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Sodium in PDB 7kou: 1.83 Angstroms Resolution Crystal Structure of Putative Pterin Binding Protein Prur (ATU3496) From Agrobacterium Fabrum Str. C58

Protein crystallography data

The structure of 1.83 Angstroms Resolution Crystal Structure of Putative Pterin Binding Protein Prur (ATU3496) From Agrobacterium Fabrum Str. C58, PDB code: 7kou was solved by G.Minasov, L.Shuvalova, I.Dubrovska, S.Pshenychnyi, M.Endres, K.J.F.Satchell, Center For Structural Genomics Of Infectious Diseases(Csgid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.80 / 1.83
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 120.928, 62.022, 101.916, 90, 90, 90
R / Rfree (%) 16.2 / 19.3

Other elements in 7kou:

The structure of 1.83 Angstroms Resolution Crystal Structure of Putative Pterin Binding Protein Prur (ATU3496) From Agrobacterium Fabrum Str. C58 also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the 1.83 Angstroms Resolution Crystal Structure of Putative Pterin Binding Protein Prur (ATU3496) From Agrobacterium Fabrum Str. C58 (pdb code 7kou). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 10 binding sites of Sodium where determined in the 1.83 Angstroms Resolution Crystal Structure of Putative Pterin Binding Protein Prur (ATU3496) From Agrobacterium Fabrum Str. C58, PDB code: 7kou:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Sodium binding site 1 out of 10 in 7kou

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Sodium binding site 1 out of 10 in the 1.83 Angstroms Resolution Crystal Structure of Putative Pterin Binding Protein Prur (ATU3496) From Agrobacterium Fabrum Str. C58


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of 1.83 Angstroms Resolution Crystal Structure of Putative Pterin Binding Protein Prur (ATU3496) From Agrobacterium Fabrum Str. C58 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na202

b:29.6
occ:1.00
 O A:HOH414 2.2 27.1 1.0
OXT D:GLU168 2.4 27.0 1.0
O A:GLY38 2.4 16.4 1.0
O A:GLY47 2.5 25.5 1.0
O D:HOH318 2.5 26.5 1.0
C A:GLY47 3.4 25.5 1.0
C D:GLU168 3.4 26.4 1.0
N A:GLY38 3.5 17.1 1.0
CA A:GLY47 3.5 27.6 1.0
C A:GLY38 3.6 17.6 1.0
O D:GLU168 3.8 29.1 1.0
ND2 D:ASN39 4.0 24.9 1.0
CA A:GLY38 4.0 17.1 1.0
CG1 A:ILE40 4.2 18.3 1.0
CB D:ASN39 4.3 20.9 1.0
C A:SER37 4.3 16.7 1.0
O D:HOH411 4.4 49.0 1.0
CA A:SER37 4.5 16.5 1.0
CG D:ASN39 4.5 23.1 1.0
O A:HOH466 4.6 32.0 0.5
N A:ILE40 4.6 17.6 1.0
O A:ILE40 4.6 19.7 1.0
N A:ALA48 4.7 23.5 1.0
CA D:GLU168 4.7 22.7 1.0
N A:ASN39 4.7 17.2 1.0
CB A:SER37 4.8 17.3 1.0
CD1 A:ILE40 5.0 18.4 1.0
O D:HOH439 5.0 51.7 1.0

Sodium binding site 2 out of 10 in 7kou

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Sodium binding site 2 out of 10 in the 1.83 Angstroms Resolution Crystal Structure of Putative Pterin Binding Protein Prur (ATU3496) From Agrobacterium Fabrum Str. C58


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of 1.83 Angstroms Resolution Crystal Structure of Putative Pterin Binding Protein Prur (ATU3496) From Agrobacterium Fabrum Str. C58 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na203

b:47.4
occ:1.00
 O A:HOH434 2.3 33.8 1.0
O A:HOH403 2.3 40.9 1.0
OG A:SER106 2.4 22.1 1.0
O A:SER156 2.4 21.0 0.5
O A:HOH365 2.5 43.1 1.0
O A:SER156 2.5 22.2 0.5
O A:SER158 2.5 19.7 0.5
C A:SER156 3.4 20.5 0.5
C A:SER156 3.4 21.8 0.5
CB A:SER106 3.5 19.9 1.0
C A:SER158 3.8 19.5 0.5
O A:HOH448 3.9 29.4 0.5
CA A:SER156 4.0 22.8 0.5
CA A:SER156 4.0 20.4 0.5
CA A:ALA159 4.1 18.9 0.5
N A:ALA159 4.2 18.6 0.5
C A:SER158 4.2 18.4 0.5
CA A:ALA159 4.3 19.1 0.5
O A:TYR155 4.3 21.6 1.0
O A:SER158 4.3 17.7 0.5
N A:SER158 4.3 19.1 0.5
CA A:SER106 4.4 19.3 1.0
N A:ARG157 4.5 20.9 1.0
O A:HOH398 4.5 28.6 1.0
O A:HOH448 4.5 21.6 0.5
O A:HOH410 4.5 26.4 1.0
N A:SER158 4.5 19.8 0.5
N A:ALA159 4.5 18.9 0.5
CB A:ALA159 4.5 18.4 0.5
C A:ARG157 4.6 20.0 1.0
CB A:ALA159 4.7 18.4 0.5
CA A:SER158 4.8 19.4 0.5
CA A:ARG157 4.8 20.0 1.0
CB A:SER156 4.8 24.9 0.5
O A:HOH396 4.8 31.2 1.0
CZ3 A:TRP160 4.9 43.1 1.0
CA A:SER158 4.9 18.6 0.5
CB A:SER156 4.9 20.8 0.5
O A:VAL105 4.9 20.1 1.0

Sodium binding site 3 out of 10 in 7kou

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Sodium binding site 3 out of 10 in the 1.83 Angstroms Resolution Crystal Structure of Putative Pterin Binding Protein Prur (ATU3496) From Agrobacterium Fabrum Str. C58


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of 1.83 Angstroms Resolution Crystal Structure of Putative Pterin Binding Protein Prur (ATU3496) From Agrobacterium Fabrum Str. C58 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na204

b:23.6
occ:1.00
 O A:HOH395 2.3 31.6 1.0
OE1 A:GLU133 2.4 24.1 1.0
O A:TYR128 2.4 20.8 1.0
OE2 A:GLU133 2.4 28.5 1.0
CD A:GLU133 2.7 26.9 1.0
C A:TYR128 3.5 20.1 1.0
CB A:ASN127 3.7 23.8 1.0
CA A:MET129 3.9 21.5 1.0
N A:MET129 4.1 20.5 1.0
O A:ASN127 4.2 20.0 1.0
CG A:GLU133 4.2 27.4 1.0
C A:ASN127 4.2 21.1 1.0
O A:HOH444 4.4 45.2 1.0
O A:HOH310 4.5 51.8 1.0
N A:TYR128 4.5 20.9 1.0
N A:THR130 4.5 21.5 1.0
CA A:ASN127 4.6 22.9 1.0
CG A:MET129 4.7 23.4 1.0
CA A:TYR128 4.7 20.1 1.0
C A:MET129 4.8 21.9 1.0
CG A:ASN127 4.8 26.4 1.0
CB A:GLU133 4.8 26.6 1.0
CB A:MET129 4.8 22.5 1.0
O A:LEU124 4.9 20.6 1.0
ND2 A:ASN127 4.9 26.4 1.0

Sodium binding site 4 out of 10 in 7kou

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Sodium binding site 4 out of 10 in the 1.83 Angstroms Resolution Crystal Structure of Putative Pterin Binding Protein Prur (ATU3496) From Agrobacterium Fabrum Str. C58


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of 1.83 Angstroms Resolution Crystal Structure of Putative Pterin Binding Protein Prur (ATU3496) From Agrobacterium Fabrum Str. C58 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na202

b:20.4
occ:0.50
 O B:HOH411 1.7 21.1 0.5
O C:HOH305 2.2 30.4 1.0
O B:GLY38 2.4 18.6 1.0
O C:HOH301 2.4 33.2 1.0
O B:GLY47 2.5 29.2 1.0
O C:GLU168 3.4 40.1 1.0
C B:GLY47 3.5 28.0 1.0
C B:GLY38 3.5 18.0 1.0
N B:GLY38 3.5 17.1 1.0
CA B:GLY47 3.6 30.7 1.0
CA B:GLY38 3.9 17.8 1.0
ND2 C:ASN39 4.0 27.2 1.0
CG1 B:ILE40 4.2 19.2 1.0
O B:HOH421 4.3 27.1 0.5
C C:GLU168 4.3 36.7 1.0
C B:SER37 4.4 17.0 1.0
CB C:ASN39 4.4 24.2 1.0
CG C:ASN39 4.6 26.3 1.0
N B:ILE40 4.6 17.7 1.0
N B:ASN39 4.6 18.1 1.0
CA B:SER37 4.7 16.7 1.0
N B:ALA48 4.7 23.6 1.0
CD1 B:ILE40 4.8 20.0 1.0
O B:HOH356 4.8 47.3 1.0
CA C:GLU168 4.9 28.7 1.0

Sodium binding site 5 out of 10 in 7kou

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Sodium binding site 5 out of 10 in the 1.83 Angstroms Resolution Crystal Structure of Putative Pterin Binding Protein Prur (ATU3496) From Agrobacterium Fabrum Str. C58


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of 1.83 Angstroms Resolution Crystal Structure of Putative Pterin Binding Protein Prur (ATU3496) From Agrobacterium Fabrum Str. C58 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na203

b:53.6
occ:1.00
 O B:HOH372 2.3 50.0 1.0
O B:HOH448 2.3 42.3 1.0
O B:HOH373 2.3 42.0 1.0
OG B:SER106 2.5 21.5 1.0
O B:SER156 2.7 19.9 1.0
O B:HOH400 3.5 31.0 0.5
CB B:SER106 3.6 21.2 1.0
C B:SER156 3.7 19.6 1.0
O B:HOH446 3.9 32.6 0.3
CA B:ALA159 4.1 18.4 0.5
CA B:ALA159 4.1 17.7 0.5
O B:HOH400 4.2 27.8 0.5
CA B:SER156 4.2 19.9 1.0
N B:ALA159 4.3 18.9 0.5
O B:HOH376 4.3 26.9 1.0
N B:ALA159 4.3 18.5 0.5
C B:SER158 4.4 18.7 1.0
O B:SER158 4.4 20.5 1.0
O B:TYR155 4.4 17.2 1.0
O B:HOH383 4.5 25.1 1.0
CB B:ALA159 4.5 18.3 0.5
CB B:ALA159 4.6 17.7 0.5
O B:HOH427 4.6 37.3 0.5
N B:SER158 4.6 19.1 1.0
CA B:SER106 4.7 20.4 1.0
N B:ARG157 4.7 19.1 1.0
C B:ARG157 4.9 18.8 1.0
CZ3 B:TRP160 4.9 36.7 0.7
CH2 B:TRP160 4.9 36.7 0.7

Sodium binding site 6 out of 10 in 7kou

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Sodium binding site 6 out of 10 in the 1.83 Angstroms Resolution Crystal Structure of Putative Pterin Binding Protein Prur (ATU3496) From Agrobacterium Fabrum Str. C58


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of 1.83 Angstroms Resolution Crystal Structure of Putative Pterin Binding Protein Prur (ATU3496) From Agrobacterium Fabrum Str. C58 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na201

b:23.8
occ:1.00
 O C:HOH421 2.2 22.2 1.0
O C:GLY38 2.4 20.3 1.0
O B:HOH323 2.4 23.9 1.0
O B:GLU168 2.4 22.6 1.0
O C:GLY47 2.5 27.5 1.0
C C:GLY47 3.4 26.7 1.0
N C:GLY38 3.4 18.0 1.0
C C:GLY38 3.4 20.0 1.0
C B:GLU168 3.5 23.9 1.0
CA C:GLY47 3.5 29.4 1.0
ND2 B:ASN39 3.7 24.8 1.0
OXT B:GLU168 3.8 23.3 1.0
CA C:GLY38 3.9 18.7 1.0
CG1 C:ILE40 4.2 20.5 1.0
CB B:ASN39 4.2 20.8 1.0
C C:SER37 4.2 16.8 1.0
O C:HOH398 4.3 30.4 1.0
CG B:ASN39 4.3 22.3 1.0
CA C:SER37 4.5 16.9 1.0
N C:ILE40 4.5 22.0 1.0
O B:HOH423 4.5 36.4 1.0
N C:ASN39 4.6 21.1 1.0
N C:ALA48 4.7 24.0 1.0
CB C:SER37 4.7 18.2 1.0
CA B:GLU168 4.7 21.8 1.0
O C:ILE40 4.8 25.9 1.0
CD1 C:ILE40 4.9 20.8 1.0
N C:GLY47 5.0 30.7 1.0

Sodium binding site 7 out of 10 in 7kou

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Sodium binding site 7 out of 10 in the 1.83 Angstroms Resolution Crystal Structure of Putative Pterin Binding Protein Prur (ATU3496) From Agrobacterium Fabrum Str. C58


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of 1.83 Angstroms Resolution Crystal Structure of Putative Pterin Binding Protein Prur (ATU3496) From Agrobacterium Fabrum Str. C58 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na202

b:48.5
occ:1.00
 O C:HOH356 2.3 49.4 1.0
O C:HOH361 2.3 41.1 1.0
O2 C:PG4204 2.7 69.3 1.0
O4 C:PG4204 2.7 51.2 1.0
O1 C:PG4204 2.8 71.6 1.0
O3 C:PG4204 2.9 59.0 1.0
O5 C:PG4204 2.9 56.0 1.0
C2 C:PG4204 3.5 73.8 1.0
C1 C:PG4204 3.5 73.1 1.0
C6 C:PG4204 3.6 57.7 1.0
C5 C:PG4204 3.6 58.3 1.0
C7 C:PG4204 3.6 49.4 1.0
C8 C:PG4204 3.7 57.0 1.0
C4 C:PG4204 3.7 60.4 1.0
C3 C:PG4204 3.8 64.7 1.0
O C:ARG132 4.3 30.5 1.0
O C:TRP70 4.5 22.2 1.0
O C:HOH354 5.0 50.1 1.0

Sodium binding site 8 out of 10 in 7kou

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Sodium binding site 8 out of 10 in the 1.83 Angstroms Resolution Crystal Structure of Putative Pterin Binding Protein Prur (ATU3496) From Agrobacterium Fabrum Str. C58


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of 1.83 Angstroms Resolution Crystal Structure of Putative Pterin Binding Protein Prur (ATU3496) From Agrobacterium Fabrum Str. C58 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na203

b:23.9
occ:1.00
 O C:PRO69 2.3 20.0 1.0
C C:PRO69 3.3 18.8 1.0
CB C:PRO69 3.9 19.9 1.0
CA C:PRO69 4.0 18.5 1.0
N C:TRP70 4.4 17.6 1.0
CD1 C:TRP70 4.4 22.1 1.0
CA C:TRP70 4.6 19.3 1.0
NE1 C:TRP70 5.0 22.5 1.0

Sodium binding site 9 out of 10 in 7kou

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Sodium binding site 9 out of 10 in the 1.83 Angstroms Resolution Crystal Structure of Putative Pterin Binding Protein Prur (ATU3496) From Agrobacterium Fabrum Str. C58


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 9 of 1.83 Angstroms Resolution Crystal Structure of Putative Pterin Binding Protein Prur (ATU3496) From Agrobacterium Fabrum Str. C58 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na201

b:27.6
occ:1.00
 O A:HOH424 2.1 29.0 1.0
O D:GLY47 2.4 26.8 1.0
O D:GLY38 2.4 16.6 1.0
OXT A:GLU168 2.4 24.1 1.0
O A:HOH304 2.5 24.7 1.0
C D:GLY47 3.4 26.9 1.0
N D:GLY38 3.4 16.3 1.0
C A:GLU168 3.5 26.1 1.0
C D:GLY38 3.5 17.1 1.0
CA D:GLY47 3.6 27.8 1.0
ND2 A:ASN39 3.6 27.0 1.0
O A:GLU168 3.8 26.1 1.0
CA D:GLY38 3.9 16.8 1.0
CG1 D:ILE40 4.0 18.1 1.0
CB A:ASN39 4.1 20.3 1.0
C D:SER37 4.2 16.1 1.0
CG A:ASN39 4.2 23.8 1.0
O A:HOH458 4.4 38.8 0.5
CA D:SER37 4.4 15.8 1.0
O A:HOH393 4.5 35.5 1.0
N D:ILE40 4.6 18.1 1.0
N D:ALA48 4.6 22.6 1.0
O D:HOH407 4.6 32.7 1.0
CD1 D:ILE40 4.6 18.6 1.0
N D:ASN39 4.7 17.9 1.0
CB D:SER37 4.7 17.6 1.0
CA A:GLU168 4.8 22.2 1.0
O D:ILE40 4.9 20.1 1.0

Sodium binding site 10 out of 10 in 7kou

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Sodium binding site 10 out of 10 in the 1.83 Angstroms Resolution Crystal Structure of Putative Pterin Binding Protein Prur (ATU3496) From Agrobacterium Fabrum Str. C58


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 10 of 1.83 Angstroms Resolution Crystal Structure of Putative Pterin Binding Protein Prur (ATU3496) From Agrobacterium Fabrum Str. C58 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na202

b:49.7
occ:1.00
 O D:HOH344 2.3 47.5 1.0
O D:HOH392 2.3 41.0 1.0
O D:HOH368 2.4 49.8 1.0
O5 D:PG4203 2.7 53.3 1.0
O3 D:PG4203 2.7 42.1 1.0
O2 D:PG4203 2.8 46.8 1.0
O4 D:PG4203 2.8 39.6 1.0
C4 D:PG4203 3.6 44.1 1.0
C3 D:PG4203 3.6 46.2 1.0
C5 D:PG4203 3.6 40.5 1.0
C8 D:PG4203 3.6 51.2 1.0
C2 D:PG4203 3.6 55.4 1.0
C6 D:PG4203 3.7 40.3 1.0
C7 D:PG4203 3.7 47.1 1.0
O D:ARG132 4.3 20.6 1.0
O D:TRP70 4.6 21.4 1.0
C1 D:PG4203 4.8 57.0 1.0
O1 D:PG4203 5.0 57.6 1.0

Reference:

G.Minasov, L.Shuvalova, I.Dubrovska, S.Pshenychnyi, M.Endres, K.J.F.Satchell, Center For Structural Genomics Of Infectious Diseases(Csgid). 1.83 Angstroms Resolution Crystal Structure of Putative Pterin Binding Protein Prur (ATU3496) From Agrobacterium Fabrum Str. C58. To Be Published.
Page generated: Tue Oct 8 17:25:33 2024

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