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Bromine 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:

Calcium (Ca) 4 atoms
Sodium (Na) 1 atom

Bromine Binding Sites:

The binding sites of Bromine 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 Bromine atom.
In total only one binding site of Bromine 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:

Bromine binding site 1 out of 1 in 5jix

Go back to Bromine Binding Sites List in 5jix
Bromine 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 Bromine with other atoms in the Br 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:Br511

b:17.4
occ:0.55
 BR A:6J7511 0.0 17.4 0.6
C9 A:6J7511 1.9 16.4 1.0
H7 A:6J7511 2.6 18.5 1.0
N A:6J7511 2.8 15.8 1.0
N4 A:6J7511 2.9 18.0 1.0
HD2 A:LYS347 3.0 22.7 1.0
HD11 A:LEU349 3.0 22.6 1.0
HG21 A:VAL333 3.1 19.4 1.0
HD21 A:LEU349 3.1 24.8 1.0
C4 A:6J7511 3.2 15.4 1.0
HH A:TYR404 3.7 23.8 1.0
HZ2 A:LYS347 3.7 26.1 1.0
O A:HOH650 3.8 23.5 1.0
O A:HOH615 3.9 21.7 1.0
HG11 A:VAL333 3.9 18.5 1.0
CG2 A:VAL333 3.9 16.2 1.0
OH A:TYR404 3.9 19.8 1.0
HG22 A:VAL333 3.9 19.4 1.0
CD1 A:LEU349 3.9 18.9 1.0
HB3 A:PHE355 3.9 16.7 1.0
CD A:LYS347 4.0 18.9 1.0
C8 A:6J7511 4.0 16.2 1.0
C5 A:6J7511 4.0 13.8 1.0
HO4 A:6J7511 4.0 18.5 1.0
CD2 A:LEU349 4.0 20.6 1.0
H21 A:EDO509 4.0 39.5 1.0
H22 A:EDO509 4.1 39.5 1.0
O5 A:6J7511 4.2 15.2 1.0
HD13 A:LEU349 4.2 22.6 1.0
HD22 A:LEU349 4.3 24.8 1.0
C2 A:6J7511 4.3 14.4 1.0
HD11 A:ILE370 4.3 18.2 1.0
CG A:LEU349 4.4 16.7 1.0
HD3 A:LYS347 4.4 22.7 1.0
NZ A:LYS347 4.5 21.7 1.0
HG23 A:VAL333 4.5 19.4 1.0
O4 A:6J7511 4.5 15.4 1.0
HG A:LEU349 4.5 20.1 1.0
HB2 A:PHE355 4.5 16.7 1.0
HE3 A:LYS347 4.5 23.0 1.0
HG3 A:LYS347 4.5 21.0 1.0
H3 A:6J7511 4.6 17.3 1.0
HD12 A:LEU349 4.6 22.6 1.0
C2 A:EDO509 4.6 32.9 1.0
CE A:LYS347 4.6 19.2 1.0
CG1 A:VAL333 4.6 15.4 1.0
HG2 A:LYS347 4.6 21.0 1.0
HG13 A:VAL333 4.6 18.5 1.0
HD12 A:ILE370 4.6 18.2 1.0
CG A:LYS347 4.7 17.5 1.0
CB A:PHE355 4.7 13.9 1.0
HD23 A:LEU349 4.7 24.8 1.0
O A:TYR354 4.8 15.7 1.0
HZ3 A:LYS347 4.8 26.1 1.0
CB A:VAL333 4.8 14.8 1.0
HD21 A:LEU408 4.9 25.4 1.0
CD1 A:ILE370 4.9 15.1 1.0
HA A:PHE355 5.0 16.1 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: Thu Jul 11 00:07:08 2024

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