Sodium 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:

Chlorine

(Cl)

3 atoms

The binding sites of Sodium 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 Sodium atom.
In total only one binding site of Sodium was determined in the Crystal Structure of the Cgmp-Dependent Protein Kinase Pkg From Plasmodium Vivax - Amppnp Bound, PDB code: 5dzc:

Sodium binding site 1 out of 1 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 Sodium with other atoms in the Na 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:Na1006 b:78.0 occ:1.00 O1G A:ANP1001 2.2 99.5 1.0 O2A A:ANP1001 2.2 91.6 1.0 OD1 A:ASN662 2.3 80.8 1.0 OD2 A:ASP675 3.3 70.4 1.0 CG A:ASN662 3.4 67.2 1.0 PG A:ANP1001 3.7 0.6 1.0 PA A:ANP1001 3.7 95.0 1.0 O3' A:ANP1001 3.8 81.3 1.0 CB A:ASP675 3.9 64.9 1.0 O1B A:ANP1001 3.9 92.6 1.0 O A:GLU661 4.0 62.0 1.0 CG A:ASP675 4.0 68.5 1.0 CA A:ASN662 4.2 61.0 1.0 ND2 A:ASN662 4.3 67.0 1.0 CD1 A:ILE674 4.3 60.2 1.0 CB A:ASN662 4.4 63.2 1.0 C A:GLU661 4.4 60.5 1.0 O3G A:ANP1001 4.4 98.1 1.0 O3A A:ANP1001 4.4 95.3 1.0 N3B A:ANP1001 4.5 98.2 1.0 N A:ASN662 4.5 59.9 1.0 C3' A:ANP1001 4.5 76.9 1.0 O2G A:ANP1001 4.5 95.3 1.0 PB A:ANP1001 4.6 97.6 1.0 O1A A:ANP1001 4.6 96.0 1.0 O5' A:ANP1001 4.6 86.6 1.0 CG1 A:ILE674 4.9 58.4 1.0 CB A:GLU661 4.9 62.0 1.0 C5' A:ANP1001 4.9 82.2 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