ALA424 5.0 22.8 1.0

Sodium binding site 8 out of 15 in 9lr7

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Sodium binding site 8 out of 15 in the Crystal Structure of the Basal Pilin Ebpb From Enterococcus Faecalis.


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 the Basal Pilin Ebpb From Enterococcus Faecalis. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na504

b:23.1
occ:1.00
 OD1 A:ASN208 2.5 18.1 1.0
O A:HOH604 2.7 24.8 1.0
O A:HOH608 3.0 22.1 1.0
CG A:ASN208 3.5 17.1 1.0
CG A:GLN286 3.7 15.6 1.0
CB A:ASN208 4.0 16.7 1.0
NE2 A:GLN286 4.0 16.1 1.0
O A:TYR285 4.1 17.5 1.0
CD A:GLN286 4.2 15.8 1.0
C A:TYR285 4.4 16.9 1.0
CB A:SER284 4.4 16.4 1.0
CA A:ASN208 4.5 16.5 1.0
ND2 A:ASN208 4.5 17.0 1.0
N A:TYR285 4.6 16.9 1.0
CA A:TYR285 4.8 17.0 1.0
N A:GLN286 4.9 16.5 1.0
C A:SER284 5.0 16.7 1.0
O A:TYR209 5.0 17.3 1.0

Sodium binding site 9 out of 15 in 9lr7

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Sodium binding site 9 out of 15 in the Crystal Structure of the Basal Pilin Ebpb From Enterococcus Faecalis.


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 the Basal Pilin Ebpb From Enterococcus Faecalis. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na501

b:42.5
occ:1.00
 OH C:TYR222 2.4 39.9 1.0
O C:ASP186 2.5 43.5 1.0
OD1 C:ASN218 2.5 36.5 1.0
CG C:ASN218 3.3 36.8 1.0
ND2 C:ASN218 3.4 40.7 1.0
CB C:PRO216 3.4 33.3 1.0
CZ C:TYR222 3.5 35.5 1.0
C C:ASP186 3.6 42.3 1.0
CE1 C:TYR222 3.7 33.2 1.0
CB C:TYR185 3.7 50.6 1.0
CG C:PRO216 4.0 32.5 1.0
C C:TYR185 4.2 51.3 1.0
O C:TYR185 4.2 53.5 1.0
N C:LEU187 4.3 38.4 1.0
CA C:LEU187 4.4 36.0 1.0
N C:ASP186 4.4 48.8 1.0
CD C:PRO188 4.6 30.3 1.0
CA C:TYR185 4.6 52.0 1.0
CA C:ASP186 4.6 47.0 1.0
CG C:TYR185 4.7 51.9 1.0
CE2 C:TYR222 4.8 35.6 1.0
CB C:ASN218 4.8 36.4 1.0
C C:LEU187 4.9 31.0 1.0
CA C:PRO216 4.9 32.0 1.0
N C:PRO188 4.9 29.9 1.0

Sodium binding site 10 out of 15 in 9lr7

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Sodium binding site 10 out of 15 in the Crystal Structure of the Basal Pilin Ebpb From Enterococcus Faecalis.


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 the Basal Pilin Ebpb From Enterococcus Faecalis. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na502

b:21.2
occ:1.00
 OG1 C:THR259 2.4 20.1 1.0
O C:GLN260 2.5 20.0 1.0
O B:TYR255 2.5 20.6 1.0
CG C:PRO239 3.2 18.4 1.0
CB C:THR259 3.3 19.2 1.0
C C:GLN260 3.3 19.8 1.0
CA B:THR256 3.5 20.4 1.0
C B:TYR255 3.6 20.3 1.0
N C:GLN260 3.9 19.4 1.0
CG2 B:THR256 3.9 20.7 1.0
C C:THR259 3.9 18.9 1.0
N B:THR256 4.0 20.3 1.0
CA C:GLN260 4.0 19.6 1.0
CB B:THR256 4.1 20.7 1.0
N C:LYS261 4.2 20.0 1.0
CA C:THR259 4.2 18.8 1.0
CB C:PRO239 4.3 18.6 1.0
O C:THR259 4.3 19.1 1.0
CD C:PRO239 4.3 18.3 1.0
CD2 C:LEU237 4.4 18.4 1.0
CA C:LYS261 4.4 20.3 1.0
CG2 C:THR259 4.4 19.1 1.0
C B:THR256 4.6 20.4 1.0
N B:LEU257 4.6 20.1 1.0
O C:LEU237 4.7 19.2 1.0
CA B:TYR255 5.0 20.2 1.0

Reference:

V.Sharma, V.Krishnan. Structural Basis of Ebp Pilus Shaft Formation and Anchoring in Vancomycin-Resistant Enterococci. Febs J. 2025.
ISSN: ISSN 1742-464X
PubMed: 40608565
DOI: 10.1111/FEBS.70173
Page generated: Mon Aug 18 17:22:10 2025

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