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Sodium in PDB 4xda: Vibrio Cholerae O395 Ribokinase Complexed with Ribose, Adp and Sodium Ion.

Enzymatic activity of Vibrio Cholerae O395 Ribokinase Complexed with Ribose, Adp and Sodium Ion.

All present enzymatic activity of Vibrio Cholerae O395 Ribokinase Complexed with Ribose, Adp and Sodium Ion.:
2.7.1.15;

Protein crystallography data

The structure of Vibrio Cholerae O395 Ribokinase Complexed with Ribose, Adp and Sodium Ion., PDB code: 4xda was solved by R.Paul, M.D.Patra, U.Sen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 27.42 / 1.75
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 59.420, 70.700, 79.880, 106.29, 97.65, 98.68
R / Rfree (%) 18.7 / 22.5

Sodium Binding Sites:

The binding sites of Sodium atom in the Vibrio Cholerae O395 Ribokinase Complexed with Ribose, Adp and Sodium Ion. (pdb code 4xda). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Vibrio Cholerae O395 Ribokinase Complexed with Ribose, Adp and Sodium Ion., PDB code: 4xda:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 4xda

Go back to Sodium Binding Sites List in 4xda
Sodium binding site 1 out of 4 in the Vibrio Cholerae O395 Ribokinase Complexed with Ribose, Adp and Sodium Ion.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Vibrio Cholerae O395 Ribokinase Complexed with Ribose, Adp and Sodium Ion. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na403

b:23.8
occ:1.00
 O A:ARG285 2.2 18.8 1.0
O A:HOH565 2.2 22.9 1.0
O A:SER282 2.3 16.5 1.0
O A:ASP246 2.3 19.1 1.0
O A:HOH568 2.3 28.8 1.0
CB A:SER291 3.3 13.6 1.0
C A:ARG285 3.4 16.4 1.0
C A:SER282 3.4 19.9 1.0
C A:ASP246 3.4 21.0 1.0
OG A:SER291 3.4 18.0 1.0
O A:THR248 3.5 25.8 1.0
CB A:ASP246 3.7 22.4 1.0
CA A:VAL283 4.0 19.8 1.0
CA A:ASP246 4.0 19.4 1.0
N A:VAL283 4.0 18.3 1.0
N A:ARG285 4.0 23.5 1.0
CG A:ASP246 4.1 23.0 1.0
C A:VAL283 4.1 18.5 1.0
O A:GLY287 4.2 22.2 1.0
O A:VAL283 4.2 22.5 1.0
CA A:ARG285 4.2 20.9 1.0
N A:PHE286 4.3 18.7 1.0
OD2 A:ASP246 4.4 21.6 1.0
N A:ASP246 4.4 19.6 1.0
N A:THR247 4.4 20.8 1.0
CA A:SER282 4.4 14.0 1.0
CA A:PHE286 4.5 21.9 1.0
N A:THR248 4.6 23.9 1.0
CA A:THR247 4.6 22.0 1.0
C A:THR248 4.7 24.6 1.0
N A:GLY287 4.7 16.3 1.0
CB A:SER282 4.7 18.5 1.0
C A:PHE286 4.7 18.6 1.0
CB A:ARG285 4.7 16.6 1.0
OG A:SER282 4.7 19.7 1.0
C A:THR247 4.7 21.8 1.0
OD1 A:ASP246 4.8 22.3 1.0
CA A:SER291 4.8 15.0 1.0
N A:THR284 4.8 22.4 1.0

Sodium binding site 2 out of 4 in 4xda

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Sodium binding site 2 out of 4 in the Vibrio Cholerae O395 Ribokinase Complexed with Ribose, Adp and Sodium Ion.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Vibrio Cholerae O395 Ribokinase Complexed with Ribose, Adp and Sodium Ion. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na403

b:30.4
occ:1.00
 O B:ARG285 2.2 24.2 1.0
O B:SER282 2.2 18.8 1.0
O B:HOH593 2.2 28.9 1.0
O B:ASP246 2.3 31.0 1.0
O B:HOH633 2.4 34.4 1.0
C B:SER282 3.2 22.1 1.0
C B:ARG285 3.3 24.8 1.0
C B:ASP246 3.3 25.1 1.0
CB B:SER291 3.4 18.5 1.0
CB B:ASP246 3.6 23.0 1.0
OG B:SER291 3.7 21.7 1.0
CA B:VAL283 3.7 21.3 1.0
N B:ARG285 3.9 21.6 1.0
N B:VAL283 3.9 20.9 1.0
CA B:ASP246 4.0 26.5 1.0
CG B:ASP246 4.0 25.3 1.0
C B:VAL283 4.0 22.1 1.0
CA B:ARG285 4.1 27.1 1.0
O B:GLY287 4.1 33.3 1.0
CA B:SER282 4.3 19.3 1.0
N B:PHE286 4.3 21.5 1.0
N B:THR247 4.3 23.6 1.0
O B:VAL283 4.3 27.2 1.0
N B:THR248 4.3 20.6 1.0
OD1 B:ASP246 4.4 27.9 1.0
OD2 B:ASP246 4.5 31.2 1.0
CA B:PHE286 4.5 29.9 1.0
CB B:ARG285 4.5 23.0 1.0
CA B:THR247 4.5 23.0 1.0
N B:ASP246 4.6 30.6 1.0
OG B:SER282 4.6 28.2 1.0
CB B:SER282 4.6 20.8 1.0
N B:THR284 4.6 23.5 1.0
N B:ALA249 4.6 21.9 1.0
N B:GLY287 4.6 26.4 1.0
C B:PHE286 4.7 23.6 1.0
C B:THR247 4.7 22.8 1.0
CA B:SER291 4.9 19.3 1.0

Sodium binding site 3 out of 4 in 4xda

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Sodium binding site 3 out of 4 in the Vibrio Cholerae O395 Ribokinase Complexed with Ribose, Adp and Sodium Ion.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Vibrio Cholerae O395 Ribokinase Complexed with Ribose, Adp and Sodium Ion. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na403

b:26.3
occ:1.00
 O C:ASP246 2.2 23.8 1.0
O C:ARG285 2.2 24.8 1.0
O C:HOH687 2.3 23.0 1.0
O C:HOH643 2.3 28.1 1.0
O C:SER282 2.4 24.4 1.0
O C:HOH733 3.1 31.0 1.0
CB C:SER291 3.3 22.5 1.0
C C:SER282 3.3 26.7 1.0
C C:ASP246 3.3 26.2 1.0
C C:ARG285 3.4 25.8 1.0
OG C:SER291 3.5 24.0 1.0
CA C:VAL283 3.9 26.8 1.0
N C:VAL283 4.0 19.9 1.0
CB C:ASP246 4.0 21.1 1.0
O C:VAL283 4.0 29.6 1.0
C C:VAL283 4.1 30.8 1.0
N C:ARG285 4.1 28.4 1.0
CA C:ASP246 4.1 26.3 1.0
O C:GLY287 4.2 27.9 1.0
CA C:ARG285 4.3 25.0 1.0
N C:THR247 4.3 28.8 1.0
CG C:ASP246 4.3 23.1 1.0
N C:PHE286 4.4 28.3 1.0
CA C:SER282 4.4 22.1 1.0
OD2 C:ASP246 4.5 25.3 1.0
N C:ASP246 4.5 26.1 1.0
CA C:THR247 4.5 26.8 1.0
OG C:SER282 4.5 29.6 1.0
N C:THR248 4.5 22.8 1.0
CA C:PHE286 4.6 24.4 1.0
CB C:SER282 4.6 21.4 1.0
C C:THR247 4.7 16.9 1.0
CB C:ARG285 4.7 19.4 1.0
CA C:SER291 4.8 27.3 1.0
C C:PHE286 4.8 23.1 1.0
N C:THR284 4.8 27.6 1.0
N C:GLY287 4.8 29.1 1.0
OD1 C:ASP246 4.9 23.8 1.0
N C:ALA249 5.0 22.4 1.0

Sodium binding site 4 out of 4 in 4xda

Go back to Sodium Binding Sites List in 4xda
Sodium binding site 4 out of 4 in the Vibrio Cholerae O395 Ribokinase Complexed with Ribose, Adp and Sodium Ion.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Vibrio Cholerae O395 Ribokinase Complexed with Ribose, Adp and Sodium Ion. within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na403

b:27.1
occ:1.00
 OG D:SER291 2.1 46.8 1.0
O D:SER282 2.3 18.5 1.0
O D:ASP246 2.4 28.6 1.0
O D:ARG285 2.4 30.0 1.0
O D:GLY287 2.5 28.0 1.0
CB D:SER291 3.3 27.5 1.0
O D:HOH652 3.3 26.7 1.0
C D:SER282 3.4 15.6 1.0
CB D:ASP246 3.5 25.1 1.0
C D:ASP246 3.5 30.5 1.0
C D:ARG285 3.5 28.8 1.0
C D:GLY287 3.7 34.6 1.0
CA D:ASP246 3.9 30.7 1.0
OG D:SER282 4.0 20.4 1.0
CG D:ASP246 4.1 28.6 1.0
N D:ASP246 4.2 27.1 1.0
C D:PHE286 4.2 36.1 1.0
CA D:ARG285 4.2 31.3 1.0
O D:VAL283 4.3 19.7 1.0
N D:GLY287 4.3 27.9 1.0
CA D:VAL283 4.3 21.4 1.0
N D:ARG285 4.3 22.2 1.0
CA D:SER282 4.3 13.3 1.0
N D:VAL283 4.3 15.1 1.0
C D:VAL283 4.3 18.1 1.0
CB D:ARG285 4.3 30.2 1.0
O D:PHE286 4.3 33.0 1.0
OD1 D:ASP246 4.4 26.4 1.0
CA D:SER291 4.5 25.5 1.0
N D:PHE286 4.5 31.6 1.0
CA D:GLY287 4.5 27.1 1.0
N D:ALA288 4.6 33.5 1.0
N D:THR247 4.6 23.4 1.0
CA D:ALA288 4.6 28.4 1.0
CA D:PHE286 4.7 29.9 1.0
OD2 D:ASP246 4.7 26.1 1.0
CB D:SER282 4.8 15.8 1.0
O D:ALA288 4.8 23.1 1.0
N D:THR284 4.9 16.6 1.0

Reference:

R.Paul, M.D.Patra, U.Sen. Crystal Structure of Apo and Ligand Bound Vibrio Cholerae Ribokinase (Vc-Rk): Role of Monovalent Cation Induced Activation and Structural Flexibility in Sugar Phosphorylation Adv.Exp.Med.Biol. V. 842 293 2015.
ISSN: ISSN 0065-2598
PubMed: 25408351
DOI: 10.1007/978-3-319-11280-0_19
Page generated: Mon Oct 7 19:03:54 2024

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