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Sodium in PDB 8wxd: Crystal Structure of Shaft Pilin Pila From Streptococcus Sanguinis

Protein crystallography data

The structure of Crystal Structure of Shaft Pilin Pila From Streptococcus Sanguinis, PDB code: 8wxd was solved by S.Yadav, P.Parijat, V.Krishnan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 58.35 / 2.00
Space group P 2 21 21
Cell size a, b, c (Å), α, β, γ (°) 60.593, 89.949, 216.408, 90, 90, 90
R / Rfree (%) 20.9 / 25.9

Other elements in 8wxd:

The structure of Crystal Structure of Shaft Pilin Pila From Streptococcus Sanguinis also contains other interesting chemical elements:

Cadmium (Cd) 6 atoms
Chlorine (Cl) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Shaft Pilin Pila From Streptococcus Sanguinis (pdb code 8wxd). 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 Shaft Pilin Pila From Streptococcus Sanguinis, PDB code: 8wxd:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6;

Sodium binding site 1 out of 6 in 8wxd

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Sodium binding site 1 out of 6 in the Crystal Structure of Shaft Pilin Pila From Streptococcus Sanguinis


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 Shaft Pilin Pila From Streptococcus Sanguinis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na501

b:24.2
occ:0.74
 O A:HOH608 2.2 11.2 1.0
NA A:NA502 2.6 25.7 0.8
SD A:MET225 3.4 31.2 1.0
CE A:MET225 3.4 30.7 1.0
CB A:ASN297 3.4 16.8 1.0
OD1 A:ASN297 3.5 16.6 1.0
CZ A:PHE197 3.6 23.3 1.0
CD A:PRO222 3.7 16.8 1.0
CG A:ASN297 3.7 17.6 1.0
CG A:MET225 3.7 28.9 1.0
CE1 A:PHE197 4.0 23.3 1.0
CG A:PRO222 4.0 17.7 1.0
CE2 A:PHE197 4.1 23.5 1.0
CB A:MET225 4.1 26.0 1.0
N A:ASN297 4.2 16.6 1.0
O A:ASN295 4.2 17.2 1.0
CA A:ASN297 4.4 16.6 1.0
NZ A:LYS173 4.6 18.7 1.0
CG2 A:ILE221 4.7 21.6 1.0
C A:PRO296 4.7 16.0 1.0
CD1 A:ILE221 4.7 22.1 1.0
CD1 A:PHE197 4.8 23.2 1.0
CD2 A:PHE197 4.9 24.2 1.0
CB A:ALA282 5.0 27.0 1.0

Sodium binding site 2 out of 6 in 8wxd

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Sodium binding site 2 out of 6 in the Crystal Structure of Shaft Pilin Pila From Streptococcus Sanguinis


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 Shaft Pilin Pila From Streptococcus Sanguinis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na502

b:25.7
occ:0.75
 NA A:NA501 2.6 24.2 0.7
OH A:TYR280 2.8 22.7 1.0
CE2 A:PHE197 3.3 23.5 1.0
CE2 A:TYR280 3.4 25.2 1.0
CZ A:PHE197 3.4 23.3 1.0
CG A:ASN297 3.4 17.6 1.0
CD2 A:PHE197 3.4 24.2 1.0
CZ A:TYR280 3.5 24.4 1.0
CE1 A:PHE197 3.5 23.3 1.0
CG A:PHE197 3.5 24.4 1.0
NZ A:LYS173 3.6 18.7 1.0
CD1 A:PHE197 3.6 23.2 1.0
CD1 A:ILE221 3.6 22.1 1.0
OD1 A:ASN297 3.6 16.6 1.0
CB A:ASN297 3.6 16.8 1.0
O A:HOH608 4.1 11.2 1.0
CE A:LYS173 4.1 20.5 1.0
CB A:ALA282 4.3 27.0 1.0
CB A:PHE197 4.4 26.3 1.0
CD2 A:TYR280 4.7 26.7 1.0
CE1 A:TYR280 4.8 25.6 1.0
OD2 A:ASP219 4.8 20.6 1.0
CG2 A:ILE221 5.0 21.6 1.0
CG1 A:ILE221 5.0 22.3 1.0

Sodium binding site 3 out of 6 in 8wxd

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Sodium binding site 3 out of 6 in the Crystal Structure of Shaft Pilin Pila From Streptococcus Sanguinis


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 Shaft Pilin Pila From Streptococcus Sanguinis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na503

b:24.2
occ:0.96
 O A:HOH606 2.6 19.4 1.0
O A:SER304 2.9 18.5 1.0
OH A:TYR213 3.0 19.4 1.0
CE1 A:TYR213 3.5 20.4 1.0
CG A:PRO204 3.6 28.5 1.0
CD A:PRO169 3.6 26.6 1.0
CZ A:TYR213 3.7 20.3 1.0
CD1 A:TYR303 3.7 17.8 1.0
O A:ASP167 3.8 27.4 1.0
CZ A:PHE210 3.8 20.6 1.0
CB A:PRO204 3.9 29.1 1.0
CE1 A:TYR303 4.1 18.1 1.0
C A:SER304 4.1 19.1 1.0
CE1 A:PHE210 4.2 21.3 1.0
CA A:ASN305 4.4 21.0 1.0
CB A:ALA148 4.4 26.1 1.0
CD A:PRO204 4.5 28.4 1.0
CA A:VAL168 4.5 26.6 1.0
CG A:PRO169 4.6 25.4 1.0
CE2 A:PHE210 4.6 20.2 1.0
N A:PRO169 4.6 26.5 1.0
C A:ASP167 4.7 29.8 1.0
CG A:TYR303 4.7 18.3 1.0
N A:ASN305 4.7 19.5 1.0
CD1 A:TYR213 4.8 20.8 1.0
C A:VAL168 4.9 26.8 1.0
OD1 A:ASN206 5.0 24.3 1.0
CB A:TYR303 5.0 18.6 1.0

Sodium binding site 4 out of 6 in 8wxd

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Sodium binding site 4 out of 6 in the Crystal Structure of Shaft Pilin Pila From Streptococcus Sanguinis


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 Shaft Pilin Pila From Streptococcus Sanguinis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na504

b:23.9
occ:1.00
 CD A:CD507 2.4 25.4 0.8
OE1 A:GLU102 2.9 35.4 1.0
NE2 A:HIS75 3.8 39.9 1.0
CD A:GLU102 3.9 33.9 1.0
NZ A:LYS82 4.0 22.1 1.0
OE2 A:GLU102 4.1 40.2 1.0
CE1 A:PHE76 4.2 25.4 1.0
CD1 A:PHE76 4.3 25.3 1.0
CD2 A:HIS75 4.5 36.8 1.0
CE1 A:HIS75 4.8 38.7 1.0

Sodium binding site 5 out of 6 in 8wxd

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Sodium binding site 5 out of 6 in the Crystal Structure of Shaft Pilin Pila From Streptococcus Sanguinis


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 Shaft Pilin Pila From Streptococcus Sanguinis within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na501

b:23.8
occ:0.78
 OD2 B:ASP136 2.4 25.8 1.0
OH B:TYR43 2.8 24.3 1.0
O B:ALA148 2.8 22.6 1.0
CG B:ASP136 3.2 26.0 1.0
OD1 B:ASP136 3.3 28.6 1.0
ND1 B:HIS41 3.3 32.7 1.0
CB B:ALA166 3.3 35.0 1.0
N B:THR150 3.3 21.2 1.0
CE1 B:TYR43 3.5 26.5 1.0
CZ B:TYR43 3.5 25.8 1.0
CE1 B:HIS41 3.5 35.7 1.0
CB B:THR150 3.8 20.5 1.0
C B:TYR149 3.8 21.1 1.0
C B:ALA148 3.9 22.5 1.0
CA B:THR150 4.0 20.3 1.0
CA B:TYR149 4.0 22.2 1.0
CG2 B:THR150 4.3 21.0 1.0
N B:TYR149 4.4 22.1 1.0
CG B:HIS41 4.5 34.8 1.0
CG2 B:VAL164 4.5 29.0 1.0
O B:TYR149 4.6 20.3 1.0
CB B:ASP136 4.6 25.1 1.0
NE2 B:HIS41 4.7 37.2 1.0
CD1 B:TYR43 4.8 26.6 1.0
CA B:ALA166 4.8 34.4 1.0
CE2 B:TYR43 4.8 26.9 1.0
O B:HOH617 4.9 13.1 1.0
CD1 B:LEU141 4.9 36.8 1.0
OG1 B:THR150 5.0 20.1 1.0

Sodium binding site 6 out of 6 in 8wxd

Go back to Sodium Binding Sites List in 8wxd
Sodium binding site 6 out of 6 in the Crystal Structure of Shaft Pilin Pila From Streptococcus Sanguinis


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 Shaft Pilin Pila From Streptococcus Sanguinis within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na502

b:24.1
occ:1.00
 O B:SER304 2.5 18.0 1.0
O B:HOH603 2.9 15.3 1.0
OH B:TYR213 2.9 17.1 1.0
CD2 B:TYR303 3.3 17.4 1.0
CD B:PRO169 3.5 21.8 1.0
C B:SER304 3.7 18.3 1.0
CE1 B:TYR213 3.7 18.1 1.0
CZ B:TYR213 3.7 17.5 1.0
CZ B:PHE210 3.7 20.4 1.0
CE2 B:TYR303 3.8 18.1 1.0
CA B:ASN305 3.9 20.3 1.0
CG B:PRO204 3.9 23.7 1.0
O B:ASP167 4.1 27.1 1.0
CE1 B:PHE210 4.2 20.6 1.0
N B:ASN305 4.3 19.1 1.0
CB B:PRO204 4.3 24.6 1.0
CG B:TYR303 4.3 17.1 1.0
CG B:PRO169 4.4 21.1 1.0
CE2 B:PHE210 4.4 20.6 1.0
C B:ASN305 4.6 21.8 1.0
CB B:TYR303 4.7 17.0 1.0
N B:PRO169 4.7 22.3 1.0
CB B:ALA148 4.7 21.9 1.0
CA B:VAL168 4.7 25.4 1.0
CD B:PRO204 4.7 23.7 1.0
CB B:ASN305 4.8 20.1 1.0
CA B:SER304 4.9 18.0 1.0
N B:SER304 4.9 17.5 1.0
CD1 B:TYR213 5.0 18.4 1.0

Reference:

S.Yadav, P.Parijat, V.Krishnan. Crystal Structure of Shaft Pilin Pila From Streptococcus Sanguinis To Be Published.
Page generated: Mon Aug 18 16:20:48 2025

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