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Sodium in PDB 5bv6: Pkg II'S Carboxyl Terminal Cyclic Nucleotide Binding Domain (Cnb-B) in A Complex with Cgmp

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

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

Protein crystallography data

The structure of Pkg II'S Carboxyl Terminal Cyclic Nucleotide Binding Domain (Cnb-B) in A Complex with Cgmp, PDB code: 5bv6 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) 40.77 / 1.94
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 40.344, 50.479, 69.167, 90.00, 90.00, 90.00
R / Rfree (%) 17.7 / 21.1

Other elements in 5bv6:

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

Calcium (Ca) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Pkg II'S Carboxyl Terminal Cyclic Nucleotide Binding Domain (Cnb-B) in A Complex with Cgmp (pdb code 5bv6). 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 Carboxyl Terminal Cyclic Nucleotide Binding Domain (Cnb-B) in A Complex with Cgmp, PDB code: 5bv6:

Sodium binding site 1 out of 1 in 5bv6

Go back to Sodium Binding Sites List in 5bv6
Sodium binding site 1 out of 1 in the Pkg II'S Carboxyl Terminal Cyclic Nucleotide Binding Domain (Cnb-B) in A Complex with Cgmp


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 Carboxyl Terminal Cyclic Nucleotide Binding Domain (Cnb-B) in A Complex with Cgmp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na505

b:35.8
occ:1.00
 N A:TYR354 3.2 21.2 1.0
O A:TYR354 3.2 25.9 1.0
OH A:TYR404 3.4 44.6 1.0
CD2 A:TYR354 3.5 23.2 1.0
CE2 A:TYR354 3.6 33.9 1.0
CB A:GLU353 3.6 23.6 1.0
CG A:TYR354 3.6 21.3 1.0
CZ A:TYR354 3.7 38.1 1.0
CD1 A:TYR354 3.7 23.8 1.0
CE1 A:TYR354 3.8 33.5 1.0
CA A:GLU353 3.9 23.6 1.0
C A:TYR354 4.0 23.2 1.0
CA A:TYR354 4.0 17.4 1.0
C A:GLU353 4.0 24.7 1.0
CZ A:TYR404 4.1 39.2 1.0
OE2 A:GLU353 4.1 48.9 1.0
CE1 A:TYR404 4.4 45.4 1.0
O A:HOH629 4.4 25.8 1.0
CG A:GLU353 4.4 26.5 1.0
OH A:TYR354 4.4 39.6 1.0
CB A:TYR354 4.4 17.4 1.0
CD A:GLU353 4.7 40.6 1.0
CD2 A:LEU349 4.8 30.0 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: Tue Dec 15 10:29:50 2020

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