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Cobalt 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:

Cadmium (Cd) 6 atoms
Calcium (Ca) 2 atoms
Sodium (Na) 1 atom

Cobalt Binding Sites:

The binding sites of Cobalt 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 Cobalt atom.
In total 4 binding sites of Cobalt where determined in the Pkg II'S Amino Terminal Cyclic Nucleotide Binding Domain (Cnb-A) in A Complex with Camp, PDB code: 5c6c:
Jump to Cobalt binding site number: 1; 2; 3; 4;

Cobalt binding site 1 out of 4 in 5c6c

Go back to Cobalt Binding Sites List in 5c6c
Cobalt binding site 1 out of 4 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 Cobalt with other atoms in the Co 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
A:Co305

b:59.7
occ:1.00
 OE2 A:GLU210 3.0 23.1 1.0
OE1 A:GLU210 3.1 27.1 1.0
CD A:GLU210 3.3 21.6 1.0
O A:HOH430 3.9 21.5 1.0
CG A:GLU210 4.6 17.2 1.0
CO A:CO307 4.8 30.8 1.0

Cobalt binding site 2 out of 4 in 5c6c

Go back to Cobalt Binding Sites List in 5c6c
Cobalt binding site 2 out of 4 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 Cobalt with other atoms in the Co binding site number 2 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
A:Co306

b:42.3
occ:1.00
 CD A:CD303 2.4 18.5 1.0
NH1 A:ARG187 3.1 22.5 1.0
NH2 A:ARG187 3.4 33.7 1.0
CZ A:ARG187 3.7 36.6 1.0
O A:HOH468 3.9 31.8 1.0
NE2 A:HIS204 4.0 20.0 1.0
O A:HOH453 4.1 30.9 1.0
O A:HOH414 4.2 15.9 1.0
O A:HOH463 4.3 33.8 1.0
O2 A:EDO309 4.6 58.1 1.0
CE1 A:HIS204 4.6 25.5 1.0
HO2 A:EDO309 4.8 69.7 1.0
O A:HOH409 4.9 19.5 1.0
CD2 A:HIS204 4.9 18.1 1.0

Cobalt binding site 3 out of 4 in 5c6c

Go back to Cobalt Binding Sites List in 5c6c
Cobalt binding site 3 out of 4 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 Cobalt with other atoms in the Co binding site number 3 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
A:Co307

b:30.8
occ:1.00
 N A:GLY211 3.5 17.7 1.0
OE1 A:GLU210 3.5 27.1 1.0
CA A:GLY211 3.5 22.6 1.0
OE2 A:GLU210 3.6 23.1 1.0
CD A:GLU210 3.7 21.6 1.0
CE A:MET227 4.0 18.1 1.0
C A:GLY211 4.0 23.0 1.0
O A:GLY211 4.2 26.9 1.0
CG A:ARG212 4.7 25.5 1.0
C A:GLU210 4.7 17.0 1.0
N A:ARG212 4.8 20.1 1.0
CO A:CO305 4.8 59.7 1.0
CG A:GLU210 4.9 17.2 1.0
OG1 A:THR250 5.0 18.6 1.0

Cobalt binding site 4 out of 4 in 5c6c

Go back to Cobalt Binding Sites List in 5c6c
Cobalt binding site 4 out of 4 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 Cobalt with other atoms in the Co binding site number 4 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:Co305

b:61.6
occ:0.75
 O B:HOH405 2.5 33.7 1.0
NZ B:LYS156 4.1 48.8 1.0
O B:VAL149 4.4 37.1 1.0
CE B:LYS156 4.4 44.0 1.0
O B:GLU182 4.6 45.8 1.0
CA B:ARG150 4.8 64.8 1.0
N B:LYS151 4.8 36.2 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 Jul 30 17:43:23 2024

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