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Sodium in PDB 6a8c: Ribokinase From Leishmania Donovani with Adp

Enzymatic activity of Ribokinase From Leishmania Donovani with Adp

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

Protein crystallography data

The structure of Ribokinase From Leishmania Donovani with Adp, PDB code: 6a8c 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) 51.14 / 1.98
Space group P 61
Cell size a, b, c (Å), α, β, γ (°) 100.700, 100.700, 126.280, 90.00, 90.00, 120.00
R / Rfree (%) 17 / 20.9

Other elements in 6a8c:

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

Chlorine (Cl) 9 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Ribokinase From Leishmania Donovani with Adp (pdb code 6a8c). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 9 binding sites of Sodium where determined in the Ribokinase From Leishmania Donovani with Adp, PDB code: 6a8c:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Sodium binding site 1 out of 9 in 6a8c

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Sodium binding site 1 out of 9 in the Ribokinase From Leishmania Donovani with Adp


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

b:15.5
occ:1.00
 O A:ALA67 2.3 14.1 1.0
O A:HOH519 2.4 15.9 1.0
O A:GLY92 2.4 11.3 1.0
O A:HOH600 2.4 22.3 1.0
C A:GLY92 3.3 13.1 1.0
C A:ALA67 3.4 14.8 1.0
CA A:GLY92 3.6 12.3 1.0
O A:GLY66 3.8 15.7 1.0
C A:GLY66 4.1 14.0 1.0
N A:LYS68 4.2 14.1 1.0
N A:ALA67 4.2 13.7 1.0
CA A:LYS68 4.3 17.1 1.0
CA A:ALA67 4.4 14.6 1.0
O A:GLY63 4.5 13.1 1.0
N A:VAL69 4.5 13.3 1.0
NA A:NA406 4.6 18.3 1.0
N A:VAL93 4.6 13.3 1.0
CA A:GLY63 4.6 11.7 1.0
CA A:GLY66 4.7 13.9 1.0
CG1 A:VAL69 4.8 12.7 1.0
C A:LYS68 5.0 13.7 1.0

Sodium binding site 2 out of 9 in 6a8c

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Sodium binding site 2 out of 9 in the Ribokinase From Leishmania Donovani with Adp


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

b:19.0
occ:1.00
 O A:SER308 2.3 16.6 1.0
O A:HOH527 2.3 16.7 1.0
O A:ASP272 2.4 18.7 1.0
O A:HOH583 2.4 12.5 1.0
O A:ARG311 2.4 18.1 1.0
OG A:SER317 2.9 16.2 1.0
C A:SER308 3.2 14.9 1.0
CB A:SER317 3.4 15.1 1.0
C A:ASP272 3.5 17.9 1.0
C A:ARG311 3.6 22.6 1.0
CA A:VAL309 3.7 17.0 1.0
O A:THR274 3.9 15.5 1.0
N A:VAL309 3.9 15.6 1.0
C A:VAL309 4.2 18.6 1.0
CA A:SER308 4.3 16.7 1.0
CB A:ASP272 4.3 25.9 1.0
N A:ARG311 4.3 22.6 1.0
CG A:ASP272 4.3 28.7 1.0
OG A:SER308 4.3 20.3 1.0
O A:VAL309 4.4 20.5 1.0
N A:THR273 4.4 19.1 1.0
CA A:ASP272 4.4 21.5 1.0
CB A:SER308 4.5 17.5 1.0
CA A:THR273 4.5 18.4 1.0
N A:LYS312 4.5 24.8 1.0
N A:THR274 4.5 18.9 1.0
OD1 A:ASP272 4.5 26.2 1.0
CA A:ARG311 4.5 25.0 1.0
C A:THR273 4.6 18.4 1.0
CA A:LYS312 4.6 25.6 1.0
C A:LYS312 4.7 21.3 1.0
OD2 A:ASP272 4.7 40.1 1.0
N A:THR314 4.8 17.8 1.0
N A:THR310 4.8 17.4 1.0
C A:THR274 4.9 17.6 1.0
N A:ASP272 4.9 21.5 1.0
CA A:SER317 4.9 15.5 1.0
N A:GLY313 5.0 19.8 1.0
CB A:VAL309 5.0 18.1 1.0

Sodium binding site 3 out of 9 in 6a8c

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Sodium binding site 3 out of 9 in the Ribokinase From Leishmania Donovani with Adp


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

b:30.0
occ:1.00
 O A:THR222 2.2 26.3 1.0
O A:HOH643 2.2 28.3 1.0
O A:HOH633 2.3 28.9 1.0
O A:HOH509 2.4 28.0 1.0
O A:HOH608 2.4 28.8 1.0
OE1 A:GLU210 2.5 27.5 1.0
C A:THR222 3.1 26.0 1.0
CD A:GLU210 3.4 27.5 1.0
CA A:THR222 3.5 26.5 1.0
OE2 A:GLU210 3.5 28.6 1.0
CB A:THR222 4.0 29.4 1.0
O A:HOH614 4.0 30.0 1.0
N A:ASP223 4.2 24.2 1.0
O A:HOH594 4.4 26.1 1.0
N A:THR222 4.8 25.1 1.0
CG A:GLU210 4.8 22.0 1.0
CA A:ASP223 4.8 21.6 1.0
CG2 A:THR222 4.9 30.9 1.0

Sodium binding site 4 out of 9 in 6a8c

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Sodium binding site 4 out of 9 in the Ribokinase From Leishmania Donovani with Adp


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

b:27.3
occ:1.00
 O A:HOH582 2.7 28.3 1.0
O A:HOH621 3.0 19.8 1.0
OD1 A:ASN293 3.4 31.8 1.0
ND2 A:ASN293 3.8 18.7 1.0
CG A:GLU296 3.9 23.7 1.0
CD2 A:LEU295 4.0 22.2 1.0
CG A:ASN293 4.0 23.8 1.0
CB A:LEU295 4.2 19.4 1.0
CD A:GLU296 4.4 28.7 1.0
CG A:LEU295 4.4 20.9 1.0
OE2 A:GLU296 4.4 31.9 1.0
N A:GLU296 4.7 17.2 1.0

Sodium binding site 5 out of 9 in 6a8c

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Sodium binding site 5 out of 9 in the Ribokinase From Leishmania Donovani with Adp


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 Adp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na406

b:18.3
occ:1.00
 O A:HOH519 2.8 15.9 1.0
O A:HOH651 3.2 16.2 1.0
CA A:GLY66 3.9 13.9 1.0
O A:GLY63 4.3 13.1 1.0
O A:HOH635 4.4 22.0 1.0
O A:HOH600 4.4 22.3 1.0
NA A:NA402 4.6 15.5 1.0
N A:GLY66 4.7 13.3 1.0
C A:GLY66 4.8 14.0 1.0
O A:GLY66 4.8 15.7 1.0
O A:HOH513 4.8 25.2 1.0

Sodium binding site 6 out of 9 in 6a8c

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Sodium binding site 6 out of 9 in the Ribokinase From Leishmania Donovani with Adp


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 Adp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na407

b:20.7
occ:1.00
 NH1 A:ARG5 3.3 21.2 1.0
N A:ARG100 3.3 15.1 1.0
CA A:PHE99 3.7 18.6 1.0
O A:ARG100 3.7 16.2 1.0
NE2 A:GLN140 3.8 44.7 1.0
C A:PHE99 4.0 16.6 1.0
CD1 A:PHE99 4.0 30.5 1.0
O A:HOH611 4.1 28.5 1.0
CB A:PHE99 4.1 21.0 1.0
CZ A:ARG5 4.2 26.6 1.0
CA A:ARG100 4.2 17.0 1.0
NH2 A:ARG5 4.3 23.9 1.0
C A:ARG100 4.4 17.6 1.0
CB A:ARG100 4.4 17.6 1.0
O A:MET98 4.5 26.7 1.0
CG A:PHE99 4.6 23.3 1.0
CG A:ARG100 4.8 17.3 1.0
CD A:GLN140 4.9 43.2 1.0
N A:PHE99 4.9 17.5 1.0

Sodium binding site 7 out of 9 in 6a8c

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Sodium binding site 7 out of 9 in the Ribokinase From Leishmania Donovani with Adp


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 with Adp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na502

b:20.9
occ:1.00
 O B:HOH633 2.2 16.3 1.0
O B:ALA67 2.3 14.5 1.0
O B:HOH710 2.3 29.9 1.0
O B:GLY92 2.4 12.1 1.0
C B:GLY92 3.3 14.2 1.0
C B:ALA67 3.4 15.2 1.0
CA B:GLY92 3.7 13.4 1.0
O B:GLY66 4.1 14.4 1.0
N B:LYS68 4.2 16.3 1.0
C B:GLY66 4.2 15.5 1.0
CA B:LYS68 4.3 17.5 1.0
N B:ALA67 4.3 15.6 1.0
N B:VAL69 4.3 14.3 1.0
CA B:ALA67 4.4 16.7 1.0
O B:GLY63 4.5 13.8 1.0
N B:VAL93 4.5 14.1 1.0
CA B:GLY63 4.6 12.6 1.0
CG1 B:VAL69 4.6 12.8 1.0
O B:HOH732 4.6 11.4 1.0
CA B:GLY66 4.9 14.6 1.0
C B:LYS68 4.9 15.7 1.0

Sodium binding site 8 out of 9 in 6a8c

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Sodium binding site 8 out of 9 in the Ribokinase From Leishmania Donovani with Adp


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of Ribokinase From Leishmania Donovani with Adp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na503

b:16.1
occ:1.00
 O B:ARG311 2.3 16.9 1.0
O B:SER308 2.3 18.0 1.0
O B:HOH630 2.4 13.0 1.0
O B:HOH678 2.5 16.5 1.0
O B:ASP272 2.5 18.2 1.0
OG B:SER317 3.0 13.3 1.0
C B:SER308 3.3 15.3 1.0
CB B:SER317 3.4 14.8 1.0
C B:ARG311 3.5 21.2 1.0
C B:ASP272 3.6 18.0 1.0
CA B:VAL309 3.8 16.2 1.0
N B:VAL309 4.0 16.0 1.0
O B:THR274 4.0 16.6 1.0
C B:VAL309 4.2 16.9 1.0
CB B:ASP272 4.3 21.6 1.0
N B:ARG311 4.3 21.4 1.0
CG B:ASP272 4.3 23.1 1.0
CA B:SER308 4.3 15.7 1.0
OD2 B:ASP272 4.3 29.0 1.0
OG B:SER308 4.4 17.1 1.0
N B:LYS312 4.4 20.7 1.0
O B:VAL309 4.5 16.4 1.0
CA B:ASP272 4.5 20.6 1.0
CB B:SER308 4.5 14.8 1.0
C B:LYS312 4.5 20.8 1.0
CA B:LYS312 4.5 24.4 1.0
CA B:ARG311 4.5 21.1 1.0
N B:THR273 4.6 17.8 1.0
N B:THR314 4.6 13.3 1.0
N B:THR274 4.6 17.8 1.0
CA B:THR273 4.6 18.8 1.0
C B:THR273 4.7 19.4 1.0
OD1 B:ASP272 4.8 29.0 1.0
N B:GLY313 4.8 18.6 1.0
N B:THR310 4.8 17.2 1.0
O B:LYS312 4.9 23.1 1.0
N B:ASP272 4.9 22.3 1.0
CA B:SER317 4.9 14.2 1.0

Sodium binding site 9 out of 9 in 6a8c

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Sodium binding site 9 out of 9 in the Ribokinase From Leishmania Donovani with Adp


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 9 of Ribokinase From Leishmania Donovani with Adp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na504

b:21.6
occ:1.00
 O B:HOH658 3.0 19.6 1.0
O A:HOH518 3.2 25.1 1.0
CG B:LYS49 3.9 16.5 1.0
CZ B:PHE51 4.1 11.7 1.0
CE1 B:PHE51 4.2 12.8 1.0
CB B:LYS49 4.3 15.8 1.0
CB A:ASP78 4.3 13.6 1.0
OD2 B:ASP83 4.6 12.6 1.0
NZ B:LYS49 5.0 17.8 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 01:45:31 2024

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