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Sodium in PDB 6jch: Crystal Structure of Spae Basal Pilin From Lactobacillus Rhamnosus Gg - Orthorhombic Form

Protein crystallography data

The structure of Crystal Structure of Spae Basal Pilin From Lactobacillus Rhamnosus Gg - Orthorhombic Form, PDB code: 6jch was solved by A.K.Megta, A.K.Mishra, A.Palva, I.Von Ossowski, V.Krishnan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 23.74 / 1.54
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 41.382, 63.523, 130.245, 90.00, 90.00, 90.00
R / Rfree (%) 18 / 21.8

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Spae Basal Pilin From Lactobacillus Rhamnosus Gg - Orthorhombic Form (pdb code 6jch). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Crystal Structure of Spae Basal Pilin From Lactobacillus Rhamnosus Gg - Orthorhombic Form, PDB code: 6jch:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in 6jch

Go back to Sodium Binding Sites List in 6jch
Sodium binding site 1 out of 3 in the Crystal Structure of Spae Basal Pilin From Lactobacillus Rhamnosus Gg - Orthorhombic Form


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 Spae Basal Pilin From Lactobacillus Rhamnosus Gg - Orthorhombic Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na501

b:16.2
occ:1.00
OD1 A:ASP221 2.2 17.8 1.0
O A:ARG296 2.3 16.0 1.0
O A:GLY294 2.3 16.5 1.0
O A:HOH772 2.4 18.1 1.0
OG1 A:THR293 2.4 14.9 1.0
N A:GLY294 3.1 16.7 1.0
CG A:ASP221 3.2 18.0 1.0
C A:GLY294 3.2 15.0 1.0
CB A:THR293 3.3 15.5 1.0
CB A:ASP221 3.4 16.0 1.0
C A:THR293 3.4 14.9 1.0
C A:ARG296 3.5 16.5 1.0
CA A:GLY294 3.6 16.5 1.0
O A:HOH610 3.7 23.9 1.0
CA A:ASP221 3.8 16.1 1.0
CA A:THR293 3.9 15.2 1.0
O A:THR293 4.0 16.0 1.0
N A:ARG296 4.2 16.6 1.0
O A:HOH881 4.3 22.4 1.0
OD1 A:ASN292 4.3 15.4 1.0
C A:ASP221 4.3 15.6 1.0
OD2 A:ASP221 4.4 18.9 1.0
N A:GLU295 4.4 18.5 1.0
N A:PHE297 4.4 17.9 1.0
N A:THR293 4.4 15.2 1.0
C A:GLU295 4.4 19.9 1.0
CA A:ARG296 4.4 15.1 1.0
CA A:PHE297 4.5 18.0 1.0
O A:GLY354 4.6 16.5 1.0
CG2 A:THR293 4.6 15.7 1.0
O A:HOH683 4.7 25.9 1.0
O A:PRO222 4.7 14.6 1.0
CA A:GLU295 4.8 19.5 1.0
N A:PRO222 4.8 14.4 1.0
O A:ASP221 4.8 15.5 1.0
O A:GLU295 4.9 19.9 1.0

Sodium binding site 2 out of 3 in 6jch

Go back to Sodium Binding Sites List in 6jch
Sodium binding site 2 out of 3 in the Crystal Structure of Spae Basal Pilin From Lactobacillus Rhamnosus Gg - Orthorhombic Form


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 Spae Basal Pilin From Lactobacillus Rhamnosus Gg - Orthorhombic Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na502

b:27.8
occ:1.00
OE1 A:GLN346 2.2 36.1 1.0
O A:HOH906 2.7 30.5 1.0
O A:HOH650 2.8 18.2 1.0
N A:ARG367 3.0 16.4 1.0
CD A:GLN346 3.3 29.4 1.0
CD1 A:TYR365 3.3 16.3 1.0
O A:ARG367 3.6 17.8 1.0
CA A:PRO366 3.6 16.4 1.0
C A:PRO366 3.8 15.0 1.0
CG A:ARG367 3.8 33.5 1.0
NE2 A:GLN346 3.8 23.8 1.0
CE1 A:TYR365 3.9 15.0 1.0
CA A:ARG367 4.0 16.3 1.0
CB A:PRO366 4.2 18.6 1.0
C A:ARG367 4.2 15.9 1.0
CG A:TYR365 4.3 17.4 1.0
CB A:ARG367 4.4 30.1 1.0
CG A:GLN346 4.5 30.6 1.0
CB A:TYR365 4.5 16.7 1.0
O A:HOH949 4.6 32.3 1.0
OH A:TYR369 4.8 16.1 1.0
CA A:TYR365 4.8 15.8 1.0
CB A:GLN346 4.9 22.4 1.0
O A:HOH612 4.9 35.2 1.0
N A:PRO366 4.9 15.3 1.0
O A:PRO366 5.0 15.6 1.0

Sodium binding site 3 out of 3 in 6jch

Go back to Sodium Binding Sites List in 6jch
Sodium binding site 3 out of 3 in the Crystal Structure of Spae Basal Pilin From Lactobacillus Rhamnosus Gg - Orthorhombic Form


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 Spae Basal Pilin From Lactobacillus Rhamnosus Gg - Orthorhombic Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na503

b:30.8
occ:1.00
O A:HOH652 2.3 24.6 1.0
OG A:SER189 2.5 26.1 1.0
O A:GLN110 2.6 21.5 1.0
CB A:SER189 3.4 22.4 1.0
C A:GLN110 3.7 21.0 1.0
O A:HOH770 4.0 38.6 1.0
CG A:GLN110 4.2 39.1 1.0
CA A:ASN111 4.2 19.2 1.0
O A:HOH968 4.3 36.6 1.0
O A:HOH687 4.3 34.3 1.0
CA A:SER189 4.4 16.5 1.0
N A:ASN111 4.5 18.4 1.0
O A:MET112 4.5 19.5 1.0
OD1 A:ASN111 4.6 31.7 1.0
O A:HOH653 4.7 35.5 1.0
CA A:GLN110 4.8 18.6 1.0
C A:ASN111 4.8 20.7 1.0

Reference:

A.K.Megta, A.K.Mishra, A.Palva, I.Von Ossowski, V.Krishnan. Crystal Structure of Basal Pilin Spae Reveals the Molecular Basis of Its Incorporation in the Lactobacillar Spafed Pilus. J.Struct.Biol. V. 207 74 2019.
ISSN: ESSN 1095-8657
PubMed: 31026587
DOI: 10.1016/J.JSB.2019.04.016
Page generated: Tue Dec 15 12:25:19 2020

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