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Sodium in PDB 5org: Structure of the Periplasmic Binding Protein (Pbp) Occj From A. Tumefaciens B6 in Complex with Octopine.

Protein crystallography data

The structure of Structure of the Periplasmic Binding Protein (Pbp) Occj From A. Tumefaciens B6 in Complex with Octopine., PDB code: 5org was solved by A.Vigouroux, S.Morera, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.14 / 1.99
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 99.490, 99.490, 157.600, 90.00, 90.00, 90.00
R / Rfree (%) 19.6 / 22.1

Other elements in 5org:

The structure of Structure of the Periplasmic Binding Protein (Pbp) Occj From A. Tumefaciens B6 in Complex with Octopine. also contains other interesting chemical elements:

Chlorine (Cl) 14 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Structure of the Periplasmic Binding Protein (Pbp) Occj From A. Tumefaciens B6 in Complex with Octopine. (pdb code 5org). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 9 binding sites of Sodium where determined in the Structure of the Periplasmic Binding Protein (Pbp) Occj From A. Tumefaciens B6 in Complex with Octopine., PDB code: 5org:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Sodium binding site 1 out of 9 in 5org

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Sodium binding site 1 out of 9 in the Structure of the Periplasmic Binding Protein (Pbp) Occj From A. Tumefaciens B6 in Complex with Octopine.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of the Periplasmic Binding Protein (Pbp) Occj From A. Tumefaciens B6 in Complex with Octopine. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na303

b:37.5
occ:1.00
 O A:GLY32 2.6 31.9 1.0
OE1 A:GLU30 2.7 29.7 1.0
N A:VAL184 3.0 25.8 1.0
OE2 A:GLU30 3.0 24.7 1.0
O A:HOH466 3.1 26.1 1.0
CD A:GLU30 3.2 33.2 1.0
NAQ A:6DB321 3.5 28.0 1.0
C A:GLY32 3.5 31.4 1.0
NE2 A:GLN159 3.5 27.9 1.0
CB A:VAL184 3.6 29.4 1.0
CG2 A:VAL184 3.7 29.6 1.0
CA A:SER183 3.7 27.2 1.0
CB A:SER183 3.7 29.1 1.0
C A:SER183 3.8 29.2 1.0
CA A:VAL184 3.9 25.6 1.0
OE1 A:GLN159 4.0 25.0 1.0
CD A:GLN159 4.0 30.8 1.0
CA A:GLY32 4.0 26.1 1.0
CD1 A:TYR33 4.4 25.5 1.0
O B:HOH428 4.5 41.4 1.0
N A:TYR33 4.6 27.9 1.0
CAP A:6DB321 4.7 27.4 1.0
CG A:GLU30 4.7 30.4 1.0
N A:GLU185 4.7 27.3 1.0
OG A:SER183 4.8 28.1 1.0
O A:HOH410 4.8 26.4 1.0
CB A:TYR33 4.8 26.1 1.0
C A:VAL184 4.9 28.8 1.0
CA A:TYR33 4.9 27.0 1.0
N A:GLY32 4.9 24.4 1.0
CG1 A:VAL184 5.0 29.1 1.0

Sodium binding site 2 out of 9 in 5org

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Sodium binding site 2 out of 9 in the Structure of the Periplasmic Binding Protein (Pbp) Occj From A. Tumefaciens B6 in Complex with Octopine.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structure of the Periplasmic Binding Protein (Pbp) Occj From A. Tumefaciens B6 in Complex with Octopine. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na304

b:43.7
occ:1.00
 O A:ARG238 2.8 27.6 1.0
O A:ASP241 3.0 32.0 1.0
CB A:LYS245 3.4 32.1 1.0
C A:ASP241 3.5 32.1 1.0
CB A:LEU237 3.7 26.3 1.0
N A:ASP241 3.7 30.9 1.0
O A:LYS239 3.8 33.6 1.0
CD A:LYS245 4.0 39.4 1.0
C A:ARG238 4.0 28.5 1.0
CA A:ASP241 4.0 29.8 1.0
CD1 A:LEU237 4.0 31.6 1.0
C A:LYS239 4.2 32.8 1.0
CG A:LYS245 4.2 34.3 1.0
CB A:ASP241 4.2 30.1 1.0
N A:THR242 4.3 30.5 1.0
CA A:GLY101 4.4 27.1 1.0
CA A:LYS245 4.5 30.2 1.0
CG A:LEU237 4.5 31.4 1.0
O A:HOH524 4.5 58.6 1.0
N A:LYS245 4.6 29.8 1.0
C A:LEU237 4.6 28.4 1.0
CA A:LYS239 4.6 28.4 1.0
CA A:THR242 4.6 30.4 1.0
C A:GLU240 4.7 34.6 1.0
N A:GLU240 4.7 29.9 1.0
N A:ARG238 4.7 26.4 1.0
C A:GLY101 4.7 31.6 1.0
N A:LYS239 4.7 25.8 1.0
O A:LEU237 4.8 29.6 1.0
CA A:LEU237 4.8 25.2 1.0
N A:PHE102 4.8 29.4 1.0

Sodium binding site 3 out of 9 in 5org

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Sodium binding site 3 out of 9 in the Structure of the Periplasmic Binding Protein (Pbp) Occj From A. Tumefaciens B6 in Complex with Octopine.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Structure of the Periplasmic Binding Protein (Pbp) Occj From A. Tumefaciens B6 in Complex with Octopine. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na305

b:43.5
occ:1.00
 O A:HOH417 2.7 27.0 1.0
ND2 A:ASN111 2.8 29.9 1.0
OG1 A:THR163 2.9 35.2 1.0
N A:ALA164 3.3 28.5 1.0
CB A:ALA164 3.4 28.2 1.0
CAK A:6DB321 3.5 28.9 1.0
CAI A:6DB321 3.5 29.6 1.0
C A:6DB321 3.6 35.8 1.0
OXT A:6DB321 3.6 34.4 1.0
O A:6DB321 3.8 38.3 1.0
CG A:ASN111 3.8 40.2 1.0
CA A:ALA164 3.9 28.0 1.0
OD1 A:ASN111 4.0 36.5 1.0
CA A:6DB321 4.1 32.2 1.0
CB A:THR163 4.2 31.0 1.0
C A:THR163 4.2 32.0 1.0
N A:THR163 4.3 27.5 1.0
N A:6DB321 4.3 31.1 1.0
OH A:TYR33 4.3 32.9 1.0
N A:ASN202 4.4 30.0 1.0
CB A:THR162 4.4 29.4 1.0
CD1 A:PHE230 4.4 38.5 1.0
CA A:THR163 4.5 28.7 1.0
OG1 A:THR162 4.5 28.6 1.0
O A:HOH467 4.5 27.3 1.0
CE1 A:PHE230 4.6 38.7 1.0
CAE A:6DB321 4.6 26.6 1.0
OAB A:6DB321 4.7 25.2 1.0
CA A:ALA201 4.7 28.4 1.0
C A:ALA201 4.8 32.2 1.0
CAL A:6DB321 5.0 25.3 1.0

Sodium binding site 4 out of 9 in 5org

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Sodium binding site 4 out of 9 in the Structure of the Periplasmic Binding Protein (Pbp) Occj From A. Tumefaciens B6 in Complex with Octopine.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Structure of the Periplasmic Binding Protein (Pbp) Occj From A. Tumefaciens B6 in Complex with Octopine. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na306

b:50.0
occ:1.00
 O A:GLY109 2.6 41.8 1.0
O A:GLY231 2.6 47.8 1.0
N A:GLY227 3.0 38.9 1.0
N A:GLY109 3.3 41.4 1.0
C A:GLY109 3.6 42.5 1.0
C A:GLY231 3.7 46.7 1.0
CA A:GLY227 3.8 39.1 1.0
CB A:SER226 3.8 43.0 1.0
CA A:SER226 3.8 39.5 1.0
C A:SER226 3.9 42.8 1.0
CB A:ALA108 3.9 45.8 1.0
CA A:GLY109 3.9 40.2 1.0
N A:GLY231 3.9 43.0 1.0
C A:ALA108 4.0 47.0 1.0
CB A:PHE230 4.1 40.9 1.0
CA A:GLY231 4.1 43.0 1.0
CA A:ALA108 4.2 42.7 1.0
C A:PHE230 4.2 43.8 1.0
O A:GLY227 4.6 42.6 1.0
O A:PHE230 4.7 42.4 1.0
C A:GLY227 4.7 43.8 1.0
N A:ILE110 4.8 39.3 1.0
CA A:PHE230 4.8 39.7 1.0
N A:VAL232 4.8 40.5 1.0
O A:HOH442 4.8 50.2 1.0
OG A:SER226 4.9 48.3 1.0
O A:ALA108 4.9 47.8 1.0

Sodium binding site 5 out of 9 in 5org

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Sodium binding site 5 out of 9 in the Structure of the Periplasmic Binding Protein (Pbp) Occj From A. Tumefaciens B6 in Complex with Octopine.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Structure of the Periplasmic Binding Protein (Pbp) Occj From A. Tumefaciens B6 in Complex with Octopine. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na307

b:43.4
occ:1.00
 OD1 A:ASP241 2.8 33.8 1.0
N A:ALA243 3.0 29.6 1.0
N A:THR242 3.1 30.5 1.0
C A:ASP241 3.4 32.1 1.0
CB A:ALA243 3.5 31.4 1.0
CA A:ASP241 3.5 29.8 1.0
CA A:ALA243 3.8 30.3 1.0
CG A:ASP241 3.8 38.9 1.0
O A:HOH420 3.9 37.4 1.0
C A:THR242 4.0 31.9 1.0
OG1 A:THR242 4.0 32.1 1.0
CA A:THR242 4.0 30.4 1.0
O A:GLU240 4.1 32.4 1.0
O A:ASP241 4.2 32.0 1.0
CB A:ASP241 4.3 30.1 1.0
N A:LEU244 4.4 30.4 1.0
CB A:THR242 4.6 34.6 1.0
C A:ALA243 4.7 33.9 1.0
N A:ASP241 4.7 30.9 1.0
C A:GLU240 4.8 34.6 1.0
OD2 A:ASP241 4.9 33.8 1.0

Sodium binding site 6 out of 9 in 5org

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Sodium binding site 6 out of 9 in the Structure of the Periplasmic Binding Protein (Pbp) Occj From A. Tumefaciens B6 in Complex with Octopine.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Structure of the Periplasmic Binding Protein (Pbp) Occj From A. Tumefaciens B6 in Complex with Octopine. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na308

b:77.9
occ:1.00
 O A:HOH442 3.5 50.2 1.0
O A:HOH525 3.6 78.4 1.0
OG A:SER132 3.6 62.1 1.0
OG A:SER135 3.8 76.8 1.0
CB A:SER132 4.3 57.5 1.0
CB A:SER135 4.4 69.4 1.0

Sodium binding site 7 out of 9 in 5org

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Sodium binding site 7 out of 9 in the Structure of the Periplasmic Binding Protein (Pbp) Occj From A. Tumefaciens B6 in Complex with Octopine.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of Structure of the Periplasmic Binding Protein (Pbp) Occj From A. Tumefaciens B6 in Complex with Octopine. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na309

b:84.3
occ:1.00
 OXT A:ACT323 2.8 61.4 1.0
O A:HOH493 3.7 54.5 1.0
C A:ACT323 4.0 55.8 1.0
CD A:LYS182 4.4 43.8 1.0
O A:HOH426 4.5 32.5 1.0
O A:ACT323 4.7 54.2 1.0
CG A:LYS182 5.0 35.0 1.0

Sodium binding site 8 out of 9 in 5org

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Sodium binding site 8 out of 9 in the Structure of the Periplasmic Binding Protein (Pbp) Occj From A. Tumefaciens B6 in Complex with Octopine.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of Structure of the Periplasmic Binding Protein (Pbp) Occj From A. Tumefaciens B6 in Complex with Octopine. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na306

b:46.2
occ:1.00
 O B:PRO223 2.5 40.3 1.0
O B:VAL221 2.7 28.6 1.0
N B:PHE113 3.0 30.0 1.0
N B:PRO223 3.3 32.6 1.0
CD2 B:PHE113 3.3 36.8 1.0
C B:GLY222 3.4 31.9 1.0
C B:PRO223 3.5 40.1 1.0
O B:HOH475 3.6 36.2 1.0
CB B:PHE113 3.6 31.2 1.0
CD B:PRO223 3.7 34.9 1.0
CA B:GLY112 3.7 32.4 1.0
CA B:GLY222 3.7 29.1 1.0
C B:VAL221 3.8 29.8 1.0
C B:GLY112 3.8 34.0 1.0
O B:GLY222 3.8 28.8 1.0
CA B:PHE113 3.8 29.1 1.0
CG B:PHE113 3.9 34.0 1.0
CA B:PRO223 3.9 33.8 1.0
SD B:MET124 4.1 36.2 1.0
N B:GLY222 4.3 28.9 1.0
O B:PHE113 4.4 29.8 1.0
CE2 B:PHE113 4.4 39.8 1.0
CG B:PRO223 4.5 39.6 1.0
C B:PHE113 4.6 31.1 1.0
N B:LEU224 4.7 38.1 1.0
CE2 B:PHE225 4.8 41.4 1.0
CB B:PRO223 4.9 36.4 1.0
O B:HOH431 4.9 37.5 1.0

Sodium binding site 9 out of 9 in 5org

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Sodium binding site 9 out of 9 in the Structure of the Periplasmic Binding Protein (Pbp) Occj From A. Tumefaciens B6 in Complex with Octopine.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 9 of Structure of the Periplasmic Binding Protein (Pbp) Occj From A. Tumefaciens B6 in Complex with Octopine. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na307

b:41.2
occ:1.00
 O B:ASP197 2.5 31.1 1.0
O B:HOH488 2.9 53.6 1.0
N B:MET116 3.0 32.9 1.0
O B:HOH418 3.1 36.2 1.0
C B:ASP197 3.5 33.1 1.0
CB B:VAL115 3.6 31.1 1.0
CB B:MET116 3.7 38.1 1.0
OG B:SER119 3.8 48.1 1.0
CA B:VAL115 3.8 28.3 1.0
CG B:MET116 3.8 41.1 1.0
C B:VAL115 3.9 34.6 1.0
CA B:MET116 3.9 34.9 1.0
CA B:ASP197 3.9 31.5 1.0
CD1 B:LEU191 4.0 32.9 1.0
CB B:SER119 4.2 41.6 1.0
O B:MET116 4.3 41.8 1.0
CG1 B:VAL115 4.4 30.6 1.0
O B:LEU196 4.5 32.4 1.0
N B:ALA198 4.6 28.7 1.0
C B:MET116 4.6 42.2 1.0
CG2 B:VAL115 4.6 30.2 1.0
CD1 B:LEU121 4.8 41.7 1.0
CB B:ASP197 4.8 34.6 1.0
CG B:LEU191 4.9 32.4 1.0

Reference:

A.Vigouroux, A.El Sahili, J.Lang, M.Aumont-Nicaise, Y.Dessaux, D.Faure, S.Morera. Structural Basis For High Specificity of Octopine Binding in the Plant Pathogen Agrobacterium Tumefaciens. Sci Rep V. 7 18033 2017.
ISSN: ESSN 2045-2322
PubMed: 29269740
DOI: 10.1038/S41598-017-18243-8
Page generated: Mon Oct 7 23:15:06 2024

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