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Caesium in PDB 4xck: Vibrio Cholerae O395 Ribokinase Complexed with Adp, Ribose and Cesium Ion.

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

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

Protein crystallography data

The structure of Vibrio Cholerae O395 Ribokinase Complexed with Adp, Ribose and Cesium Ion., PDB code: 4xck 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) 26.64 / 2.37
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 59.304, 69.553, 78.316, 106.99, 98.77, 96.46
R / Rfree (%) 18.8 / 25.1

Caesium Binding Sites:

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

Caesium binding site 1 out of 4 in 4xck

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


Mono view


Stereo pair view

A full contact list of Caesium with other atoms in the Cs binding site number 1 of Vibrio Cholerae O395 Ribokinase Complexed with Adp, Ribose and Cesium Ion. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cs403

b:0.2
occ:1.00
O A:ASP246 2.7 37.5 1.0
O A:ARG285 2.7 35.5 1.0
O A:THR248 2.8 48.3 1.0
OG A:SER291 3.2 28.0 1.0
O A:SER282 3.3 43.6 1.0
C A:ASP246 3.4 35.2 1.0
O A:GLY287 3.5 36.1 1.0
CB A:SER291 3.5 37.0 1.0
CG A:ASP246 3.7 42.9 1.0
CB A:ASP246 3.8 41.3 1.0
C A:ARG285 3.8 36.0 1.0
OD2 A:ASP246 3.8 45.0 1.0
C A:THR248 3.9 42.4 1.0
N A:THR248 4.0 40.6 1.0
N A:THR247 4.1 31.8 1.0
CA A:ASP246 4.1 37.2 1.0
C A:SER282 4.2 41.0 1.0
OD1 A:ASP246 4.2 36.6 1.0
C A:THR247 4.2 38.7 1.0
C A:GLY287 4.3 33.8 1.0
CA A:THR247 4.3 34.3 1.0
N A:GLY287 4.3 37.6 1.0
CA A:VAL283 4.3 36.7 1.0
CA A:THR248 4.4 40.9 1.0
C A:PHE286 4.4 35.6 1.0
CA A:PHE286 4.5 37.8 1.0
CB A:THR248 4.6 35.0 1.0
N A:PHE286 4.6 30.2 1.0
N A:VAL283 4.7 38.4 1.0
C A:VAL283 4.7 35.2 1.0
N A:ASP246 4.7 40.4 1.0
O A:VAL283 4.7 34.6 1.0
N A:ARG285 4.8 34.3 1.0
CA A:ARG285 4.8 38.9 1.0
CA A:GLY287 4.9 34.2 1.0
O A:THR247 4.9 40.3 1.0
N A:ALA249 5.0 40.9 1.0
O A:PHE286 5.0 32.4 1.0

Caesium binding site 2 out of 4 in 4xck

Go back to Caesium Binding Sites List in 4xck
Caesium binding site 2 out of 4 in the Vibrio Cholerae O395 Ribokinase Complexed with Adp, Ribose and Cesium Ion.


Mono view


Stereo pair view

A full contact list of Caesium with other atoms in the Cs binding site number 2 of Vibrio Cholerae O395 Ribokinase Complexed with Adp, Ribose and Cesium Ion. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cs403

b:0.5
occ:1.00
O B:ARG285 2.7 53.8 1.0
O B:ASP246 2.8 51.5 1.0
O B:HOH575 2.9 64.5 1.0
O B:GLY287 3.2 42.8 1.0
OG B:SER291 3.2 28.1 1.0
C B:ASP246 3.5 46.6 1.0
O B:SER282 3.5 39.5 1.0
CB B:SER291 3.5 30.2 1.0
CB B:ASP246 3.7 52.7 1.0
N B:THR248 3.7 39.6 1.0
CG B:ASP246 3.7 54.9 1.0
OD1 B:ASP246 3.9 50.6 1.0
C B:ARG285 3.9 51.3 1.0
N B:ALA249 4.0 39.2 1.0
N B:GLY287 4.1 52.6 1.0
CB B:THR248 4.1 46.0 1.0
N B:THR247 4.2 38.8 1.0
C B:GLY287 4.2 46.0 1.0
CA B:ASP246 4.2 51.3 1.0
OD2 B:ASP246 4.2 61.3 1.0
C B:PHE286 4.3 50.0 1.0
C B:THR247 4.3 42.4 1.0
C B:SER282 4.3 41.2 1.0
CA B:THR248 4.4 43.7 1.0
CA B:THR247 4.4 35.8 1.0
CA B:PHE286 4.6 53.8 1.0
N B:PHE286 4.7 53.7 1.0
O B:PHE286 4.7 47.3 1.0
C B:THR248 4.7 41.9 1.0
OG B:SER282 4.7 50.7 1.0
CA B:VAL283 4.7 39.1 1.0
CA B:GLY287 4.7 49.7 1.0
OG1 B:THR248 4.8 47.5 1.0
CA B:ARG285 4.9 49.2 1.0
N B:ARG285 4.9 46.8 1.0
N B:VAL283 4.9 37.7 1.0

Caesium binding site 3 out of 4 in 4xck

Go back to Caesium Binding Sites List in 4xck
Caesium binding site 3 out of 4 in the Vibrio Cholerae O395 Ribokinase Complexed with Adp, Ribose and Cesium Ion.


Mono view


Stereo pair view

A full contact list of Caesium with other atoms in the Cs binding site number 3 of Vibrio Cholerae O395 Ribokinase Complexed with Adp, Ribose and Cesium Ion. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cs403

b:0.8
occ:1.00
O C:ASP246 2.6 44.3 1.0
O C:ARG285 2.8 49.3 1.0
O C:SER282 2.8 46.9 1.0
OG C:SER291 2.9 41.2 1.0
CB C:SER291 3.2 42.9 1.0
O C:GLY287 3.5 44.1 1.0
C C:ASP246 3.6 44.0 1.0
C C:SER282 3.6 40.2 1.0
C C:ARG285 3.9 44.9 1.0
N C:THR248 4.0 48.6 1.0
CB C:ASP246 4.1 46.3 1.0
OD2 C:ASP246 4.1 50.9 1.0
CG C:ASP246 4.1 48.5 1.0
CA C:VAL283 4.2 36.9 1.0
N C:ALA249 4.2 56.5 1.0
N C:VAL283 4.3 35.0 1.0
CA C:ASP246 4.4 45.6 1.0
N C:THR247 4.4 40.1 1.0
C C:THR247 4.4 48.5 1.0
N C:GLY287 4.4 40.2 1.0
CA C:THR247 4.5 47.4 1.0
C C:GLY287 4.5 42.3 1.0
OG C:SER282 4.5 37.3 1.0
CB C:SER282 4.5 36.7 1.0
CA C:SER282 4.5 38.8 1.0
C C:VAL283 4.6 42.2 1.0
N C:ARG285 4.7 47.5 1.0
OD1 C:ASP246 4.7 47.4 1.0
CA C:SER291 4.7 43.1 1.0
CB C:THR248 4.7 47.0 1.0
CA C:THR248 4.8 49.3 1.0
CA C:ARG285 4.8 47.2 1.0
O C:VAL283 4.8 45.9 1.0
N C:PHE286 4.8 40.7 1.0
C C:PHE286 4.8 40.3 1.0
CA C:PHE286 4.9 39.7 1.0
N C:ASP246 4.9 47.5 1.0
C C:THR248 5.0 52.4 1.0

Caesium binding site 4 out of 4 in 4xck

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


Mono view


Stereo pair view

A full contact list of Caesium with other atoms in the Cs binding site number 4 of Vibrio Cholerae O395 Ribokinase Complexed with Adp, Ribose and Cesium Ion. within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cs402

b:0.4
occ:1.00
O D:ASP246 2.7 49.0 1.0
O D:SER282 2.7 36.9 1.0
O D:GLY287 2.7 58.5 1.0
O D:ARG285 2.7 60.7 1.0
OG D:SER291 2.9 42.1 1.0
O D:HOH549 3.2 56.3 1.0
CB D:SER291 3.4 45.6 1.0
CB D:ASP246 3.5 46.4 1.0
C D:ASP246 3.6 50.4 1.0
C D:SER282 3.8 37.5 1.0
C D:ARG285 3.8 61.4 1.0
C D:GLY287 3.8 57.7 1.0
CG D:ASP246 4.0 45.8 1.0
CA D:ASP246 4.1 48.8 1.0
O D:ALA288 4.2 49.5 1.0
OG D:SER282 4.2 49.2 1.0
OD1 D:ASP246 4.3 46.6 1.0
C D:PHE286 4.4 66.0 1.0
CA D:ALA288 4.4 51.6 1.0
O D:PHE286 4.4 63.3 1.0
N D:ARG285 4.5 50.8 1.0
N D:ALA288 4.5 56.1 1.0
CA D:ARG285 4.5 56.6 1.0
N D:GLY287 4.5 63.3 1.0
OD2 D:ASP246 4.6 45.8 1.0
CA D:VAL283 4.6 39.1 1.0
CA D:SER282 4.6 40.9 1.0
N D:ASP246 4.6 48.6 1.0
N D:VAL283 4.6 34.5 1.0
C D:VAL283 4.6 45.8 1.0
CB D:ARG285 4.7 54.8 1.0
O D:VAL283 4.7 48.8 1.0
N D:THR247 4.7 49.7 1.0
N D:PHE286 4.7 68.0 1.0
C D:ALA288 4.7 50.9 1.0
CA D:GLY287 4.8 60.0 1.0
CA D:PHE286 4.8 72.5 1.0
CA D:SER291 4.8 44.6 1.0
N D:THR248 4.9 44.4 1.0
CB D:SER282 5.0 45.8 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: Sun Dec 13 10:56:40 2020

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