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Sodium in PDB 6a8b: Ribokinase From Leishmania Donovani with Amppcp

Enzymatic activity of Ribokinase From Leishmania Donovani with Amppcp

All present enzymatic activity of Ribokinase From Leishmania Donovani with Amppcp:
2.7.1.15;

Protein crystallography data

The structure of Ribokinase From Leishmania Donovani with Amppcp, PDB code: 6a8b was solved by S.Gatreddi, V.Pillalamarri, I.A.Qureshi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 31.79 / 2.01
Space group P 61
Cell size a, b, c (Å), α, β, γ (°) 100.395, 100.395, 125.785, 90.00, 90.00, 120.00
R / Rfree (%) 18.4 / 22.6

Other elements in 6a8b:

The structure of Ribokinase From Leishmania Donovani with Amppcp also contains other interesting chemical elements:

Chlorine (Cl) 7 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Ribokinase From Leishmania Donovani with Amppcp (pdb code 6a8b). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 6 binding sites of Sodium where determined in the Ribokinase From Leishmania Donovani with Amppcp, PDB code: 6a8b:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6;

Sodium binding site 1 out of 6 in 6a8b

Go back to Sodium Binding Sites List in 6a8b
Sodium binding site 1 out of 6 in the Ribokinase From Leishmania Donovani with Amppcp


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Ribokinase From Leishmania Donovani with Amppcp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na408

b:25.9
occ:1.00
 O A:HOH530 2.7 26.9 1.0
O A:HOH592 3.1 24.1 1.0
CA A:GLY66 4.0 23.4 1.0
O A:HOH575 4.4 25.9 1.0
O A:GLY63 4.4 20.7 1.0
NA A:NA409 4.5 23.9 1.0
N A:GLY66 4.8 23.0 1.0
C A:GLY66 4.8 22.3 1.0
O A:GLY66 4.9 23.3 1.0

Sodium binding site 2 out of 6 in 6a8b

Go back to Sodium Binding Sites List in 6a8b
Sodium binding site 2 out of 6 in the Ribokinase From Leishmania Donovani with Amppcp


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Ribokinase From Leishmania Donovani with Amppcp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na409

b:23.9
occ:1.00
 O A:HOH530 2.3 26.9 1.0
O A:ALA67 2.3 20.1 1.0
O A:HOH575 2.3 25.9 1.0
O A:GLY92 2.4 17.3 1.0
C A:GLY92 3.4 18.9 1.0
C A:ALA67 3.4 22.4 1.0
CA A:GLY92 3.6 18.8 1.0
O A:GLY66 4.0 23.3 1.0
C A:GLY66 4.1 22.3 1.0
N A:ALA67 4.2 21.2 1.0
N A:LYS68 4.2 22.2 1.0
CA A:LYS68 4.3 26.9 1.0
CA A:ALA67 4.4 23.0 1.0
O A:GLY63 4.4 20.7 1.0
NA A:NA408 4.5 25.9 1.0
N A:VAL69 4.5 22.3 1.0
CA A:GLY63 4.6 18.7 1.0
N A:VAL93 4.6 18.2 1.0
CA A:GLY66 4.7 23.4 1.0
CG1 A:VAL69 4.9 18.2 1.0

Sodium binding site 3 out of 6 in 6a8b

Go back to Sodium Binding Sites List in 6a8b
Sodium binding site 3 out of 6 in the Ribokinase From Leishmania Donovani with Amppcp


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Ribokinase From Leishmania Donovani with Amppcp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na410

b:29.4
occ:1.00
 O A:SER308 2.3 20.9 1.0
O A:HOH555 2.3 21.6 1.0
O A:ARG311 2.4 27.3 1.0
O A:HOH511 2.5 25.6 1.0
O A:ASP272 2.5 27.6 1.0
OG A:SER317 2.8 23.7 1.0
C A:SER308 3.2 23.5 1.0
CB A:SER317 3.3 21.7 1.0
C A:ARG311 3.6 35.2 1.0
C A:ASP272 3.7 29.2 1.0
CA A:VAL309 3.8 26.4 1.0
N A:VAL309 3.9 24.9 1.0
O A:THR274 3.9 21.3 1.0
C A:VAL309 4.2 29.4 1.0
CA A:SER308 4.2 23.7 1.0
N A:ARG311 4.3 30.3 1.0
CB A:ASP272 4.4 35.3 1.0
CB A:SER308 4.4 24.3 1.0
OG A:SER308 4.4 26.5 1.0
O A:VAL309 4.4 25.1 1.0
OD2 A:ASP272 4.4 39.1 1.0
N A:LYS312 4.5 35.1 1.0
CG A:ASP272 4.5 36.1 1.0
CA A:ASP272 4.5 34.1 1.0
CA A:ARG311 4.5 32.4 1.0
CA A:LYS312 4.5 33.4 1.0
N A:THR273 4.6 29.6 1.0
C A:LYS312 4.6 29.3 1.0
N A:THR274 4.6 30.4 1.0
C A:THR273 4.7 27.5 1.0
CA A:THR273 4.7 29.6 1.0
N A:THR314 4.7 25.1 1.0
N A:THR310 4.8 27.3 1.0
CA A:SER317 4.8 22.4 1.0
O A:LYS312 4.8 27.3 1.0
N A:ASP272 4.9 35.8 1.0
O A:THR314 4.9 23.4 1.0
C A:THR274 5.0 26.0 1.0

Sodium binding site 4 out of 6 in 6a8b

Go back to Sodium Binding Sites List in 6a8b
Sodium binding site 4 out of 6 in the Ribokinase From Leishmania Donovani with Amppcp


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Ribokinase From Leishmania Donovani with Amppcp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na406

b:28.0
occ:1.00
 O B:ALA67 2.2 20.2 1.0
O B:HOH522 2.2 21.3 1.0
O B:GLY92 2.3 17.0 1.0
C B:GLY92 3.3 21.9 1.0
C B:ALA67 3.4 23.1 1.0
CA B:GLY92 3.6 20.2 1.0
O B:GLY66 4.1 20.7 1.0
C B:GLY66 4.2 21.2 1.0
N B:LYS68 4.2 25.7 1.0
N B:ALA67 4.2 21.4 1.0
CA B:LYS68 4.3 24.6 1.0
O B:GLY63 4.3 19.9 1.0
N B:VAL69 4.4 21.5 1.0
CA B:ALA67 4.4 20.8 1.0
N B:VAL93 4.5 20.7 1.0
CA B:GLY63 4.5 18.7 1.0
NA B:NA407 4.7 30.9 1.0
CG1 B:VAL69 4.7 19.2 1.0
CA B:GLY66 4.8 20.8 1.0
C B:LYS68 4.9 24.2 1.0
C B:GLY63 5.0 19.5 1.0

Sodium binding site 5 out of 6 in 6a8b

Go back to Sodium Binding Sites List in 6a8b
Sodium binding site 5 out of 6 in the Ribokinase From Leishmania Donovani with Amppcp


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Ribokinase From Leishmania Donovani with Amppcp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na407

b:30.9
occ:1.00
 O B:HOH522 2.9 21.3 1.0
O B:HOH521 3.6 33.0 1.0
CA B:GLY66 4.0 20.8 1.0
O B:GLY63 4.3 19.9 1.0
NA B:NA406 4.7 28.0 1.0
N B:GLY66 4.7 20.9 1.0
C B:GLY66 4.9 21.2 1.0
O B:GLY66 5.0 20.7 1.0

Sodium binding site 6 out of 6 in 6a8b

Go back to Sodium Binding Sites List in 6a8b
Sodium binding site 6 out of 6 in the Ribokinase From Leishmania Donovani with Amppcp


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Ribokinase From Leishmania Donovani with Amppcp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na408

b:26.2
occ:1.00
 O B:HOH553 2.3 26.5 1.0
O B:SER308 2.3 28.1 1.0
O B:HOH512 2.4 18.4 1.0
O B:ARG311 2.4 23.8 1.0
O B:ASP272 2.6 30.8 1.0
OG B:SER317 2.7 20.9 1.0
C B:SER308 3.2 22.6 1.0
CB B:SER317 3.3 22.7 1.0
C B:ARG311 3.6 26.8 1.0
C B:ASP272 3.8 27.6 1.0
CA B:VAL309 3.8 25.1 1.0
N B:VAL309 3.9 25.1 1.0
O B:THR274 3.9 23.2 1.0
CA B:SER308 4.2 23.2 1.0
C B:VAL309 4.3 26.1 1.0
N B:ARG311 4.4 27.7 1.0
CB B:SER308 4.4 21.4 1.0
OD2 B:ASP272 4.4 37.0 1.0
CB B:ASP272 4.4 31.8 1.0
OG B:SER308 4.4 22.2 1.0
CG B:ASP272 4.5 32.6 1.0
N B:LYS312 4.5 25.3 1.0
C B:LYS312 4.6 27.3 1.0
CA B:ASP272 4.6 31.8 1.0
CA B:ARG311 4.6 26.1 1.0
CA B:LYS312 4.6 27.1 1.0
O B:VAL309 4.6 27.3 1.0
N B:THR314 4.6 20.7 1.0
N B:THR273 4.7 27.2 1.0
N B:THR274 4.7 28.0 1.0
CA B:SER317 4.7 21.4 1.0
C B:THR273 4.7 27.6 1.0
O B:LYS312 4.8 29.2 1.0
CA B:THR273 4.8 27.8 1.0
N B:GLY313 4.8 26.6 1.0
N B:THR310 4.8 25.6 1.0
O B:THR314 4.9 20.2 1.0
CA B:THR314 5.0 21.6 1.0
C B:THR274 5.0 25.7 1.0

Reference:

S.Gatreddi, V.Pillalamarri, D.Vasudevan, A.Addlagatta, I.A.Qureshi. Unraveling Structural Insights of Ribokinase From Leishmania Donovani. Int.J.Biol.Macromol. V. 136 253 2019.
ISSN: ISSN 0141-8130
PubMed: 31170491
DOI: 10.1016/J.IJBIOMAC.2019.06.001
Page generated: Tue Oct 8 01:45:28 2024

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