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Cadmium 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:

Cobalt (Co) 4 atoms
Calcium (Ca) 2 atoms
Sodium (Na) 1 atom

Cadmium Binding Sites:

The binding sites of Cadmium 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 Cadmium atom.
In total 6 binding sites of Cadmium 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 Cadmium binding site number: 1; 2; 3; 4; 5; 6;

Cadmium binding site 1 out of 6 in 5c6c

Go back to Cadmium Binding Sites List in 5c6c
Cadmium binding site 1 out of 6 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 Cadmium with other atoms in the Cd 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:Cd301

b:36.7
occ:1.00
 O A:HOH465 2.6 46.7 1.0
SG A:CYS183 2.7 44.3 1.0
CB A:CYS183 3.9 36.0 1.0
CD A:CD302 3.9 35.8 0.9
CA A:CYS183 4.1 30.9 1.0
O A:HOH470 4.5 49.6 1.0
O A:CYS183 5.0 22.9 1.0

Cadmium binding site 2 out of 6 in 5c6c

Go back to Cadmium Binding Sites List in 5c6c
Cadmium binding site 2 out of 6 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 Cadmium with other atoms in the Cd 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:Cd302

b:35.8
occ:0.86
 O A:HOH462 2.5 23.5 1.0
O A:CYS183 2.5 22.9 1.0
O A:HOH457 2.7 13.7 1.0
SG A:CYS183 2.8 44.3 1.0
C A:CYS183 3.5 28.7 1.0
CB A:CYS183 3.7 36.0 1.0
CA A:CYS183 3.9 30.9 1.0
CD A:CD301 3.9 36.7 1.0
CD1 A:LEU257 4.4 26.8 1.0
CG2 A:VAL261 4.5 52.5 1.0
CD1 A:TYR185 4.5 24.8 1.0
CG1 A:VAL261 4.6 42.1 1.0
N A:MET184 4.6 20.0 1.0
CB A:VAL261 5.0 43.9 1.0
CA A:MET184 5.0 17.7 1.0

Cadmium binding site 3 out of 6 in 5c6c

Go back to Cadmium Binding Sites List in 5c6c
Cadmium binding site 3 out of 6 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 Cadmium with other atoms in the Cd 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:Cd303

b:18.5
occ:1.00
 CO A:CO306 2.4 42.3 1.0
NE2 A:HIS204 2.4 20.0 1.0
CD2 A:HIS204 3.4 18.1 1.0
CE1 A:HIS204 3.4 25.5 1.0
O A:HOH409 4.3 19.5 1.0
CB A:ASN203 4.5 24.9 1.0
ND1 A:HIS204 4.5 20.8 1.0
NH1 A:ARG187 4.5 22.5 1.0
CG A:HIS204 4.5 20.8 1.0
ND2 A:ASN203 4.6 18.2 1.0
O A:HOH417 4.7 19.9 1.0
O A:HOH414 4.7 15.9 1.0
O A:HOH433 4.9 16.2 1.0

Cadmium binding site 4 out of 6 in 5c6c

Go back to Cadmium Binding Sites List in 5c6c
Cadmium binding site 4 out of 6 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 Cadmium with other atoms in the Cd 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:Cd301

b:47.9
occ:0.63
 O B:HOH434 2.6 22.7 1.0
SG A:CYS240 2.7 44.8 0.6
SG A:CYS240 2.8 50.6 0.4
SG B:CYS240 3.1 94.5 1.0
CB A:CYS240 3.2 39.5 0.4
CB B:CYS240 3.3 69.2 1.0
CB A:CYS240 3.3 36.7 0.6
CD B:CD302 3.4 45.8 0.6
CG2 B:THR243 4.5 64.2 1.0
CB A:TYR238 4.5 41.1 1.0
CA A:CYS240 4.8 38.8 0.4
CA B:CYS240 4.8 73.9 1.0
CA A:CYS240 4.8 38.2 0.6

Cadmium binding site 5 out of 6 in 5c6c

Go back to Cadmium Binding Sites List in 5c6c
Cadmium binding site 5 out of 6 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 Cadmium with other atoms in the Cd binding site number 5 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:Cd302

b:45.8
occ:0.64
 SG A:CYS240 2.4 44.8 0.6
O A:HOH452 2.7 37.3 1.0
CB A:CYS240 2.9 39.5 0.4
CB B:CYS240 3.1 69.2 1.0
SG B:CYS240 3.1 94.5 1.0
CB A:CYS240 3.2 36.7 0.6
CD B:CD301 3.4 47.9 0.6
CA A:CYS240 3.9 38.8 0.4
CA A:CYS240 3.9 38.2 0.6
CA B:CYS240 3.9 73.9 1.0
SG A:CYS240 4.2 50.6 0.4
N B:THR241 4.3 79.4 1.0
O A:ASN239 4.7 54.6 1.0
C B:CYS240 4.7 77.7 1.0
N A:CYS240 4.8 40.2 0.4
N A:CYS240 4.8 40.4 0.6
N A:THR241 4.9 25.5 1.0
C A:CYS240 4.9 29.5 0.4
C A:CYS240 5.0 28.5 0.6

Cadmium binding site 6 out of 6 in 5c6c

Go back to Cadmium Binding Sites List in 5c6c
Cadmium binding site 6 out of 6 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 Cadmium with other atoms in the Cd binding site number 6 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:Cd303

b:30.1
occ:0.42
 SG B:CYS183 2.2 38.3 0.6
O B:CYS183 2.2 35.3 0.4
O B:CYS183 2.3 35.4 0.6
O B:HOH415 2.6 40.8 1.0
C B:CYS183 3.3 34.4 0.4
C B:CYS183 3.3 34.3 0.6
O B:HOH430 3.4 44.7 1.0
CB B:CYS183 3.5 36.1 0.6
CB B:CYS183 3.6 36.2 0.4
CA B:CYS183 3.8 35.8 0.6
CA B:CYS183 3.8 35.7 0.4
CD1 B:TYR185 4.3 48.5 1.0
N B:MET184 4.5 32.5 1.0
CD1 B:LEU257 4.5 37.5 1.0
CG2 B:VAL261 4.6 58.4 1.0
CE1 B:TYR185 4.8 44.9 1.0
CG1 B:VAL261 4.8 53.5 1.0
CA B:MET184 4.9 34.1 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: Fri Jul 19 18:15:15 2024

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