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Sodium in PDB 7kos: 1.50 Angstroms Resolution Crystal Structure of Putative Pterin Binding Protein Prur (ATU3496) From Agrobacterium Fabrum Str. C58

Protein crystallography data

The structure of 1.50 Angstroms Resolution Crystal Structure of Putative Pterin Binding Protein Prur (ATU3496) From Agrobacterium Fabrum Str. C58, PDB code: 7kos 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) 29.04 / 1.50
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 80.462, 91.81, 99.22, 90, 90, 90
R / Rfree (%) 15.2 / 17.2

Sodium Binding Sites:

The binding sites of Sodium atom in the 1.50 Angstroms Resolution Crystal Structure of Putative Pterin Binding Protein Prur (ATU3496) From Agrobacterium Fabrum Str. C58 (pdb code 7kos). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 5 binding sites of Sodium where determined in the 1.50 Angstroms Resolution Crystal Structure of Putative Pterin Binding Protein Prur (ATU3496) From Agrobacterium Fabrum Str. C58, PDB code: 7kos:
Jump to Sodium binding site number: 1; 2; 3; 4; 5;

Sodium binding site 1 out of 5 in 7kos

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Sodium binding site 1 out of 5 in the 1.50 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 1.50 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:Na201

b:24.1
occ:1.00
 O A:HOH393 2.3 29.5 1.0
O A:HOH453 2.3 32.9 1.0
O A:HOH395 2.4 18.1 1.0
O A:HOH344 2.5 23.1 1.0
O C:HOH312 2.5 22.4 1.0
O D:HOH393 2.6 23.7 1.0
OG A:SER156 3.7 16.4 0.4
OG A:SER156 3.8 15.8 0.6
O A:HOH412 4.0 26.8 1.0
O D:VAL105 4.1 17.5 1.0
O A:THR107 4.2 20.1 1.0
OE2 C:GLU168 4.2 19.6 1.0
O D:HOH391 4.3 26.5 1.0
O C:HOH482 4.4 32.1 1.0
O A:HOH448 4.5 26.9 0.4
NE A:ARG157 4.5 17.1 1.0
OE1 C:GLU168 4.5 16.3 1.0
CB A:SER156 4.5 15.7 0.6
O C:HOH452 4.5 29.8 1.0
CG A:ARG157 4.6 16.3 1.0
CB A:SER156 4.6 16.1 0.4
CE1 D:TYR104 4.7 15.3 1.0
CD C:GLU168 4.8 17.2 1.0
O A:HOH422 4.9 24.1 1.0
O A:THR153 5.0 15.3 1.0

Sodium binding site 2 out of 5 in 7kos

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Sodium binding site 2 out of 5 in the 1.50 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 1.50 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:37.6
occ:1.00
 O B:HOH317 2.4 30.4 1.0
O A:HOH425 2.5 43.2 1.0
O A:HOH386 2.5 38.8 1.0
O A:HOH337 2.5 34.0 1.0
O B:HOH318 2.6 28.9 1.0
O B:HOH390 3.1 48.1 1.0
O A:HOH449 3.9 60.2 1.0
CA A:GLY47 4.0 26.9 1.0
O A:HOH433 4.0 36.1 1.0
O A:HOH408 4.1 26.7 1.0
O A:GLY38 4.4 17.7 1.0
OE2 A:GLU46 4.6 41.6 1.0
N A:SER20 4.6 34.9 1.0
OD1 B:ASP103 4.6 21.4 1.0
O A:HOH365 4.7 35.8 1.0
O A:HOH454 4.7 46.0 1.0
OD2 B:ASP103 4.8 23.5 1.0
O B:LEU101 4.8 18.3 1.0
O A:GLY47 4.8 25.5 1.0
O A:HOH407 4.9 39.9 0.5
N A:GLY47 5.0 27.3 1.0
C A:GLY47 5.0 25.4 1.0

Sodium binding site 3 out of 5 in 7kos

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Sodium binding site 3 out of 5 in the 1.50 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 1.50 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:27.7
occ:1.00
 O B:HOH387 2.3 31.7 1.0
O B:HOH330 2.3 20.9 1.0
O B:HOH458 2.4 41.7 1.0
O D:HOH335 2.5 23.9 1.0
O B:HOH348 2.5 25.2 1.0
O C:HOH421 2.6 27.7 1.0
OG B:SER156 3.5 17.0 0.4
OG B:SER156 3.9 15.4 0.6
O B:HOH423 4.1 26.8 1.0
O C:VAL105 4.1 17.6 1.0
OE1 D:GLU168 4.2 20.7 1.0
O B:THR107 4.2 20.0 1.0
O C:HOH420 4.4 28.1 1.0
O D:HOH427 4.4 25.2 0.7
OE2 D:GLU168 4.5 19.8 1.0
O B:HOH441 4.5 40.3 0.7
O D:HOH415 4.5 34.5 1.0
NE B:ARG157 4.5 17.4 1.0
CB B:SER156 4.5 16.0 0.6
CB B:SER156 4.5 16.5 0.4
O B:HOH441 4.6 34.0 0.3
CE1 C:TYR104 4.6 16.3 1.0
CG B:ARG157 4.6 15.8 1.0
CD D:GLU168 4.7 19.3 1.0
O B:HOH422 4.9 26.6 1.0
O B:THR153 5.0 17.6 1.0

Sodium binding site 4 out of 5 in 7kos

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Sodium binding site 4 out of 5 in the 1.50 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 1.50 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:26.1
occ:1.00
 O C:HOH385 2.3 30.4 1.0
O C:HOH386 2.3 18.8 1.0
O C:HOH476 2.4 34.8 1.0
O C:HOH327 2.4 27.3 1.0
O A:HOH319 2.5 22.7 1.0
O B:HOH422 2.6 26.6 1.0
OG C:SER156 3.4 15.3 0.3
OG C:SER156 3.8 16.9 0.7
O C:HOH420 4.0 28.1 1.0
O B:VAL105 4.2 17.2 1.0
OE1 A:GLU168 4.2 20.6 1.0
O C:THR107 4.3 22.1 1.0
O B:HOH423 4.3 26.8 1.0
O C:HOH440 4.4 30.4 0.4
CB C:SER156 4.5 15.8 0.7
CE1 B:TYR104 4.5 14.9 1.0
CB C:SER156 4.5 15.3 0.3
OE2 A:GLU168 4.5 16.9 1.0
O A:HOH443 4.5 36.6 1.0
O A:HOH460 4.5 27.4 0.6
NE C:ARG157 4.6 17.4 1.0
CG C:ARG157 4.6 16.7 1.0
O C:HOH440 4.8 35.6 0.6
O C:HOH421 4.8 27.7 1.0
CD A:GLU168 4.8 16.9 1.0
O C:THR153 4.9 14.8 1.0

Sodium binding site 5 out of 5 in 7kos

Go back to Sodium Binding Sites List in 7kos
Sodium binding site 5 out of 5 in the 1.50 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 1.50 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:25.2
occ:1.00
 O D:HOH426 2.3 31.7 1.0
O D:HOH369 2.3 28.2 1.0
O D:HOH384 2.4 18.5 1.0
O B:HOH315 2.4 22.2 1.0
O D:HOH342 2.4 23.6 1.0
O A:HOH422 2.6 24.1 1.0
OG D:SER156 3.7 15.3 0.4
OG D:SER156 3.9 15.2 0.6
O D:HOH391 4.0 26.5 1.0
O A:VAL105 4.1 17.9 1.0
O D:THR107 4.2 21.9 1.0
OE1 B:GLU168 4.2 19.6 1.0
O A:HOH412 4.3 26.8 1.0
O B:HOH459 4.5 34.8 1.0
NE D:ARG157 4.5 16.8 1.0
OE2 B:GLU168 4.5 16.9 1.0
CB D:SER156 4.6 14.9 0.6
O D:HOH422 4.6 26.8 0.3
O B:HOH440 4.6 31.7 1.0
CE1 A:TYR104 4.6 14.7 1.0
CG D:ARG157 4.7 16.1 1.0
CB D:SER156 4.7 15.3 0.4
CD B:GLU168 4.8 17.1 1.0
O D:HOH393 4.9 23.7 1.0
O D:THR153 5.0 15.3 1.0
NH2 D:ARG157 5.0 19.4 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). 1.50 Angstroms Resolution Crystal Structure of Putative Pterin Binding Protein Prur (ATU3496) From Agrobacterium Fabrum Str. C58. To Be Published.
Page generated: Tue Oct 8 17:25:29 2024

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