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Zinc in PDB 5xio: Crystal Structure of Cryptosporidium Parvum Prolyl-Trna Synthetase (Cpprs) in Complex with Halofuginone

Protein crystallography data

The structure of Crystal Structure of Cryptosporidium Parvum Prolyl-Trna Synthetase (Cpprs) in Complex with Halofuginone, PDB code: 5xio was solved by V.Jain, Y.Manickam, A.Sharma, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.31 / 2.46
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 82.768, 112.635, 140.494, 90.00, 90.00, 90.00
R / Rfree (%) 19.6 / 25.2

Other elements in 5xio:

The structure of Crystal Structure of Cryptosporidium Parvum Prolyl-Trna Synthetase (Cpprs) in Complex with Halofuginone also contains other interesting chemical elements:

Bromine (Br) 2 atoms
Chlorine (Cl) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Cryptosporidium Parvum Prolyl-Trna Synthetase (Cpprs) in Complex with Halofuginone (pdb code 5xio). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of Cryptosporidium Parvum Prolyl-Trna Synthetase (Cpprs) in Complex with Halofuginone, PDB code: 5xio:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 5xio

Go back to Zinc Binding Sites List in 5xio
Zinc binding site 1 out of 2 in the Crystal Structure of Cryptosporidium Parvum Prolyl-Trna Synthetase (Cpprs) in Complex with Halofuginone


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of Cryptosporidium Parvum Prolyl-Trna Synthetase (Cpprs) in Complex with Halofuginone within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn802

b:43.2
occ:0.70
SG A:CYS702 2.2 39.2 1.0
SG A:CYS657 2.2 38.5 1.0
SG A:CYS652 2.2 36.8 1.0
CB A:CYS705 2.4 41.1 1.0
CB A:CYS702 3.2 41.2 1.0
CB A:CYS657 3.3 37.6 1.0
CB A:CYS652 3.3 40.4 1.0
N A:CYS705 3.3 48.1 1.0
CA A:CYS705 3.4 50.2 1.0
SG A:CYS705 3.7 38.7 1.0
NE1 A:TRP651 4.0 36.1 1.0
CD1 A:TRP651 4.0 33.3 1.0
N A:CYS652 4.2 43.2 1.0
C A:CYS705 4.3 52.8 1.0
CA A:CYS652 4.4 39.3 1.0
C A:PHE704 4.6 43.3 1.0
CA A:CYS657 4.7 34.9 1.0
CA A:CYS702 4.7 40.7 1.0
O A:CYS705 4.7 51.5 1.0
CB A:PHE704 4.8 43.0 1.0

Zinc binding site 2 out of 2 in 5xio

Go back to Zinc Binding Sites List in 5xio
Zinc binding site 2 out of 2 in the Crystal Structure of Cryptosporidium Parvum Prolyl-Trna Synthetase (Cpprs) in Complex with Halofuginone


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of Cryptosporidium Parvum Prolyl-Trna Synthetase (Cpprs) in Complex with Halofuginone within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn801

b:43.8
occ:0.70
CB B:CYS705 2.1 41.1 1.0
SG B:CYS657 2.2 39.8 1.0
SG B:CYS702 2.2 39.0 1.0
SG B:CYS652 2.2 37.1 1.0
CA B:CYS705 3.1 46.0 1.0
CB B:CYS702 3.2 40.2 1.0
N B:CYS705 3.2 43.9 1.0
CB B:CYS652 3.2 35.7 1.0
CB B:CYS657 3.3 39.0 1.0
SG B:CYS705 3.4 41.1 1.0
O B:HOH917 3.8 47.9 1.0
C B:CYS705 4.1 50.4 1.0
CD1 B:TRP651 4.2 27.7 1.0
NE1 B:TRP651 4.2 25.4 1.0
N B:CYS652 4.3 33.9 1.0
CA B:CYS652 4.4 35.1 1.0
O B:CYS705 4.4 42.1 1.0
C B:PHE704 4.5 43.3 1.0
CA B:CYS702 4.6 40.0 1.0
CA B:CYS657 4.7 36.5 1.0
CB B:PHE704 4.8 36.9 1.0
N B:ASP706 4.9 55.4 1.0

Reference:

V.Jain, M.Yogavel, H.Kikuchi, Y.Oshima, N.Hariguchi, M.Matsumoto, P.Goel, B.Touquet, R.S.Jumani, F.Tacchini-Cottier, K.Harlos, C.D.Huston, M.A.Hakimi, A.Sharma. Targeting Prolyl-Trna Synthetase to Accelerate Drug Discovery Against Malaria, Leishmaniasis, Toxoplasmosis, Cryptosporidiosis, and Coccidiosis Structure V. 25 1495 2017.
ISSN: ISSN 1878-4186
PubMed: 28867614
DOI: 10.1016/J.STR.2017.07.015
Page generated: Wed Dec 16 11:20:29 2020

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