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Manganese in PDB 1cdk: Camp-Dependent Protein Kinase Catalytic Subunit (E.C.2.7.1.37) (Protein Kinase A) Complexed with Protein Kinase Inhibitor Peptide Fragment 5-24 (Pki(5-24) Isoelectric Variant Ca) and MN2+ Adenylyl Imidodiphosphate (Mnamp-Pnp) at pH 5.6 and 7C and 4C

Enzymatic activity of Camp-Dependent Protein Kinase Catalytic Subunit (E.C.2.7.1.37) (Protein Kinase A) Complexed with Protein Kinase Inhibitor Peptide Fragment 5-24 (Pki(5-24) Isoelectric Variant Ca) and MN2+ Adenylyl Imidodiphosphate (Mnamp-Pnp) at pH 5.6 and 7C and 4C

All present enzymatic activity of Camp-Dependent Protein Kinase Catalytic Subunit (E.C.2.7.1.37) (Protein Kinase A) Complexed with Protein Kinase Inhibitor Peptide Fragment 5-24 (Pki(5-24) Isoelectric Variant Ca) and MN2+ Adenylyl Imidodiphosphate (Mnamp-Pnp) at pH 5.6 and 7C and 4C:
2.7.11.11;

Protein crystallography data

The structure of Camp-Dependent Protein Kinase Catalytic Subunit (E.C.2.7.1.37) (Protein Kinase A) Complexed with Protein Kinase Inhibitor Peptide Fragment 5-24 (Pki(5-24) Isoelectric Variant Ca) and MN2+ Adenylyl Imidodiphosphate (Mnamp-Pnp) at pH 5.6 and 7C and 4C, PDB code: 1cdk was solved by D.Bossemeyer, R.A.Engh, V.Kinzel, H.Ponstingl, R.Huber, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 5.00 / 2.00
Space group I 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 107.610, 80.600, 110.100, 90.00, 88.59, 90.00
R / Rfree (%) 19.7 / n/a

Manganese Binding Sites:

The binding sites of Manganese atom in the Camp-Dependent Protein Kinase Catalytic Subunit (E.C.2.7.1.37) (Protein Kinase A) Complexed with Protein Kinase Inhibitor Peptide Fragment 5-24 (Pki(5-24) Isoelectric Variant Ca) and MN2+ Adenylyl Imidodiphosphate (Mnamp-Pnp) at pH 5.6 and 7C and 4C (pdb code 1cdk). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the Camp-Dependent Protein Kinase Catalytic Subunit (E.C.2.7.1.37) (Protein Kinase A) Complexed with Protein Kinase Inhibitor Peptide Fragment 5-24 (Pki(5-24) Isoelectric Variant Ca) and MN2+ Adenylyl Imidodiphosphate (Mnamp-Pnp) at pH 5.6 and 7C and 4C, PDB code: 1cdk:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in 1cdk

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Manganese binding site 1 out of 4 in the Camp-Dependent Protein Kinase Catalytic Subunit (E.C.2.7.1.37) (Protein Kinase A) Complexed with Protein Kinase Inhibitor Peptide Fragment 5-24 (Pki(5-24) Isoelectric Variant Ca) and MN2+ Adenylyl Imidodiphosphate (Mnamp-Pnp) at pH 5.6 and 7C and 4C


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Camp-Dependent Protein Kinase Catalytic Subunit (E.C.2.7.1.37) (Protein Kinase A) Complexed with Protein Kinase Inhibitor Peptide Fragment 5-24 (Pki(5-24) Isoelectric Variant Ca) and MN2+ Adenylyl Imidodiphosphate (Mnamp-Pnp) at pH 5.6 and 7C and 4C within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn401

b:18.3
occ:1.00
 O2A A:ANP400 2.0 16.9 1.0
O2G A:ANP400 2.0 18.6 1.0
OD1 A:ASN171 2.1 11.5 1.0
O A:HOH451 2.2 14.5 1.0
OD2 A:ASP184 2.6 16.9 1.0
N3B A:ANP400 2.6 16.9 1.0
PG A:ANP400 2.9 21.6 1.0
CG A:ASN171 3.1 19.6 1.0
CG A:ASP184 3.3 13.7 1.0
PA A:ANP400 3.4 19.0 1.0
ND2 A:ASN171 3.5 15.9 1.0
CB A:ASP184 3.6 13.2 1.0
PB A:ANP400 3.7 20.4 1.0
O1G A:ANP400 3.8 17.3 1.0
CE A:LYS168 3.8 11.5 1.0
MN A:MN402 3.8 16.8 1.0
O3A A:ANP400 3.9 9.4 1.0
O2B A:ANP400 3.9 25.4 1.0
O3G A:ANP400 4.1 8.1 1.0
OD1 A:ASP184 4.2 20.1 1.0
O1A A:ANP400 4.3 18.6 1.0
NZ A:LYS168 4.3 8.6 1.0
OD2 A:ASP166 4.3 23.9 1.0
O3' A:ANP400 4.4 16.7 1.0
O5' A:ANP400 4.5 23.5 1.0
CB A:ASN171 4.5 12.6 1.0
O I:HOH49 4.5 22.1 1.0
C5' A:ANP400 4.7 21.8 1.0
O A:GLU170 4.9 23.5 1.0
C3' A:ANP400 4.9 13.1 1.0
CA A:ASN171 4.9 16.0 1.0
O A:HOH436 4.9 17.1 1.0
O1B A:ANP400 5.0 14.0 1.0

Manganese binding site 2 out of 4 in 1cdk

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Manganese binding site 2 out of 4 in the Camp-Dependent Protein Kinase Catalytic Subunit (E.C.2.7.1.37) (Protein Kinase A) Complexed with Protein Kinase Inhibitor Peptide Fragment 5-24 (Pki(5-24) Isoelectric Variant Ca) and MN2+ Adenylyl Imidodiphosphate (Mnamp-Pnp) at pH 5.6 and 7C and 4C


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Camp-Dependent Protein Kinase Catalytic Subunit (E.C.2.7.1.37) (Protein Kinase A) Complexed with Protein Kinase Inhibitor Peptide Fragment 5-24 (Pki(5-24) Isoelectric Variant Ca) and MN2+ Adenylyl Imidodiphosphate (Mnamp-Pnp) at pH 5.6 and 7C and 4C within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn402

b:16.8
occ:1.00
 O1G A:ANP400 1.9 17.3 1.0
OD2 A:ASP184 2.0 16.9 1.0
O2B A:ANP400 2.1 25.4 1.0
OD1 A:ASP184 2.1 20.1 1.0
O A:HOH436 2.2 17.1 1.0
O A:HOH514 2.3 23.0 1.0
CG A:ASP184 2.4 13.7 1.0
PG A:ANP400 3.0 21.6 1.0
PB A:ANP400 3.2 20.4 1.0
N3B A:ANP400 3.3 16.9 1.0
O2G A:ANP400 3.5 18.6 1.0
MN A:MN401 3.8 18.3 1.0
CB A:ASP184 3.9 13.2 1.0
OD2 A:ASP166 4.0 23.9 1.0
CD2 A:PHE54 4.0 18.7 1.0
O1B A:ANP400 4.2 14.0 1.0
O3G A:ANP400 4.3 8.1 1.0
O A:HOH404 4.3 16.3 1.0
O3A A:ANP400 4.4 9.4 1.0
O2A A:ANP400 4.4 16.9 1.0
NZ A:LYS72 4.4 12.2 1.0
CE2 A:PHE54 4.5 13.6 1.0
CA A:GLY186 4.5 12.5 1.0
N A:GLY186 4.6 15.4 1.0
PA A:ANP400 4.7 19.0 1.0
O A:ASP184 4.7 13.2 1.0
CB I:ALA17 4.8 23.5 1.0
O1A A:ANP400 4.8 18.6 1.0
CA A:ASP184 4.8 16.1 1.0

Manganese binding site 3 out of 4 in 1cdk

Go back to Manganese Binding Sites List in 1cdk
Manganese binding site 3 out of 4 in the Camp-Dependent Protein Kinase Catalytic Subunit (E.C.2.7.1.37) (Protein Kinase A) Complexed with Protein Kinase Inhibitor Peptide Fragment 5-24 (Pki(5-24) Isoelectric Variant Ca) and MN2+ Adenylyl Imidodiphosphate (Mnamp-Pnp) at pH 5.6 and 7C and 4C


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Camp-Dependent Protein Kinase Catalytic Subunit (E.C.2.7.1.37) (Protein Kinase A) Complexed with Protein Kinase Inhibitor Peptide Fragment 5-24 (Pki(5-24) Isoelectric Variant Ca) and MN2+ Adenylyl Imidodiphosphate (Mnamp-Pnp) at pH 5.6 and 7C and 4C within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn401

b:16.1
occ:1.00
 O2G B:ANP400 2.0 11.2 1.0
O2A B:ANP400 2.0 16.1 1.0
OD1 B:ASN171 2.1 13.6 1.0
O B:HOH449 2.3 19.9 1.0
N3B B:ANP400 2.4 13.1 1.0
OD2 B:ASP184 2.5 20.8 1.0
PG B:ANP400 2.8 19.8 1.0
CG B:ASN171 3.2 16.9 1.0
PA B:ANP400 3.3 17.6 1.0
CG B:ASP184 3.4 15.9 1.0
ND2 B:ASN171 3.6 14.1 1.0
PB B:ANP400 3.6 20.2 1.0
O1G B:ANP400 3.7 20.6 1.0
CB B:ASP184 3.7 14.8 1.0
O3A B:ANP400 3.8 11.9 1.0
MN B:MN402 3.9 19.3 1.0
CE B:LYS168 3.9 7.5 1.0
O2B B:ANP400 3.9 19.4 1.0
O3G B:ANP400 4.0 10.7 1.0
NZ B:LYS168 4.2 11.3 1.0
O1A B:ANP400 4.3 17.7 1.0
OD1 B:ASP184 4.3 16.0 1.0
O J:HOH196 4.4 16.5 1.0
O3' B:ANP400 4.4 21.7 1.0
OD2 B:ASP166 4.4 25.8 1.0
O5' B:ANP400 4.4 22.1 1.0
CB B:ASN171 4.5 7.6 1.0
C5' B:ANP400 4.6 16.3 1.0
O1B B:ANP400 4.9 12.8 1.0
C3' B:ANP400 4.9 11.4 1.0
O B:HOH435 4.9 9.1 1.0
CA B:ASN171 4.9 13.1 1.0

Manganese binding site 4 out of 4 in 1cdk

Go back to Manganese Binding Sites List in 1cdk
Manganese binding site 4 out of 4 in the Camp-Dependent Protein Kinase Catalytic Subunit (E.C.2.7.1.37) (Protein Kinase A) Complexed with Protein Kinase Inhibitor Peptide Fragment 5-24 (Pki(5-24) Isoelectric Variant Ca) and MN2+ Adenylyl Imidodiphosphate (Mnamp-Pnp) at pH 5.6 and 7C and 4C


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Camp-Dependent Protein Kinase Catalytic Subunit (E.C.2.7.1.37) (Protein Kinase A) Complexed with Protein Kinase Inhibitor Peptide Fragment 5-24 (Pki(5-24) Isoelectric Variant Ca) and MN2+ Adenylyl Imidodiphosphate (Mnamp-Pnp) at pH 5.6 and 7C and 4C within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn402

b:19.3
occ:1.00
 O1G B:ANP400 1.9 20.6 1.0
OD2 B:ASP184 2.0 20.8 1.0
OD1 B:ASP184 2.1 16.0 1.0
O2B B:ANP400 2.1 19.4 1.0
O B:HOH435 2.3 9.1 1.0
O B:HOH506 2.3 11.2 1.0
CG B:ASP184 2.4 15.9 1.0
PG B:ANP400 3.1 19.8 1.0
PB B:ANP400 3.2 20.2 1.0
N3B B:ANP400 3.3 13.1 1.0
O2G B:ANP400 3.6 11.2 1.0
MN B:MN401 3.9 16.1 1.0
CB B:ASP184 3.9 14.8 1.0
CD2 B:PHE54 4.0 23.4 1.0
OD2 B:ASP166 4.0 25.8 1.0
O1B B:ANP400 4.2 12.8 1.0
O B:HOH404 4.3 15.1 1.0
O3G B:ANP400 4.3 10.7 1.0
O3A B:ANP400 4.3 11.9 1.0
NZ B:LYS72 4.4 16.4 1.0
CE2 B:PHE54 4.5 11.1 1.0
CA B:GLY186 4.5 15.7 1.0
O2A B:ANP400 4.5 16.1 1.0
N B:GLY186 4.6 17.9 1.0
PA B:ANP400 4.7 17.6 1.0
O1A B:ANP400 4.8 17.7 1.0
CA B:ASP184 4.8 24.7 1.0
CB J:ALA17 4.9 19.3 1.0

Reference:

D.Bossemeyer, R.A.Engh, V.Kinzel, H.Ponstingl, R.Huber. Phosphotransferase and Substrate Binding Mechanism of the Camp-Dependent Protein Kinase Catalytic Subunit From Porcine Heart As Deduced From the 2.0 A Structure of the Complex with MN2+ Adenylyl Imidodiphosphate and Inhibitor Peptide Pki(5-24). Embo J. V. 12 849 1993.
ISSN: ISSN 0261-4189
PubMed: 8384554
Page generated: Sat Oct 5 09:52:06 2024

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