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Sodium in PDB 5jix: Pkg II'S Carboxyl Terminal Cyclic Nucleotide Binding Domain (Cnb-B) in A Complex with 8-Br-Cgmp

Enzymatic activity of Pkg II'S Carboxyl Terminal Cyclic Nucleotide Binding Domain (Cnb-B) in A Complex with 8-Br-Cgmp

All present enzymatic activity of Pkg II'S Carboxyl Terminal Cyclic Nucleotide Binding Domain (Cnb-B) in A Complex with 8-Br-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 8-Br-Cgmp, PDB code: 5jix was solved by J.C.Campbell, C.W.Kim, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 41.49 / 1.47
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 41.620, 52.090, 68.640, 90.00, 90.00, 90.00
R / Rfree (%) 16.5 / 18.8

Other elements in 5jix:

The structure of Pkg II'S Carboxyl Terminal Cyclic Nucleotide Binding Domain (Cnb-B) in A Complex with 8-Br-Cgmp also contains other interesting chemical elements:

Bromine (Br) 1 atom
Calcium (Ca) 4 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 8-Br-Cgmp (pdb code 5jix). 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 8-Br-Cgmp, PDB code: 5jix:

Sodium binding site 1 out of 1 in 5jix

Go back to Sodium Binding Sites List in 5jix
Sodium binding site 1 out of 1 in the Pkg II'S Carboxyl Terminal Cyclic Nucleotide Binding Domain (Cnb-B) in A Complex with 8-Br-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 8-Br-Cgmp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na512

b:26.3
occ:1.00
 O A:ILE313 2.7 17.7 1.0
OH A:TYR307 2.8 16.6 1.0
HE2 A:TYR307 2.9 21.1 1.0
O A:HOH606 2.9 34.0 1.0
HA A:ILE313 3.0 18.0 1.0
HO2 A:EDO505 3.2 51.5 1.0
H21 A:EDO505 3.2 52.0 1.0
HH A:TYR307 3.4 19.9 1.0
HG23 A:ILE313 3.4 22.3 1.0
CE2 A:TYR307 3.5 17.6 1.0
HZ A:PHE324 3.6 21.6 1.0
CZ A:TYR307 3.6 14.9 1.0
OE2 A:GLU305 3.6 20.0 1.0
C A:ILE313 3.6 17.1 1.0
H22 A:EDO507 3.6 40.0 1.0
O2 A:EDO505 3.6 42.9 1.0
CA A:ILE313 3.7 15.0 1.0
HE2 A:PHE324 3.8 19.1 1.0
C2 A:EDO505 3.9 43.3 1.0
CD A:GLU305 4.1 19.3 1.0
HG22 A:ILE313 4.1 22.3 1.0
OE1 A:GLU305 4.1 20.2 1.0
CG2 A:ILE313 4.1 18.6 1.0
CZ A:PHE324 4.2 18.0 1.0
CE2 A:PHE324 4.3 15.9 1.0
O A:TYR312 4.4 23.5 1.0
CB A:ILE313 4.5 15.8 1.0
H22 A:EDO505 4.5 52.0 1.0
C2 A:EDO507 4.6 33.4 1.0
H21 A:EDO507 4.6 40.0 1.0
HG12 A:ILE313 4.8 23.5 1.0
CD2 A:TYR307 4.8 17.6 1.0
CE1 A:TYR307 4.9 14.6 1.0
N A:ILE314 4.9 15.3 1.0
N A:ILE313 4.9 16.1 1.0
HG21 A:ILE313 5.0 22.3 1.0
H11 A:EDO507 5.0 31.6 1.0

Reference:

J.C.Campbell, P.Henning, E.Franz, B.Sankaran, F.W.Herberg, C.Kim. Structural Basis of Analog Specificity in Pkg I and II. Acs Chem. Biol. V. 12 2388 2017.
ISSN: ESSN 1554-8937
PubMed: 28793191
DOI: 10.1021/ACSCHEMBIO.7B00369
Page generated: Tue Dec 15 11:08:16 2020

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