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Chlorine 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:

Sodium (Na) 7 atoms

Chlorine Binding Sites:

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

Chlorine binding site 1 out of 7 in 5zwy

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


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Ribokinase From Leishmania Donovani within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl406

b:25.7
occ:1.00
 N A:ALA4 3.2 28.3 1.0
NH1 A:ARG100 3.2 16.2 1.0
NE A:ARG5 3.2 25.9 1.0
N A:ARG5 3.4 22.6 1.0
CG A:ARG5 3.7 23.8 1.0
CG A:ARG3 3.8 39.0 1.0
CA A:ARG3 3.8 37.4 1.0
CD A:ARG100 3.9 19.1 1.0
CB A:ARG5 3.9 23.2 1.0
NH1 A:ARG5 3.9 26.0 1.0
CB A:ALA4 3.9 28.6 1.0
CA A:ALA4 4.0 26.5 1.0
C A:ARG3 4.0 32.9 1.0
CZ A:ARG5 4.0 28.2 1.0
CD A:ARG5 4.1 25.1 1.0
C A:ALA4 4.2 27.1 1.0
CA A:ARG5 4.2 23.0 1.0
CZ A:ARG100 4.3 18.7 1.0
CB A:ARG3 4.4 38.4 1.0
CD1 A:ILE85 4.4 17.2 1.0
NE A:ARG100 4.5 20.2 1.0
O A:HOH581 4.8 39.1 1.0
O A:HOH592 4.8 24.2 1.0

Chlorine binding site 2 out of 7 in 5zwy

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


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Ribokinase From Leishmania Donovani within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl407

b:22.1
occ:1.00
 O A:HOH530 2.9 32.6 1.0
O B:HOH572 3.2 27.4 1.0
N A:SER105 3.3 15.1 1.0
CB A:ASN127 3.6 16.3 1.0
CA A:SER104 3.8 17.7 1.0
CG A:ASN127 3.8 18.2 1.0
OD1 A:ASN127 3.8 16.1 1.0
CB A:SER104 3.8 16.9 1.0
O A:HOH517 3.9 27.5 1.0
CA A:ASN127 3.9 15.3 1.0
CB A:SER105 4.0 14.6 1.0
C A:SER104 4.0 16.0 1.0
O B:PHE47 4.1 20.8 1.0
CD2 B:PHE47 4.2 16.9 1.0
CA A:SER105 4.2 15.7 1.0
OG A:SER105 4.2 15.9 1.0
OG A:SER104 4.4 21.0 1.0
O A:SER105 4.4 16.1 1.0
ND2 A:ASN127 4.5 15.3 1.0
C A:ASN127 4.5 14.4 1.0
CB B:PHE47 4.5 19.5 1.0
N A:ALA128 4.7 14.4 1.0
C A:SER105 4.8 15.4 1.0
CG B:PHE47 4.8 17.8 1.0
C B:PHE47 4.8 21.6 1.0

Chlorine binding site 3 out of 7 in 5zwy

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


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Ribokinase From Leishmania Donovani within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl408

b:33.9
occ:1.00
 N A:PHE51 3.1 17.6 1.0
O A:HOH521 3.6 25.0 1.0
CA A:GLY50 3.7 20.5 1.0
CD1 A:PHE51 3.8 18.1 1.0
C A:GLY50 3.9 18.1 1.0
CB A:PHE51 4.0 16.6 1.0
CA A:PHE51 4.0 16.9 1.0
O A:PHE51 4.1 16.7 1.0
CG A:PHE51 4.4 16.6 1.0
C A:PHE51 4.5 17.7 1.0
CE1 A:PHE51 4.8 17.8 1.0
O A:LYS49 5.0 21.3 1.0
OE2 A:GLU87 5.0 18.4 1.0
NE2 A:HIS48 5.0 30.8 1.0

Chlorine binding site 4 out of 7 in 5zwy

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


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Ribokinase From Leishmania Donovani within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl406

b:25.4
occ:1.00
 O B:HOH501 3.1 20.3 1.0
NH2 B:ARG64 3.1 19.5 1.0
NH1 B:ARG64 3.2 17.4 1.0
CZ B:ARG64 3.6 20.6 1.0
CE1 B:HIS320 3.6 17.9 1.0
O B:LEU316 3.8 20.0 1.0
O B:HOH541 4.0 26.5 1.0
CD2 B:LEU316 4.1 17.7 1.0
CA B:LEU316 4.2 18.6 1.0
C B:LEU316 4.4 18.5 1.0
NE2 B:HIS320 4.5 16.6 1.0
CB B:LEU316 4.5 19.3 1.0
ND1 B:HIS320 4.6 16.0 1.0
O B:HOH576 4.7 15.6 1.0
NE B:ARG64 4.9 20.1 1.0
CG B:LEU316 4.9 19.0 1.0

Chlorine binding site 5 out of 7 in 5zwy

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


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Ribokinase From Leishmania Donovani within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl407

b:28.5
occ:1.00
 NE B:ARG5 3.1 25.3 1.0
NH1 B:ARG100 3.2 19.6 1.0
N B:ALA4 3.3 33.2 1.0
N B:ARG5 3.5 23.8 1.0
CG B:ARG5 3.6 25.0 1.0
NH1 B:ARG5 3.8 30.6 1.0
CD B:ARG100 3.9 18.9 1.0
CZ B:ARG5 3.9 29.6 1.0
CG B:ARG3 3.9 40.1 1.0
CA B:ARG3 3.9 38.5 1.0
CB B:ARG5 3.9 26.7 1.0
CD B:ARG5 3.9 27.5 1.0
C B:ARG3 4.1 34.4 1.0
CA B:ALA4 4.1 27.9 1.0
CB B:ALA4 4.2 29.9 1.0
C B:ALA4 4.3 24.9 1.0
O B:HOH566 4.3 35.1 1.0
CA B:ARG5 4.3 23.6 1.0
CZ B:ARG100 4.3 18.3 1.0
CD1 B:ILE85 4.4 17.1 1.0
CB B:ARG3 4.5 40.3 1.0
NE B:ARG100 4.6 18.9 1.0
O B:HOH602 4.8 24.7 1.0

Chlorine binding site 6 out of 7 in 5zwy

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


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Ribokinase From Leishmania Donovani within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl408

b:20.2
occ:1.00
 O B:HOH575 3.0 24.0 1.0
O B:HOH529 3.0 20.9 1.0
O B:HOH543 3.1 21.8 1.0
O B:HOH533 3.1 15.3 1.0
N B:PHE51 3.3 15.3 1.0
CG B:LEU316 3.7 19.0 1.0
CD1 B:PHE51 3.8 15.5 1.0
CA B:GLY50 3.8 17.1 1.0
CD2 B:LEU316 4.0 17.7 1.0
CB B:PHE51 4.0 15.5 1.0
C B:GLY50 4.1 15.6 1.0
CD1 B:LEU316 4.1 20.0 1.0
O B:GLY313 4.2 20.4 1.0
CA B:PHE51 4.2 14.2 1.0
O B:PHE51 4.3 15.4 1.0
CG B:PHE51 4.4 14.2 1.0
CB B:GLN315 4.4 15.7 1.0
O B:HOH521 4.4 19.9 1.0
N B:LEU316 4.6 15.7 1.0
OE2 B:GLU87 4.7 17.2 1.0
C B:PHE51 4.7 15.6 1.0
CE1 B:PHE51 4.8 16.0 1.0
N B:GLN315 4.8 17.2 1.0
O B:LYS49 4.9 19.2 1.0
OE1 B:GLN315 4.9 15.9 1.0
CB B:LEU316 5.0 19.3 1.0
O B:HOH596 5.0 19.5 1.0

Chlorine binding site 7 out of 7 in 5zwy

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


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of Ribokinase From Leishmania Donovani within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl409

b:25.9
occ:1.00
 N B:SER105 3.2 17.3 1.0
O B:HOH522 3.5 32.6 1.0
CA B:SER104 3.6 20.3 1.0
CB B:ASN127 3.6 16.4 1.0
CB B:SER104 3.7 20.6 1.0
CG B:ASN127 3.8 16.6 1.0
OD1 B:ASN127 3.9 16.1 1.0
C B:SER104 3.9 17.9 1.0
CA B:ASN127 4.0 15.0 1.0
CB B:SER105 4.1 20.0 1.0
CD2 A:PHE47 4.1 18.0 1.0
CA B:SER105 4.2 18.2 1.0
OG B:SER105 4.2 19.4 1.0
OG B:SER104 4.3 25.2 1.0
O B:SER105 4.4 17.3 1.0
ND2 B:ASN127 4.5 13.8 1.0
C B:ASN127 4.6 15.4 1.0
O A:PHE47 4.7 16.9 1.0
C B:SER105 4.7 17.4 1.0
CE2 A:PHE47 4.8 17.8 1.0
N B:ALA128 4.8 14.1 1.0
O B:HOH508 4.9 29.2 1.0
O B:LYS103 4.9 22.2 1.0
N B:SER104 5.0 19.6 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: Fri Jul 26 21:49:55 2024

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