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Sodium in PDB 5zwy: Ribokinase From Leishmania Donovani

Enzymatic activity of Ribokinase From Leishmania Donovani

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

Protein crystallography data

The structure of Ribokinase From Leishmania Donovani, PDB code: 5zwy was solved by S.Gatreddi, D.Vasudevan, I.A.Qureshi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.61 / 1.95
Space group P 61
Cell size a, b, c (Å), α, β, γ (°) 100.253, 100.253, 126.771, 90.00, 90.00, 120.00
R / Rfree (%) 18.3 / 21.8

Other elements in 5zwy:

The structure of Ribokinase From Leishmania Donovani 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 (pdb code 5zwy). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 7 binding sites of Sodium where determined in the Ribokinase From Leishmania Donovani, PDB code: 5zwy:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7;

Sodium binding site 1 out of 7 in 5zwy

Go back to Sodium Binding Sites List in 5zwy
Sodium binding site 1 out of 7 in the Ribokinase From Leishmania Donovani


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na402

b:26.2
occ:1.00
 O A:HOH520 2.8 20.4 1.0
O A:HOH593 3.2 23.4 1.0
CA A:GLY66 4.1 22.3 1.0
O A:GLY63 4.3 18.9 1.0
O A:HOH558 4.4 31.2 1.0
NA A:NA403 4.6 22.1 1.0
N A:GLY66 4.8 21.6 1.0
C A:GLY66 4.9 22.4 1.0
O A:GLY66 4.9 19.6 1.0

Sodium binding site 2 out of 7 in 5zwy

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Sodium binding site 2 out of 7 in the Ribokinase From Leishmania Donovani


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na403

b:22.1
occ:1.00
 O A:HOH520 2.3 20.4 1.0
O A:ALA67 2.3 18.1 1.0
O A:HOH558 2.3 31.2 1.0
O A:GLY92 2.4 11.7 1.0
C A:GLY92 3.3 15.7 1.0
C A:ALA67 3.4 22.9 1.0
CA A:GLY92 3.6 15.7 1.0
O A:GLY66 4.0 19.6 1.0
C A:GLY66 4.1 22.4 1.0
CA A:LYS68 4.2 22.9 1.0
N A:LYS68 4.2 20.6 1.0
N A:ALA67 4.3 22.1 1.0
N A:VAL69 4.4 18.4 1.0
O A:GLY63 4.4 18.9 1.0
CA A:ALA67 4.5 23.6 1.0
N A:VAL93 4.5 14.6 1.0
CA A:GLY63 4.6 19.1 1.0
NA A:NA402 4.6 26.2 1.0
CG1 A:VAL69 4.7 15.0 1.0
CA A:GLY66 4.9 22.3 1.0
C A:LYS68 4.9 20.0 1.0
C A:GLY63 5.0 17.8 1.0

Sodium binding site 3 out of 7 in 5zwy

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Sodium binding site 3 out of 7 in the Ribokinase From Leishmania Donovani


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na404

b:24.4
occ:1.00
 NH2 A:ARG5 3.1 26.1 1.0
N A:ARG100 3.3 17.4 1.0
CA A:PHE99 3.8 20.1 1.0
O A:ARG100 3.8 21.8 1.0
CD1 A:PHE99 4.0 32.2 1.0
OE1 A:GLN140 4.0 51.3 1.0
CZ A:ARG5 4.0 28.2 1.0
C A:PHE99 4.0 17.6 1.0
NH1 A:ARG5 4.1 26.0 1.0
O A:HOH580 4.1 35.0 1.0
CB A:PHE99 4.2 21.0 1.0
CA A:ARG100 4.3 19.2 1.0
O A:MET98 4.4 30.4 1.0
O A:HOH582 4.4 38.2 1.0
CB A:ARG100 4.5 18.9 1.0
C A:ARG100 4.5 18.9 1.0
CG A:PHE99 4.6 25.4 1.0
CG A:ARG100 4.8 20.3 1.0
N A:PHE99 4.9 18.9 1.0

Sodium binding site 4 out of 7 in 5zwy

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Sodium binding site 4 out of 7 in the Ribokinase From Leishmania Donovani


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na405

b:24.5
occ:1.00
 O A:HOH539 3.2 18.0 1.0
CE1 A:HIS131 3.6 20.5 1.0
ND1 A:HIS131 3.7 18.4 1.0
NE2 A:HIS131 3.8 20.2 1.0
CG A:HIS131 3.8 19.7 1.0
CD2 A:HIS131 3.9 20.6 1.0
CB A:LYS103 4.0 24.9 1.0
OG A:SER104 4.6 21.0 1.0
CB A:HIS131 4.6 17.1 1.0
CG A:LYS103 4.8 28.1 1.0
O A:LYS103 5.0 20.6 1.0

Sodium binding site 5 out of 7 in 5zwy

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Sodium binding site 5 out of 7 in the Ribokinase From Leishmania Donovani


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na403

b:24.9
occ:1.00
 O B:ARG311 2.2 23.5 1.0
O B:SER308 2.3 25.1 1.0
O B:ASP272 2.4 29.7 1.0
O B:HOH556 2.4 22.3 1.0
O B:HOH531 2.5 16.2 1.0
OG B:SER317 2.9 17.4 1.0
C B:SER308 3.2 23.8 1.0
CB B:SER317 3.5 17.5 1.0
C B:ARG311 3.5 31.3 1.0
C B:ASP272 3.6 27.4 1.0
CA B:VAL309 3.8 24.9 1.0
N B:VAL309 3.9 25.3 1.0
O B:THR274 3.9 23.4 1.0
C B:VAL309 4.2 25.7 1.0
CB B:ASP272 4.2 36.2 1.0
N B:ARG311 4.2 31.7 1.0
CA B:SER308 4.2 22.2 1.0
CG B:ASP272 4.4 32.4 1.0
CB B:SER308 4.4 22.2 1.0
OD2 B:ASP272 4.4 42.2 1.0
N B:LYS312 4.4 31.2 1.0
CA B:ASP272 4.5 31.6 1.0
CA B:LYS312 4.5 33.2 1.0
CA B:ARG311 4.5 29.5 1.0
N B:THR273 4.5 24.6 1.0
O B:VAL309 4.5 24.1 1.0
C B:LYS312 4.6 27.0 1.0
N B:THR274 4.6 23.6 1.0
CA B:THR273 4.6 27.5 1.0
OG B:SER308 4.6 27.4 1.0
C B:THR273 4.7 26.9 1.0
N B:THR314 4.7 21.3 1.0
O B:LYS312 4.8 30.2 1.0
N B:THR310 4.8 26.3 1.0
N B:ASP272 4.9 33.3 1.0
C B:THR274 4.9 24.0 1.0
CA B:SER317 5.0 17.7 1.0
N B:GLY313 5.0 25.4 1.0

Sodium binding site 6 out of 7 in 5zwy

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Sodium binding site 6 out of 7 in the Ribokinase From Leishmania Donovani


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na404

b:24.1
occ:1.00
 CB B:PRO162 3.5 19.7 1.0
CD B:PRO134 3.8 17.9 1.0
CG B:PRO164 3.9 20.8 1.0
CG2 B:THR133 4.0 18.0 1.0
CB B:THR133 4.1 17.4 1.0
CB B:PRO164 4.1 21.1 1.0
CD B:PRO164 4.1 20.0 1.0
CA B:THR133 4.3 15.8 1.0
CG B:PRO162 4.4 20.0 1.0
OG1 B:THR165 4.7 15.8 1.0
CG B:PRO134 4.7 21.3 1.0
CA B:PRO162 4.8 21.2 1.0
N B:PRO134 4.9 17.2 1.0

Sodium binding site 7 out of 7 in 5zwy

Go back to Sodium Binding Sites List in 5zwy
Sodium binding site 7 out of 7 in the Ribokinase From Leishmania Donovani


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of Ribokinase From Leishmania Donovani within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na405

b:20.6
occ:1.00
 O B:HOH536 2.2 22.1 1.0
O B:ALA67 2.2 19.7 1.0
O B:HOH591 2.4 30.8 1.0
O B:GLY92 2.4 17.0 1.0
C B:GLY92 3.4 16.6 1.0
C B:ALA67 3.4 19.9 1.0
CA B:GLY92 3.7 16.4 1.0
CA B:LYS68 4.1 21.2 1.0
N B:LYS68 4.1 21.2 1.0
O B:GLY66 4.2 17.0 1.0
C B:GLY66 4.3 17.7 1.0
N B:VAL69 4.3 18.6 1.0
N B:ALA67 4.4 18.4 1.0
O B:GLY63 4.4 16.9 1.0
CA B:ALA67 4.5 20.2 1.0
N B:VAL93 4.6 15.6 1.0
CA B:GLY63 4.7 15.3 1.0
CG1 B:VAL69 4.7 19.6 1.0
C B:LYS68 4.8 20.3 1.0
CA B:GLY66 4.9 17.0 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: Mon Aug 18 03:30:07 2025

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