Chlorine in PDB 5dzc: Crystal Structure of the Cgmp-Dependent Protein Kinase Pkg From Plasmodium Vivax - Amppnp Bound

The structure of Crystal Structure of the Cgmp-Dependent Protein Kinase Pkg From Plasmodium Vivax - Amppnp Bound, PDB code: 5dzc was solved by J.R.Walker, M.El Bakkouri, P.Loppnau, S.Graslund, H.He, A.Seitova, A.Hutchinson, C.Bountra, A.M.Edwards, C.H.Arrowsmith, R.Hui, M.Amani, Structural Genomics Consortium (Sgc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 2.30
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	193.111, 117.906, 67.731, 90.00, 95.08, 90.00
R / Rfree (%)	22.1 / 25.5

The structure of Crystal Structure of the Cgmp-Dependent Protein Kinase Pkg From Plasmodium Vivax - Amppnp Bound also contains other interesting chemical elements:

Sodium

(Na)

1 atom

The binding sites of Chlorine atom in the Crystal Structure of the Cgmp-Dependent Protein Kinase Pkg From Plasmodium Vivax - Amppnp Bound (pdb code 5dzc). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 3 binding sites of Chlorine where determined in the Crystal Structure of the Cgmp-Dependent Protein Kinase Pkg From Plasmodium Vivax - Amppnp Bound, PDB code: 5dzc:
Jump to Chlorine binding site number: 1; 2; 3;

Chlorine binding site 1 out of 3 in the Crystal Structure of the Cgmp-Dependent Protein Kinase Pkg From Plasmodium Vivax - Amppnp Bound


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Crystal Structure of the Cgmp-Dependent Protein Kinase Pkg From Plasmodium Vivax - Amppnp Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl1003 b:67.4 occ:1.00 O A:HOH1122 2.9 63.8 1.0 NH2 A:ARG485 3.2 61.5 1.0 N A:SER446 3.5 55.8 1.0 N A:ARG447 3.6 55.4 1.0 CB A:ARG447 3.7 58.4 1.0 CA A:GLY445 3.8 58.2 1.0 OH A:TYR449 3.8 61.1 1.0 CG A:ARG447 4.1 59.8 1.0 NH1 A:ARG447 4.1 66.5 1.0 CA A:ARG447 4.2 55.8 1.0 C A:GLY445 4.2 56.1 1.0 CZ A:ARG485 4.3 62.4 1.0 CD A:ARG447 4.3 63.0 1.0 CE2 A:TYR449 4.3 59.6 1.0 NE A:ARG485 4.4 64.5 1.0 C A:SER446 4.4 54.5 1.0 O A:ARG447 4.5 55.7 1.0 CA A:SER446 4.5 54.5 1.0 CZ A:TYR449 4.6 60.3 1.0 OG A:SER446 4.6 56.1 1.0 C A:ARG447 4.8 54.9 1.0 CG1 A:ILE439 4.8 70.8 1.0

Chlorine binding site 2 out of 3 in the Crystal Structure of the Cgmp-Dependent Protein Kinase Pkg From Plasmodium Vivax - Amppnp Bound


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Crystal Structure of the Cgmp-Dependent Protein Kinase Pkg From Plasmodium Vivax - Amppnp Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl1004 b:97.0 occ:1.00 N A:ALA176 3.2 61.7 1.0 CB A:ALA176 3.4 60.7 1.0 CB A:GLU175 3.7 65.1 1.0 CA A:ALA176 3.9 61.4 1.0 N A:GLU175 3.9 60.5 1.0 CA A:GLU175 4.1 63.0 1.0 C A:GLU175 4.1 62.8 1.0 CB A:THR174 4.1 56.9 1.0 O A:HOH1234 4.2 73.3 1.0 OG1 A:THR174 4.4 57.3 1.0 C A:THR174 4.7 58.8 1.0 CG2 A:THR174 5.0 55.5 1.0

Chlorine binding site 3 out of 3 in the Crystal Structure of the Cgmp-Dependent Protein Kinase Pkg From Plasmodium Vivax - Amppnp Bound


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Crystal Structure of the Cgmp-Dependent Protein Kinase Pkg From Plasmodium Vivax - Amppnp Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl1005 b:93.0 occ:1.00 N A:VAL306 3.0 47.7 1.0 O A:VAL306 3.5 49.0 1.0 CB A:VAL306 3.8 47.1 1.0 CA A:ILE305 3.8 49.4 1.0 CA A:VAL306 3.8 47.1 1.0 O A:ALA304 3.8 48.6 1.0 C A:ILE305 3.9 48.1 1.0 C A:VAL306 4.1 47.9 1.0 NH1 A:ARG307 4.2 56.0 1.0 CG2 A:VAL306 4.2 47.0 1.0 CG2 A:ILE305 4.7 51.2 1.0 C A:ALA304 4.7 47.9 1.0 CB A:ILE305 4.8 50.6 1.0 N A:ILE305 4.8 48.8 1.0

M.El Bakkouri, I.Kouidmi, A.K.Wernimont, M.Amani, A.Hutchinson, P.Loppnau, J.J.Kim, C.Flueck, J.R.Walker, A.Seitova, G.Senisterra, Y.Kakihara, C.Kim, M.J.Blackman, C.Calmettes, D.A.Baker, R.Hui. Structures of the Cgmp-Dependent Protein Kinase in Malaria Parasites Reveal A Unique Structural Relay Mechanism For Activation. Proc.Natl.Acad.Sci.Usa V. 116 14164 2019.
ISSN: ESSN 1091-6490
PubMed: 31239348
DOI: 10.1073/PNAS.1905558116