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

Go back to Chlorine Binding Sites List in 5zwy
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

Go back to Chlorine Binding Sites List in 5zwy
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

Go back to Chlorine Binding Sites List in 5zwy
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

Go back to Chlorine Binding Sites List in 5zwy
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

Go back to Chlorine Binding Sites List in 5zwy
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: Sat Dec 12 12:42:45 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy