Atomistry » Cobalt » PDB 4xim-5d6e » 5c6c
Atomistry »
  Cobalt »
    PDB 4xim-5d6e »
      5c6c »

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

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy