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Sodium in PDB 5hbb: Crystal Structure of Shaft Pilin Spaa From Lactobacillus Rhamnosus Gg - E139A Mutant

Protein crystallography data

The structure of Crystal Structure of Shaft Pilin Spaa From Lactobacillus Rhamnosus Gg - E139A Mutant, PDB code: 5hbb was solved by P.Chaurasia, S.Pratap, I.Von Ossowski, A.Palva, V.Krishnan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 111.80 / 2.47
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 223.950, 63.488, 104.453, 90.00, 94.99, 90.00
R / Rfree (%) 20 / 21.7

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 Shaft Pilin Spaa From Lactobacillus Rhamnosus Gg - E139A Mutant (pdb code 5hbb). 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 Shaft Pilin Spaa From Lactobacillus Rhamnosus Gg - E139A Mutant, PDB code: 5hbb:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Sodium binding site 1 out of 17 in 5hbb

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Sodium binding site 1 out of 17 in the Crystal Structure of Shaft Pilin Spaa From Lactobacillus Rhamnosus Gg - E139A Mutant


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 Spaa From Lactobacillus Rhamnosus Gg - E139A Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na402

b:7.9
occ:1.00
O B:GLY223 2.6 8.7 1.0
O B:GLY221 2.8 10.9 1.0
N B:THR246 3.1 10.9 1.0
N B:GLY223 3.3 9.9 1.0
C B:GLU222 3.4 10.4 1.0
O B:THR246 3.5 10.4 1.0
CA B:PHE245 3.6 11.1 1.0
C B:GLY223 3.6 8.9 1.0
CA B:GLU222 3.7 11.2 1.0
CD1 B:ILE225 3.8 9.0 1.0
C B:PHE245 3.8 11.3 1.0
CB B:PHE245 3.8 10.4 1.0
C B:GLY221 3.9 11.7 1.0
CG1 B:ILE225 3.9 8.6 1.0
O B:GLU222 4.0 10.4 1.0
CD2 B:PHE245 4.0 9.7 1.0
CA B:GLY223 4.0 9.5 1.0
O B:HOH518 4.1 2.0 1.0
CA B:THR246 4.1 11.4 1.0
C B:THR246 4.1 10.9 1.0
CB B:PHE253 4.2 9.3 1.0
N B:GLU222 4.2 11.9 1.0
CG B:PHE245 4.4 10.4 1.0
CG2 B:ILE220 4.5 10.8 1.0
CB B:THR246 4.6 12.3 1.0
N B:PHE224 4.9 8.8 1.0
CA B:PHE253 4.9 9.1 1.0
O B:VAL244 5.0 12.8 1.0
N B:PHE245 5.0 12.3 1.0
O B:PHE245 5.0 12.0 1.0

Sodium binding site 2 out of 17 in 5hbb

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Sodium binding site 2 out of 17 in the Crystal Structure of Shaft Pilin Spaa From Lactobacillus Rhamnosus Gg - E139A Mutant


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 Spaa From Lactobacillus Rhamnosus Gg - E139A Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na403

b:11.6
occ:1.00
O B:GLY75 2.6 14.3 1.0
O B:ASN141 3.1 13.4 1.0
NH2 B:ARG233 3.1 16.0 1.0
ND2 B:ASN231 3.2 15.0 1.0
O B:PRO142 3.3 14.9 1.0
C B:GLY75 3.6 14.0 1.0
C B:PRO142 3.6 14.1 1.0
OD1 B:ASN231 3.7 13.8 1.0
N B:ARG143 3.8 13.8 1.0
ND2 B:ASN141 3.8 16.8 1.0
CG B:ASN141 3.9 16.1 1.0
CG B:ASN231 3.9 13.9 1.0
C B:ASN141 4.0 13.8 1.0
CA B:ARG143 4.0 14.3 1.0
CB B:LYS213 4.0 18.7 1.0
OD1 B:ASN141 4.0 16.4 1.0
CA B:VAL76 4.1 12.6 1.0
CE B:LYS213 4.1 29.6 1.0
CD B:LYS213 4.2 22.6 1.0
N B:VAL76 4.2 13.2 1.0
CZ B:ARG233 4.4 15.2 1.0
CB B:ASN141 4.5 15.1 1.0
CA B:PRO142 4.5 13.5 1.0
CA B:GLY75 4.6 14.8 1.0
N B:PRO142 4.6 13.9 1.0
NZ B:LYS213 4.7 27.0 1.0
CG B:LYS213 4.7 20.5 1.0
NH1 B:ARG233 4.8 14.0 1.0
N B:ASP77 4.8 12.6 1.0
CA B:ASN141 4.9 14.4 1.0
C B:ARG143 4.9 15.3 1.0
CG2 B:VAL76 4.9 12.4 1.0
C B:VAL76 5.0 12.4 1.0

Sodium binding site 3 out of 17 in 5hbb

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Sodium binding site 3 out of 17 in the Crystal Structure of Shaft Pilin Spaa From Lactobacillus Rhamnosus Gg - E139A Mutant


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 Spaa From Lactobacillus Rhamnosus Gg - E139A Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na404

b:19.3
occ:1.00
OD1 B:ASN86 2.4 16.1 1.0
O B:HOH525 2.6 2.0 1.0
CA B:ALA101 3.4 16.6 1.0
CB B:ALA85 3.5 17.2 1.0
CG B:ASN86 3.6 16.3 1.0
O B:ASN82 3.7 13.9 1.0
CB B:ALA101 3.7 15.1 1.0
N B:ASN86 3.8 15.9 1.0
CD B:PRO102 3.9 17.0 1.0
O B:SER100 4.0 19.9 1.0
N B:ALA101 4.0 17.8 1.0
N B:ALA85 4.2 15.2 1.0
CA B:ALA85 4.2 16.3 1.0
C B:SER100 4.2 19.4 1.0
C B:ALA85 4.4 16.4 1.0
CA B:VAL83 4.4 12.9 1.0
ND2 B:ASN86 4.5 17.2 1.0
O B:ASP99 4.5 19.0 1.0
CB B:ASN86 4.5 15.9 1.0
C B:ALA101 4.6 16.8 1.0
C B:VAL83 4.7 13.2 1.0
CA B:ASN86 4.7 16.4 1.0
N B:PRO102 4.7 17.0 1.0
C B:ASN82 4.7 13.0 1.0
N B:THR84 5.0 13.3 1.0

Sodium binding site 4 out of 17 in 5hbb

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Sodium binding site 4 out of 17 in the Crystal Structure of Shaft Pilin Spaa From Lactobacillus Rhamnosus Gg - E139A Mutant


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 Spaa From Lactobacillus Rhamnosus Gg - E139A Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na405

b:21.6
occ:1.00
OG1 B:THR140 2.8 14.0 1.0
O B:HOH583 2.9 16.5 1.0
OG1 B:THR79 3.0 13.8 1.0
O B:PHE78 3.3 12.3 1.0
C B:PHE78 3.5 11.7 1.0
N B:THR79 3.7 11.7 1.0
CG2 B:THR140 3.7 13.9 1.0
CB B:THR140 3.8 14.2 1.0
CB B:ASP77 3.9 13.7 1.0
N B:PHE78 3.9 11.8 1.0
O B:HOH566 4.1 12.1 1.0
CB B:THR79 4.2 12.9 1.0
CA B:PHE78 4.2 11.3 1.0
CB B:THR106 4.2 15.8 1.0
CA B:THR79 4.2 12.1 1.0
CG2 B:THR106 4.2 16.0 1.0
C B:ASP77 4.2 12.0 1.0
CA B:ASP77 4.6 12.7 1.0
O B:ASP77 4.7 11.8 1.0
O B:GLY107 4.7 13.4 1.0
CG B:ASP77 4.8 22.0 1.0
N B:GLY107 4.9 14.2 1.0
CA B:THR106 4.9 14.7 1.0

Sodium binding site 5 out of 17 in 5hbb

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Sodium binding site 5 out of 17 in the Crystal Structure of Shaft Pilin Spaa From Lactobacillus Rhamnosus Gg - E139A Mutant


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 Spaa From Lactobacillus Rhamnosus Gg - E139A Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na406

b:21.1
occ:1.00
O B:SER149 2.5 13.4 1.0
OD1 B:ASP151 2.6 12.5 1.0
N B:ALA139 3.2 11.2 1.0
O B:HOH580 3.5 11.7 1.0
N B:ASP151 3.5 13.2 1.0
C B:SER149 3.5 13.5 1.0
CG B:ASP151 3.7 14.7 1.0
C B:ALA150 3.7 13.2 1.0
ND1 B:HIS138 3.8 13.1 1.0
CB B:ALA139 3.8 11.5 1.0
CA B:ASP151 3.9 12.5 1.0
CA B:HIS138 4.0 11.0 1.0
OG1 B:THR148 4.0 27.1 1.0
O B:ALA139 4.0 12.9 1.0
CA B:ALA139 4.0 11.4 1.0
C B:HIS138 4.0 11.1 1.0
O B:ALA150 4.1 12.5 1.0
CA B:ALA150 4.3 14.3 1.0
N B:ALA150 4.3 14.0 1.0
CE1 B:HIS138 4.4 14.1 1.0
O B:PHE137 4.4 10.6 1.0
CA B:SER149 4.4 13.2 1.0
CB B:ASP151 4.4 13.0 1.0
C B:ALA139 4.5 12.3 1.0
N B:SER149 4.5 13.3 1.0
CG B:HIS138 4.5 12.6 1.0
CB B:SER149 4.5 12.2 1.0
OD2 B:ASP151 4.6 18.4 1.0
CB B:HIS138 4.8 11.7 1.0
N B:HIS138 5.0 10.5 1.0

Sodium binding site 6 out of 17 in 5hbb

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Sodium binding site 6 out of 17 in the Crystal Structure of Shaft Pilin Spaa From Lactobacillus Rhamnosus Gg - E139A Mutant


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 Spaa From Lactobacillus Rhamnosus Gg - E139A Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na408

b:39.1
occ:1.00
O B:THR130 2.7 19.5 1.0
OG1 A:THR189 2.9 21.7 1.0
NZ B:LYS129 3.2 56.5 1.0
OD2 A:ASP186 3.3 20.8 1.0
CB A:ASP186 3.7 19.6 1.0
CB A:GLU191 3.8 25.5 1.0
C B:THR130 3.9 19.1 1.0
CG A:ASP186 3.9 20.5 1.0
CB A:THR189 4.0 23.0 1.0
CG2 A:THR189 4.1 23.4 1.0
OH A:TYR276 4.1 20.1 1.0
OE1 A:GLU191 4.3 60.7 1.0
CD B:ARG131 4.4 17.9 1.0
O A:GLU191 4.5 18.6 1.0
NH1 B:ARG131 4.5 19.9 1.0
CG B:LYS129 4.5 37.0 1.0
CE B:LYS129 4.5 0.3 1.0
CA A:GLU191 4.6 20.4 1.0
CA B:ARG131 4.7 17.3 1.0
C A:GLU191 4.7 19.0 1.0
N B:ARG131 4.7 18.0 1.0
O A:HOH514 4.7 2.0 1.0
O A:VAL192 4.7 18.1 1.0
CG A:GLU191 4.7 34.1 1.0
CA B:THR130 4.8 20.0 1.0
N A:GLU191 4.8 20.8 1.0
CD B:LYS129 4.8 52.2 1.0
CD1 A:LEU193 4.9 18.1 1.0
NE B:ARG131 4.9 18.6 1.0
CD A:GLU191 4.9 63.0 1.0
CB B:THR130 4.9 21.1 1.0
N B:THR130 4.9 20.8 1.0
CZ B:ARG131 5.0 19.5 1.0
OD1 A:ASP186 5.0 21.1 1.0

Sodium binding site 7 out of 17 in 5hbb

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Sodium binding site 7 out of 17 in the Crystal Structure of Shaft Pilin Spaa From Lactobacillus Rhamnosus Gg - E139A Mutant


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 Shaft Pilin Spaa From Lactobacillus Rhamnosus Gg - E139A Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na402

b:19.5
occ:1.00
O A:GLY221 2.7 17.7 1.0
O A:GLY223 2.7 13.8 1.0
N A:THR246 3.2 16.0 1.0
N A:GLY223 3.3 14.7 1.0
C A:GLU222 3.4 15.4 1.0
O A:THR246 3.6 15.0 1.0
CA A:PHE245 3.6 16.7 1.0
CD1 A:ILE225 3.7 15.1 1.0
CA A:GLU222 3.7 21.8 1.0
C A:GLY223 3.7 13.8 1.0
C A:GLY221 3.8 19.3 1.0
CG1 A:ILE225 3.8 14.8 1.0
C A:PHE245 3.9 16.4 1.0
CB A:PHE245 3.9 16.1 1.0
O A:GLU222 4.0 15.6 1.0
CD2 A:PHE245 4.0 15.9 1.0
O A:HOH521 4.0 4.2 1.0
CA A:GLY223 4.1 14.2 1.0
CA A:THR246 4.2 16.0 1.0
N A:GLU222 4.2 19.6 1.0
C A:THR246 4.3 15.2 1.0
CG2 A:ILE220 4.3 25.8 1.0
CG A:PHE245 4.4 16.5 1.0
CB A:PHE253 4.4 13.9 1.0
CB A:THR246 4.7 16.9 1.0
O A:VAL244 4.8 18.9 1.0
N A:PHE245 4.9 18.0 1.0
N A:PHE224 4.9 13.5 1.0

Sodium binding site 8 out of 17 in 5hbb

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Sodium binding site 8 out of 17 in the Crystal Structure of Shaft Pilin Spaa From Lactobacillus Rhamnosus Gg - E139A Mutant


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 Shaft Pilin Spaa From Lactobacillus Rhamnosus Gg - E139A Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na403

b:24.7
occ:1.00
O A:GLY75 2.5 19.6 1.0
O A:ASN141 3.0 18.7 1.0
ND2 A:ASN231 3.2 21.0 1.0
NH2 A:ARG233 3.3 23.0 1.0
O A:PRO142 3.4 20.4 1.0
C A:GLY75 3.5 18.9 1.0
C A:PRO142 3.6 19.0 1.0
ND2 A:ASN141 3.8 23.7 1.0
CG A:ASN141 3.8 22.7 1.0
N A:ARG143 3.8 18.2 1.0
C A:ASN141 3.9 19.2 1.0
OD1 A:ASN231 3.9 19.8 1.0
CA A:VAL76 4.0 16.9 1.0
CG A:ASN231 4.0 20.0 1.0
CA A:ARG143 4.0 18.9 1.0
OD1 A:ASN141 4.0 23.1 1.0
CE A:LYS213 4.1 27.7 1.0
CB A:LYS213 4.1 24.9 1.0
N A:VAL76 4.1 17.6 1.0
CD A:LYS213 4.2 26.1 1.0
CB A:ASN141 4.3 21.2 1.0
CA A:PRO142 4.5 18.3 1.0
N A:PRO142 4.5 19.1 1.0
CZ A:ARG233 4.5 22.4 1.0
CA A:GLY75 4.6 19.7 1.0
NZ A:LYS213 4.6 29.8 1.0
N A:ASP77 4.7 17.3 1.0
CA A:ASN141 4.8 20.2 1.0
CG A:LYS213 4.8 26.9 1.0
C A:VAL76 4.8 16.8 1.0
CG2 A:VAL76 4.9 16.1 1.0
CB A:VAL76 5.0 15.8 1.0
C A:ARG143 5.0 19.9 1.0
NH1 A:ARG233 5.0 20.9 1.0

Sodium binding site 9 out of 17 in 5hbb

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Sodium binding site 9 out of 17 in the Crystal Structure of Shaft Pilin Spaa From Lactobacillus Rhamnosus Gg - E139A Mutant


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 Shaft Pilin Spaa From Lactobacillus Rhamnosus Gg - E139A Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na404

b:15.6
occ:1.00
O A:HOH559 2.8 7.3 1.0
OG1 A:THR140 3.0 19.3 1.0
OG1 A:THR79 3.1 18.1 1.0
O A:PHE78 3.3 16.1 1.0
C A:PHE78 3.5 15.6 1.0
N A:THR79 3.8 15.6 1.0
N A:PHE78 3.9 15.9 1.0
CB A:ASP77 3.9 22.6 1.0
CG2 A:THR140 4.0 19.0 1.0
O A:HOH579 4.0 12.9 1.0
CB A:THR106 4.0 19.1 1.0
CB A:THR140 4.0 19.6 1.0
CG2 A:THR106 4.1 19.4 1.0
CA A:PHE78 4.2 15.2 1.0
C A:ASP77 4.2 16.4 1.0
CB A:THR79 4.2 16.9 1.0
CA A:THR79 4.2 15.8 1.0
O A:GLY107 4.5 18.8 1.0
CA A:ASP77 4.5 17.4 1.0
CG A:ASP77 4.7 40.0 1.0
N A:GLY107 4.7 17.6 1.0
O A:ASP77 4.7 16.3 1.0
CA A:THR106 4.8 17.7 1.0

Sodium binding site 10 out of 17 in 5hbb

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Sodium binding site 10 out of 17 in the Crystal Structure of Shaft Pilin Spaa From Lactobacillus Rhamnosus Gg - E139A Mutant


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 Shaft Pilin Spaa From Lactobacillus Rhamnosus Gg - E139A Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na405

b:26.1
occ:1.00
O A:SER149 2.6 16.0 1.0
OD1 A:ASP151 2.7 23.1 1.0
N A:ALA139 3.1 15.0 1.0
O A:HOH545 3.3 5.4 1.0
N A:ASP151 3.5 15.4 1.0
C A:SER149 3.5 15.4 1.0
C A:ALA150 3.7 14.9 1.0
CB A:ALA139 3.7 15.3 1.0
CG A:ASP151 3.8 16.4 1.0
ND1 A:HIS138 3.8 17.4 1.0
CA A:ASP151 3.9 14.9 1.0
CA A:ALA139 3.9 15.5 1.0
CA A:HIS138 3.9 14.7 1.0
O A:ALA139 3.9 17.6 1.0
OG1 A:THR148 4.0 17.9 1.0
C A:HIS138 4.0 15.0 1.0
O A:ALA150 4.0 14.1 1.0
CA A:ALA150 4.3 15.7 1.0
O A:PHE137 4.3 13.4 1.0
N A:ALA150 4.3 15.3 1.0
O A:HOH526 4.4 18.5 1.0
CA A:SER149 4.4 15.1 1.0
C A:ALA139 4.4 16.9 1.0
CB A:ASP151 4.4 15.8 1.0
CE1 A:HIS138 4.4 18.8 1.0
CB A:SER149 4.5 14.1 1.0
N A:SER149 4.5 15.8 1.0
CG A:HIS138 4.5 16.9 1.0
OD2 A:ASP151 4.7 17.4 1.0
CB A:HIS138 4.8 15.7 1.0
N A:HIS138 4.9 13.8 1.0

Reference:

P.Chaurasia, S.Pratap, I.Von Ossowski, A.Palva, V.Krishnan. New Insights About Pilus Formation in Gut-Adapted Lactobacillus Rhamnosus Gg From the Crystal Structure of the Spaa Backbone-Pilin Subunit Sci Rep V. 6 28664 2016.
ISSN: ESSN 2045-2322
PubMed: 27349405
DOI: 10.1038/SREP28664
Page generated: Tue Dec 15 11:02:48 2020

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