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Calcium 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
Sodium (Na) 1 atom

Calcium Binding Sites:

The binding sites of Calcium 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 Calcium atom.
In total 4 binding sites of Calcium where determined in the Pkg II'S Carboxyl Terminal Cyclic Nucleotide Binding Domain (Cnb-B) in A Complex with 8-Br-Cgmp, PDB code: 5jix:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 5jix

Go back to Calcium Binding Sites List in 5jix
Calcium binding site 1 out of 4 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 Calcium with other atoms in the Ca 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:Ca501

b:31.8
occ:1.00
 O A:HOH700 2.3 40.5 1.0
O A:HOH639 2.4 25.4 1.0
O A:THR348 2.4 18.1 1.0
O A:HOH617 2.4 27.0 1.0
H A:THR348 3.6 20.8 1.0
C A:THR348 3.6 19.1 1.0
HA A:LEU349 3.8 21.2 1.0
HG1 A:THR348 3.9 29.0 1.0
HD23 A:LEU349 3.9 24.8 1.0
HB2 A:LYS347 3.9 20.9 1.0
OG1 A:THR348 4.2 24.2 1.0
N A:THR348 4.2 17.3 1.0
O A:HOH649 4.3 26.9 1.0
OE1 A:GLU353 4.5 21.6 1.0
CA A:THR348 4.5 17.1 1.0
N A:LEU349 4.5 15.7 1.0
CA A:LEU349 4.6 17.6 1.0
OE2 A:GLU353 4.7 24.8 1.0
HD3 A:LYS347 4.9 22.7 1.0
CD2 A:LEU349 4.9 20.6 1.0
CB A:LYS347 4.9 17.4 1.0
HG3 A:LYS347 4.9 21.0 1.0

Calcium binding site 2 out of 4 in 5jix

Go back to Calcium Binding Sites List in 5jix
Calcium binding site 2 out of 4 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 Calcium with other atoms in the Ca binding site number 2 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:Ca502

b:46.2
occ:1.00
 O A:HOH718 2.9 42.5 1.0
O A:HOH702 3.4 47.3 1.0
HB3 A:ASN407 4.0 24.4 1.0
OD2 A:ASP411 4.3 27.1 1.0
OD1 A:ASP411 4.5 23.8 1.0
CB A:ASN407 4.9 20.4 1.0
CG A:ASP411 4.9 24.1 1.0

Calcium binding site 3 out of 4 in 5jix

Go back to Calcium Binding Sites List in 5jix
Calcium binding site 3 out of 4 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 Calcium with other atoms in the Ca binding site number 3 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:Ca503

b:32.9
occ:1.00
 O A:HOH711 2.3 28.4 1.0
O A:HOH607 2.5 29.2 1.0
O A:HOH682 2.5 30.1 1.0
O A:HOH605 3.0 32.9 1.0
O A:HOH716 3.3 45.1 1.0
OD2 A:ASP412 4.1 18.5 1.0
HZ2 A:LYS358 4.2 23.9 1.0
O A:HOH612 4.4 33.2 1.0
HZ1 A:LYS358 4.4 23.9 1.0
HB3 A:ASP412 4.5 20.0 1.0
HB2 A:SER367 4.5 21.3 1.0
O A:HOH640 4.5 21.3 1.0
OD1 A:ASN409 4.6 19.2 1.0
NZ A:LYS358 4.7 19.9 1.0
HB2 A:ASP412 4.8 20.0 1.0
HB3 A:SER367 4.9 21.3 1.0
HE3 A:LYS358 4.9 23.6 1.0
CB A:ASP412 5.0 16.7 1.0
CG A:ASP412 5.0 19.8 1.0

Calcium binding site 4 out of 4 in 5jix

Go back to Calcium Binding Sites List in 5jix
Calcium binding site 4 out of 4 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 Calcium with other atoms in the Ca binding site number 4 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:Ca504

b:20.8
occ:1.00
 OE1 A:GLU395 2.3 22.1 1.0
O A:HOH657 2.3 22.7 1.0
OE1 A:GLN398 2.5 20.5 1.0
HE22 A:GLN398 3.3 26.2 1.0
CD A:GLN398 3.4 20.5 1.0
CD A:GLU395 3.5 21.4 1.0
HB2 A:GLU395 3.7 29.2 1.0
NE2 A:GLN398 3.8 21.9 1.0
HA A:GLU395 3.9 20.9 1.0
OE2 A:GLU395 4.3 24.2 1.0
CB A:GLU395 4.4 24.3 1.0
CA A:GLU395 4.4 17.4 1.0
CG A:GLU395 4.5 24.0 1.0
H A:GLU395 4.5 21.7 1.0
O A:THR393 4.5 21.8 1.0
N A:GLU395 4.5 18.1 1.0
O A:GLY392 4.6 22.8 1.0
HE21 A:GLN398 4.6 26.2 1.0
HA A:THR393 4.7 23.1 1.0
O A:HOH717 4.7 46.4 1.0
CG A:GLN398 4.8 19.7 1.0
C A:THR393 4.9 19.9 1.0
HG2 A:GLU395 4.9 28.8 1.0
HG3 A:GLN398 4.9 23.7 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: Wed Jul 9 07:07:49 2025

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