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Sodium in PDB 5c6c: Pkg II'S Amino Terminal Cyclic Nucleotide Binding Domain (Cnb-A) in A Complex with Camp

Enzymatic activity of Pkg II'S Amino Terminal Cyclic Nucleotide Binding Domain (Cnb-A) in A Complex with Camp

All present enzymatic activity of Pkg II'S Amino Terminal Cyclic Nucleotide Binding Domain (Cnb-A) in A Complex with Camp:
2.7.11.12;

Protein crystallography data

The structure of Pkg II'S Amino Terminal Cyclic Nucleotide Binding Domain (Cnb-A) in A Complex with Camp, PDB code: 5c6c was solved by J.C.Campbell, A.S.Reger, G.Y.Huang, B.Sankaran, J.J.Kim, C.W.Kim, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.23 / 2.05
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 46.710, 63.760, 99.540, 90.00, 90.00, 90.00
R / Rfree (%) 18.6 / 24.3

Other elements in 5c6c:

The structure of Pkg II'S Amino Terminal Cyclic Nucleotide Binding Domain (Cnb-A) in A Complex with Camp also contains other interesting chemical elements:

Cobalt (Co) 4 atoms
Cadmium (Cd) 6 atoms
Calcium (Ca) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Pkg II'S Amino Terminal Cyclic Nucleotide Binding Domain (Cnb-A) in A Complex with Camp (pdb code 5c6c). 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 Pkg II'S Amino Terminal Cyclic Nucleotide Binding Domain (Cnb-A) in A Complex with Camp, PDB code: 5c6c:

Sodium binding site 1 out of 1 in 5c6c

Go back to Sodium Binding Sites List in 5c6c
Sodium binding site 1 out of 1 in the Pkg II'S Amino Terminal Cyclic Nucleotide Binding Domain (Cnb-A) in A Complex with Camp


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Pkg II'S Amino Terminal Cyclic Nucleotide Binding Domain (Cnb-A) in A Complex with Camp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na307

b:55.4
occ:1.00
 N6 A:CMP304 2.7 26.4 1.0
O B:PHE168 2.8 35.7 1.0
CD B:ARG171 3.0 55.1 1.0
NH1 B:ARG171 3.1 50.9 1.0
OH B:TYR238 3.2 45.3 1.0
C B:PHE168 3.7 30.4 1.0
C6 A:CMP304 3.8 26.1 1.0
CA B:PHE168 3.9 35.0 1.0
NE B:ARG171 3.9 49.2 1.0
CZ B:ARG171 3.9 53.8 1.0
CB B:PHE168 3.9 30.4 1.0
CG B:ARG171 4.1 49.6 1.0
O B:HOH409 4.1 33.4 1.0
CZ B:TYR238 4.2 47.6 1.0
N7 A:CMP304 4.2 31.6 1.0
CD2 A:LEU222 4.3 33.8 1.0
C5 A:CMP304 4.3 26.9 1.0
CD1 B:LEU237 4.3 42.5 1.0
CG A:LEU222 4.4 38.7 1.0
CE1 B:TYR238 4.5 49.6 1.0
CD2 B:LEU237 4.5 45.4 1.0
CD1 B:PHE168 4.6 33.3 1.0
CG B:PHE168 4.7 31.7 1.0
CB B:ARG171 4.7 44.4 1.0
N B:LEU169 4.9 27.4 1.0
CG B:LEU237 4.9 49.2 1.0
N1 A:CMP304 5.0 26.7 1.0

Reference:

J.C.Campbell, J.J.Kim, K.Y.Li, G.Y.Huang, A.S.Reger, S.Matsuda, B.Sankaran, T.M.Link, K.Yuasa, J.E.Ladbury, D.E.Casteel, C.Kim. Structural Basis of Cyclic Nucleotide Selectivity in Cgmp-Dependent Protein Kinase II. J.Biol.Chem. V. 291 5623 2016.
ISSN: ESSN 1083-351X
PubMed: 26769964
DOI: 10.1074/JBC.M115.691303
Page generated: Mon Oct 7 20:15:19 2024

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